Starting phenix.real_space_refine on Tue Apr 7 08:03:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pit_71677/04_2026/9pit_71677_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pit_71677/04_2026/9pit_71677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pit_71677/04_2026/9pit_71677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pit_71677/04_2026/9pit_71677.map" model { file = "/net/cci-nas-00/data/ceres_data/9pit_71677/04_2026/9pit_71677_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pit_71677/04_2026/9pit_71677_neut.cif" } resolution = 3.1 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= 0.007 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 15987 2.51 5 N 4317 2.21 5 O 5091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25533 Number of models: 1 Model: "" Number of chains: 57 Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 97} Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "B" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3517 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "A" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "Q" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 97} Chain: "M" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "E" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3517 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Chain: "I" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "O" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "C" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "R" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 97} Chain: "N" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "F" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3517 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "P" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "S" 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: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: 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: "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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: 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: "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: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.65, per 1000 atoms: 0.22 Number of scatterers: 25533 At special positions: 0 Unit cell: (142.12, 137.94, 152.57, 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 138 16.00 O 5091 8.00 N 4317 7.00 C 15987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN d 4 " - " MAN d 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA d 3 " - " MAN d 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA d 3 " - " MAN d 6 " " BMA o 3 " - " MAN o 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 611 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 339 " " NAG B 602 " - " ASN B 295 " " NAG B 603 " - " ASN B 301 " " NAG B 604 " - " ASN B 160 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 611 " " NAG C 703 " - " ASN C 637 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 611 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 339 " " NAG E 602 " - " ASN E 295 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 160 " " NAG F 601 " - " ASN F 339 " " NAG F 602 " - " ASN F 295 " " NAG F 603 " - " ASN F 301 " " NAG F 604 " - " ASN F 160 " " NAG S 1 " - " ASN B 276 " " NAG T 1 " - " ASN B 234 " " NAG U 1 " - " ASN B 88 " " NAG V 1 " - " ASN B 386 " " NAG W 1 " - " ASN B 133 " " NAG X 1 " - " ASN B 156 " " NAG Y 1 " - " ASN B 262 " " NAG Z 1 " - " ASN B 448 " " NAG a 1 " - " ASN B 392 " " NAG b 1 " - " ASN B 332 " " NAG c 1 " - " ASN B 197 " " NAG d 1 " - " ASN E 276 " " NAG e 1 " - " ASN E 234 " " NAG f 1 " - " ASN E 88 " " NAG g 1 " - " ASN E 386 " " NAG h 1 " - " ASN E 133 " " NAG i 1 " - " ASN E 156 " " NAG j 1 " - " ASN E 262 " " NAG k 1 " - " ASN E 448 " " NAG l 1 " - " ASN E 392 " " NAG m 1 " - " ASN E 332 " " NAG n 1 " - " ASN E 197 " " NAG o 1 " - " ASN F 276 " " NAG p 1 " - " ASN F 234 " " NAG q 1 " - " ASN F 88 " " NAG r 1 " - " ASN F 386 " " NAG s 1 " - " ASN F 133 " " NAG t 1 " - " ASN F 156 " " NAG u 1 " - " ASN F 262 " " NAG v 1 " - " ASN F 448 " " NAG w 1 " - " ASN F 392 " " NAG x 1 " - " ASN F 332 " " NAG y 1 " - " ASN F 197 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 985.7 milliseconds 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5634 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.0% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 25 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.761A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.559A pdb=" N ALA B 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.119A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.797A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.807A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.542A pdb=" N VAL G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.962A pdb=" N SER J 65 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 570 through 596 removed outlier: 4.145A pdb=" N LYS A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.529A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'M' and resid 25 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.766A pdb=" N THR M 87 " --> pdb=" O SER M 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.539A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.123A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.798A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.811A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.540A pdb=" N VAL I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 65 removed outlier: 4.970A pdb=" N SER O 65 " --> pdb=" O SER O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 570 through 596 removed outlier: 4.147A pdb=" N LYS C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 659 removed outlier: 3.511A pdb=" N ASP C 659 " --> pdb=" O LYS C 655 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'N' and resid 25 through 32 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.762A pdb=" N THR N 87 " --> pdb=" O SER N 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.552A pdb=" N ALA F 73 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.121A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.797A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 483 removed outlier: 3.811A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.532A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 61 through 65 removed outlier: 4.968A pdb=" N SER P 65 " --> pdb=" O SER P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.150A pdb=" N LYS D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 659 removed outlier: 3.509A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.519A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.501A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.501A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.233A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.119A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 100 through 100A Processing sheet with id=AA8, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.372A pdb=" N VAL A 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL B 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR A 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR B 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N CYS A 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.635A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 177 Processing sheet with id=AB4, first strand: chain 'B' and resid 200 through 203 Processing sheet with id=AB5, first strand: chain 'B' and resid 259 through 261 removed outlier: 10.028A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.761A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 271 through 274 removed outlier: 6.667A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.761A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 467 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 303 through 308 removed outlier: 7.126A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.569A pdb=" N GLU G 105 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU G 13 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.315A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU J 45 " --> pdb=" O THR J 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'Q' and resid 5 through 6 removed outlier: 3.517A pdb=" N THR Q 5 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.620A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.214A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.131A pdb=" N VAL M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 100 through 100A Processing sheet with id=AD2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.635A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD6, first strand: chain 'E' and resid 170 through 177 Processing sheet with id=AD7, first strand: chain 'E' and resid 200 through 203 Processing sheet with id=AD8, first strand: chain 'E' and resid 259 through 261 removed outlier: 10.019A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.676A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 303 through 308 removed outlier: 7.140A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.563A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.310A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR O 40 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU O 45 " --> pdb=" O THR O 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'R' and resid 5 through 6 removed outlier: 3.519A pdb=" N THR R 5 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.628A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.221A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.124A pdb=" N VAL N 102 " --> pdb=" O ARG N 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 100 through 100A Processing sheet with id=AF5, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.343A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.640A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AF8, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AF9, first strand: chain 'F' and resid 170 through 177 Processing sheet with id=AG1, first strand: chain 'F' and resid 200 through 203 Processing sheet with id=AG2, first strand: chain 'F' and resid 259 through 261 removed outlier: 10.013A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.374A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.658A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.374A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR F 467 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 303 through 308 removed outlier: 7.134A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AG6, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.565A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU K 13 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.314A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR P 40 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU P 45 " --> pdb=" O THR P 40 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 11 through 12 1051 hydrogen bonds defined for protein. 2610 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: 5.54 Time building geometry restraints manager: 3.32 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: 7991 1.34 - 1.46: 6491 1.46 - 1.58: 11432 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 26100 Sorted by residual: bond pdb=" N ASP R 31 " pdb=" CA ASP R 31 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.21e+00 bond pdb=" N ASP Q 31 " pdb=" CA ASP Q 31 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.13e+00 bond pdb=" N ASP L 31 " pdb=" CA ASP L 31 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.04e+00 bond pdb=" C1 MAN S 6 " pdb=" O5 MAN S 6 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 MAN o 6 " pdb=" O5 MAN o 6 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 26095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 34502 1.70 - 3.40: 832 3.40 - 5.11: 88 5.11 - 6.81: 23 6.81 - 8.51: 9 Bond angle restraints: 35454 Sorted by residual: angle pdb=" C ASP F 140 " pdb=" CA ASP F 140 " pdb=" CB ASP F 140 " ideal model delta sigma weight residual 115.79 109.59 6.20 1.19e+00 7.06e-01 2.72e+01 angle pdb=" C ASP B 140 " pdb=" CA ASP B 140 " pdb=" CB ASP B 140 " ideal model delta sigma weight residual 115.79 109.64 6.15 1.19e+00 7.06e-01 2.67e+01 angle pdb=" C ASP E 140 " pdb=" CA ASP E 140 " pdb=" CB ASP E 140 " ideal model delta sigma weight residual 115.79 109.65 6.14 1.19e+00 7.06e-01 2.66e+01 angle pdb=" N ASP O 101 " pdb=" CA ASP O 101 " pdb=" C ASP O 101 " ideal model delta sigma weight residual 107.23 114.53 -7.30 1.67e+00 3.59e-01 1.91e+01 angle pdb=" N ASP P 101 " pdb=" CA ASP P 101 " pdb=" C ASP P 101 " ideal model delta sigma weight residual 107.23 114.52 -7.29 1.67e+00 3.59e-01 1.91e+01 ... (remaining 35449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 15981 17.84 - 35.68: 669 35.68 - 53.52: 141 53.52 - 71.36: 63 71.36 - 89.20: 30 Dihedral angle restraints: 16884 sinusoidal: 8100 harmonic: 8784 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.74 -55.74 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.55 -55.55 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.49 -55.49 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 16881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3096 0.044 - 0.088: 761 0.088 - 0.132: 319 0.132 - 0.175: 34 0.175 - 0.219: 5 Chirality restraints: 4215 Sorted by residual: chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.06 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C5 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C6 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.06 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C5 BMA o 3 " pdb=" C4 BMA o 3 " pdb=" C6 BMA o 3 " pdb=" O5 BMA o 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.06 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4212 not shown) Planarity restraints: 4455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY O 104 " 0.077 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO O 105 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO O 105 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO O 105 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 104 " 0.077 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO J 105 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO J 105 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO J 105 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY P 104 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO P 105 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO P 105 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO P 105 " -0.063 5.00e-02 4.00e+02 ... (remaining 4452 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 13271 2.99 - 3.47: 23132 3.47 - 3.95: 42734 3.95 - 4.42: 46957 4.42 - 4.90: 79173 Nonbonded interactions: 205267 Sorted by model distance: nonbonded pdb=" O5 NAG h 1 " pdb=" O6 NAG h 1 " model vdw 2.518 2.432 nonbonded pdb=" O5 NAG W 1 " pdb=" O6 NAG W 1 " model vdw 2.519 2.432 nonbonded pdb=" O5 NAG s 1 " pdb=" O6 NAG s 1 " model vdw 2.520 2.432 nonbonded pdb=" O5 MAN S 4 " pdb=" O6 MAN S 4 " model vdw 2.521 2.432 nonbonded pdb=" O5 MAN d 4 " pdb=" O6 MAN d 4 " model vdw 2.523 2.432 ... (remaining 205262 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'd' selection = chain 'o' } ncs_group { reference = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'V' selection = chain 'Y' selection = chain 'g' selection = chain 'j' selection = chain 'r' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.470 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.003 0.042 26250 Z= 0.137 Angle : 0.659 8.511 35859 Z= 0.344 Chirality : 0.046 0.219 4215 Planarity : 0.006 0.118 4401 Dihedral : 11.351 89.196 11115 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.22 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3021 helix: 0.23 (0.26), residues: 432 sheet: 0.19 (0.15), residues: 1053 loop : 0.11 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 56 TYR 0.016 0.001 TYR L 91 PHE 0.019 0.002 PHE E 176 TRP 0.024 0.001 TRP E 479 HIS 0.004 0.001 HIS F 66 Details of bonding type rmsd covalent geometry : bond 0.00282 (26100) covalent geometry : angle 0.62921 (35454) SS BOND : bond 0.00247 ( 45) SS BOND : angle 1.18879 ( 90) hydrogen bonds : bond 0.18570 ( 983) hydrogen bonds : angle 8.56940 ( 2610) link_ALPHA1-2 : bond 0.00624 ( 3) link_ALPHA1-2 : angle 1.30081 ( 9) link_ALPHA1-3 : bond 0.01318 ( 3) link_ALPHA1-3 : angle 0.96849 ( 9) link_ALPHA1-6 : bond 0.02246 ( 3) link_ALPHA1-6 : angle 3.21746 ( 9) link_BETA1-4 : bond 0.00766 ( 42) link_BETA1-4 : angle 1.98755 ( 126) link_NAG-ASN : bond 0.00266 ( 54) link_NAG-ASN : angle 2.19893 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.912 Fit side-chains REVERT: H 32 TYR cc_start: 0.9095 (m-80) cc_final: 0.8743 (m-80) REVERT: H 72 ASP cc_start: 0.8791 (t0) cc_final: 0.8429 (t0) REVERT: H 96 SER cc_start: 0.9021 (m) cc_final: 0.8772 (t) REVERT: B 150 MET cc_start: 0.7007 (mtp) cc_final: 0.6758 (mtm) REVERT: J 47 TRP cc_start: 0.5176 (t-100) cc_final: 0.2640 (t60) REVERT: A 577 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6407 (pt0) REVERT: A 659 ASP cc_start: 0.8416 (t70) cc_final: 0.8150 (t0) REVERT: Q 45 ARG cc_start: 0.8218 (ttp80) cc_final: 0.8017 (ptm160) REVERT: M 81 GLU cc_start: 0.8550 (tt0) cc_final: 0.8287 (tt0) REVERT: M 96 SER cc_start: 0.9057 (m) cc_final: 0.8824 (t) REVERT: I 45 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7733 (ttp80) REVERT: O 32 ASN cc_start: 0.7979 (m-40) cc_final: 0.7777 (m-40) REVERT: O 47 TRP cc_start: 0.5329 (t-100) cc_final: 0.2754 (t60) REVERT: O 108 ARG cc_start: 0.5999 (ppt170) cc_final: 0.5592 (ppt170) REVERT: C 577 GLN cc_start: 0.6824 (mm-40) cc_final: 0.6351 (pt0) REVERT: N 72 ASP cc_start: 0.8771 (t0) cc_final: 0.8518 (t0) REVERT: F 170 GLN cc_start: 0.6729 (pt0) cc_final: 0.6520 (pm20) REVERT: K 60 ASP cc_start: 0.8351 (t0) cc_final: 0.8133 (t0) REVERT: P 39 GLN cc_start: 0.7590 (tt0) cc_final: 0.7351 (tt0) REVERT: P 81 LYS cc_start: 0.7421 (mmtm) cc_final: 0.7218 (mmmm) REVERT: P 101 ASP cc_start: 0.9189 (p0) cc_final: 0.8974 (p0) REVERT: D 577 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6551 (pt0) REVERT: D 620 SER cc_start: 0.8981 (t) cc_final: 0.8773 (p) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2166 time to fit residues: 119.7462 Evaluate side-chains 249 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 64 GLN Q 89 GLN E 195 ASN O 64 GLN C 607 ASN R 89 GLN F 195 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.135642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096348 restraints weight = 39372.311| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.99 r_work: 0.3174 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 26250 Z= 0.245 Angle : 0.714 8.557 35859 Z= 0.358 Chirality : 0.049 0.262 4215 Planarity : 0.005 0.068 4401 Dihedral : 7.248 66.441 5496 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 0.45 % Allowed : 5.89 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3021 helix: 0.72 (0.26), residues: 438 sheet: 0.19 (0.15), residues: 1020 loop : 0.05 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 56 TYR 0.014 0.002 TYR O 50 PHE 0.019 0.003 PHE E 176 TRP 0.020 0.002 TRP F 479 HIS 0.004 0.002 HIS M 74 Details of bonding type rmsd covalent geometry : bond 0.00577 (26100) covalent geometry : angle 0.68446 (35454) SS BOND : bond 0.00443 ( 45) SS BOND : angle 0.83286 ( 90) hydrogen bonds : bond 0.04763 ( 983) hydrogen bonds : angle 6.28439 ( 2610) link_ALPHA1-2 : bond 0.00455 ( 3) link_ALPHA1-2 : angle 1.51673 ( 9) link_ALPHA1-3 : bond 0.01157 ( 3) link_ALPHA1-3 : angle 1.54052 ( 9) link_ALPHA1-6 : bond 0.02402 ( 3) link_ALPHA1-6 : angle 3.34890 ( 9) link_BETA1-4 : bond 0.00548 ( 42) link_BETA1-4 : angle 2.14716 ( 126) link_NAG-ASN : bond 0.00412 ( 54) link_NAG-ASN : angle 2.33902 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 263 time to evaluate : 0.967 Fit side-chains REVERT: H 72 ASP cc_start: 0.8539 (t0) cc_final: 0.8293 (t0) REVERT: B 173 TYR cc_start: 0.6939 (m-80) cc_final: 0.6284 (t80) REVERT: J 101 ASP cc_start: 0.8961 (p0) cc_final: 0.8723 (p0) REVERT: A 577 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6439 (pt0) REVERT: M 81 GLU cc_start: 0.8399 (tt0) cc_final: 0.8094 (tt0) REVERT: E 95 MET cc_start: 0.9414 (ptm) cc_final: 0.9201 (ptm) REVERT: E 173 TYR cc_start: 0.7129 (m-80) cc_final: 0.6408 (t80) REVERT: O 91 TYR cc_start: 0.8354 (m-80) cc_final: 0.8112 (m-80) REVERT: O 100 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8433 (mtpp) REVERT: O 101 ASP cc_start: 0.9074 (p0) cc_final: 0.8860 (p0) REVERT: O 108 ARG cc_start: 0.6134 (ppt170) cc_final: 0.5810 (ppt170) REVERT: C 577 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6291 (pt0) REVERT: R 103 ARG cc_start: 0.7198 (tpt-90) cc_final: 0.6975 (tpp-160) REVERT: N 72 ASP cc_start: 0.8607 (t0) cc_final: 0.8311 (t0) REVERT: F 161 MET cc_start: 0.7650 (tpt) cc_final: 0.7348 (tpt) REVERT: K 60 ASP cc_start: 0.8393 (t0) cc_final: 0.8125 (t0) REVERT: D 577 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6539 (pt0) REVERT: D 654 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7551 (mt-10) outliers start: 12 outliers final: 9 residues processed: 269 average time/residue: 0.1980 time to fit residues: 79.2603 Evaluate side-chains 239 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 114 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 195 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN E 195 ASN O 32 ASN O 64 GLN N 100DHIS F 114 GLN K 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.135109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096230 restraints weight = 39658.459| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.03 r_work: 0.3176 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26250 Z= 0.183 Angle : 0.632 8.944 35859 Z= 0.312 Chirality : 0.046 0.235 4215 Planarity : 0.004 0.046 4401 Dihedral : 6.838 59.826 5496 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 1.16 % Allowed : 7.06 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3021 helix: 1.01 (0.27), residues: 438 sheet: 0.19 (0.16), residues: 1020 loop : -0.06 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 56 TYR 0.012 0.001 TYR O 50 PHE 0.019 0.002 PHE P 100C TRP 0.019 0.002 TRP K 94 HIS 0.007 0.001 HIS N 100D Details of bonding type rmsd covalent geometry : bond 0.00424 (26100) covalent geometry : angle 0.60113 (35454) SS BOND : bond 0.00335 ( 45) SS BOND : angle 0.68196 ( 90) hydrogen bonds : bond 0.04183 ( 983) hydrogen bonds : angle 5.82676 ( 2610) link_ALPHA1-2 : bond 0.00470 ( 3) link_ALPHA1-2 : angle 1.48850 ( 9) link_ALPHA1-3 : bond 0.01331 ( 3) link_ALPHA1-3 : angle 1.15321 ( 9) link_ALPHA1-6 : bond 0.02686 ( 3) link_ALPHA1-6 : angle 4.04329 ( 9) link_BETA1-4 : bond 0.00666 ( 42) link_BETA1-4 : angle 2.04861 ( 126) link_NAG-ASN : bond 0.00293 ( 54) link_NAG-ASN : angle 2.14175 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: L 27 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7545 (tm-30) REVERT: H 72 ASP cc_start: 0.8730 (t0) cc_final: 0.8502 (t0) REVERT: B 308 ARG cc_start: 0.7546 (mtp85) cc_final: 0.7283 (mmm-85) REVERT: Q 27 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7467 (tm-30) REVERT: M 81 GLU cc_start: 0.8669 (tt0) cc_final: 0.8417 (tt0) REVERT: E 308 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7279 (mmm-85) REVERT: O 91 TYR cc_start: 0.8469 (m-80) cc_final: 0.8207 (m-80) REVERT: O 108 ARG cc_start: 0.6205 (ppt170) cc_final: 0.5866 (ppt170) REVERT: N 72 ASP cc_start: 0.8743 (t0) cc_final: 0.8496 (t0) REVERT: F 308 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7390 (mtp-110) REVERT: K 60 ASP cc_start: 0.8492 (t0) cc_final: 0.8205 (t0) REVERT: P 47 TRP cc_start: 0.6025 (t-100) cc_final: 0.3863 (t60) REVERT: D 577 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6397 (pt0) REVERT: D 654 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7713 (mt-10) outliers start: 31 outliers final: 18 residues processed: 267 average time/residue: 0.1828 time to fit residues: 74.5630 Evaluate side-chains 232 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain C residue 607 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 116 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 276 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 280 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 90 GLN J 64 GLN O 64 GLN N 3 GLN K 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.134289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095418 restraints weight = 39646.338| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.02 r_work: 0.3160 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26250 Z= 0.194 Angle : 0.637 9.303 35859 Z= 0.311 Chirality : 0.046 0.230 4215 Planarity : 0.004 0.043 4401 Dihedral : 6.708 59.716 5496 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 1.65 % Allowed : 7.66 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3021 helix: 1.05 (0.27), residues: 438 sheet: 0.12 (0.16), residues: 1014 loop : -0.11 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 45 TYR 0.012 0.001 TYR O 50 PHE 0.015 0.002 PHE P 100C TRP 0.020 0.001 TRP F 479 HIS 0.004 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00455 (26100) covalent geometry : angle 0.60413 (35454) SS BOND : bond 0.00387 ( 45) SS BOND : angle 1.08964 ( 90) hydrogen bonds : bond 0.03971 ( 983) hydrogen bonds : angle 5.69250 ( 2610) link_ALPHA1-2 : bond 0.00473 ( 3) link_ALPHA1-2 : angle 1.51090 ( 9) link_ALPHA1-3 : bond 0.01367 ( 3) link_ALPHA1-3 : angle 1.21356 ( 9) link_ALPHA1-6 : bond 0.02597 ( 3) link_ALPHA1-6 : angle 4.07598 ( 9) link_BETA1-4 : bond 0.00615 ( 42) link_BETA1-4 : angle 2.08414 ( 126) link_NAG-ASN : bond 0.00507 ( 54) link_NAG-ASN : angle 2.16829 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.720 Fit side-chains REVERT: L 54 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7713 (mtt90) REVERT: H 72 ASP cc_start: 0.8774 (t0) cc_final: 0.8560 (t0) REVERT: B 173 TYR cc_start: 0.7499 (m-80) cc_final: 0.6166 (t80) REVERT: J 47 TRP cc_start: 0.7534 (t-100) cc_final: 0.6741 (t-100) REVERT: J 101 ASP cc_start: 0.9222 (p0) cc_final: 0.9010 (p0) REVERT: M 81 GLU cc_start: 0.8687 (tt0) cc_final: 0.8425 (tt0) REVERT: E 173 TYR cc_start: 0.7440 (m-80) cc_final: 0.6287 (t80) REVERT: O 43 LYS cc_start: 0.7456 (ptmt) cc_final: 0.6871 (mptt) REVERT: O 81 LYS cc_start: 0.7459 (mmmm) cc_final: 0.7243 (mmmm) REVERT: O 91 TYR cc_start: 0.8473 (m-80) cc_final: 0.8199 (m-80) REVERT: O 100 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8603 (mtpp) REVERT: O 108 ARG cc_start: 0.6013 (ppt170) cc_final: 0.5747 (ppt170) REVERT: N 48 MET cc_start: 0.9077 (mtp) cc_final: 0.8875 (mtm) REVERT: N 97 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8249 (m-10) REVERT: F 308 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7351 (mtp-110) REVERT: P 47 TRP cc_start: 0.6175 (t-100) cc_final: 0.4103 (t60) REVERT: P 81 LYS cc_start: 0.7306 (mmmm) cc_final: 0.7100 (mmmm) REVERT: D 654 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7893 (mt-10) outliers start: 44 outliers final: 28 residues processed: 266 average time/residue: 0.1804 time to fit residues: 73.3478 Evaluate side-chains 248 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 287 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 71 optimal weight: 0.0020 chunk 186 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN N 3 GLN K 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093325 restraints weight = 39748.877| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.90 r_work: 0.3139 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 26250 Z= 0.235 Angle : 0.660 9.763 35859 Z= 0.321 Chirality : 0.047 0.218 4215 Planarity : 0.004 0.045 4401 Dihedral : 6.695 56.026 5496 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 2.25 % Allowed : 7.55 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3021 helix: 0.90 (0.26), residues: 438 sheet: 0.01 (0.15), residues: 1029 loop : -0.21 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 45 TYR 0.013 0.001 TYR E 217 PHE 0.017 0.002 PHE P 100C TRP 0.016 0.002 TRP I 94 HIS 0.005 0.001 HIS R 32 Details of bonding type rmsd covalent geometry : bond 0.00556 (26100) covalent geometry : angle 0.62781 (35454) SS BOND : bond 0.00409 ( 45) SS BOND : angle 0.87521 ( 90) hydrogen bonds : bond 0.04079 ( 983) hydrogen bonds : angle 5.69357 ( 2610) link_ALPHA1-2 : bond 0.00456 ( 3) link_ALPHA1-2 : angle 1.48905 ( 9) link_ALPHA1-3 : bond 0.01366 ( 3) link_ALPHA1-3 : angle 1.21852 ( 9) link_ALPHA1-6 : bond 0.02739 ( 3) link_ALPHA1-6 : angle 4.18661 ( 9) link_BETA1-4 : bond 0.00609 ( 42) link_BETA1-4 : angle 2.14701 ( 126) link_NAG-ASN : bond 0.00407 ( 54) link_NAG-ASN : angle 2.25078 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 0.738 Fit side-chains REVERT: L 27 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7521 (tm-30) REVERT: H 23 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: H 72 ASP cc_start: 0.8768 (t0) cc_final: 0.8556 (t0) REVERT: H 97 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: J 47 TRP cc_start: 0.7501 (t-100) cc_final: 0.6800 (t-100) REVERT: J 101 ASP cc_start: 0.9170 (p0) cc_final: 0.8935 (p0) REVERT: Q 27 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7558 (tm-30) REVERT: M 81 GLU cc_start: 0.8677 (tt0) cc_final: 0.8425 (tt0) REVERT: M 97 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: I 45 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7764 (ttp80) REVERT: O 27 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: O 43 LYS cc_start: 0.7599 (ptmt) cc_final: 0.7020 (mptt) REVERT: N 97 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: F 161 MET cc_start: 0.7702 (tpt) cc_final: 0.7489 (tpt) REVERT: F 308 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7330 (mtp-110) REVERT: D 654 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7892 (mt-10) outliers start: 60 outliers final: 42 residues processed: 270 average time/residue: 0.1803 time to fit residues: 75.4990 Evaluate side-chains 255 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 PHE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 607 ASN Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 98 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 195 optimal weight: 0.0270 chunk 255 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS J 64 GLN Q 32 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN R 32 HIS N 3 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN P 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097015 restraints weight = 39596.331| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.94 r_work: 0.3183 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26250 Z= 0.124 Angle : 0.600 9.823 35859 Z= 0.290 Chirality : 0.045 0.312 4215 Planarity : 0.004 0.043 4401 Dihedral : 6.280 52.022 5496 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 1.61 % Allowed : 8.63 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3021 helix: 1.46 (0.27), residues: 420 sheet: 0.12 (0.16), residues: 984 loop : -0.19 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 45 TYR 0.011 0.001 TYR O 50 PHE 0.012 0.001 PHE Q 49 TRP 0.019 0.001 TRP K 94 HIS 0.004 0.001 HIS Q 32 Details of bonding type rmsd covalent geometry : bond 0.00278 (26100) covalent geometry : angle 0.56441 (35454) SS BOND : bond 0.00265 ( 45) SS BOND : angle 1.18327 ( 90) hydrogen bonds : bond 0.03529 ( 983) hydrogen bonds : angle 5.45790 ( 2610) link_ALPHA1-2 : bond 0.00485 ( 3) link_ALPHA1-2 : angle 1.66464 ( 9) link_ALPHA1-3 : bond 0.01506 ( 3) link_ALPHA1-3 : angle 0.90648 ( 9) link_ALPHA1-6 : bond 0.02914 ( 3) link_ALPHA1-6 : angle 4.55140 ( 9) link_BETA1-4 : bond 0.00637 ( 42) link_BETA1-4 : angle 1.99104 ( 126) link_NAG-ASN : bond 0.00270 ( 54) link_NAG-ASN : angle 2.18701 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: L 27 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7560 (tm-30) REVERT: H 23 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: H 72 ASP cc_start: 0.8751 (t0) cc_final: 0.8529 (t0) REVERT: H 97 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: B 173 TYR cc_start: 0.7402 (m-80) cc_final: 0.6091 (t80) REVERT: G 37 GLN cc_start: 0.8647 (tt0) cc_final: 0.7878 (tt0) REVERT: J 27 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: J 47 TRP cc_start: 0.7438 (t-100) cc_final: 0.6709 (t-100) REVERT: J 101 ASP cc_start: 0.9061 (p0) cc_final: 0.8768 (p0) REVERT: Q 27 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7739 (tm-30) REVERT: M 81 GLU cc_start: 0.8614 (tt0) cc_final: 0.8370 (tt0) REVERT: M 97 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: E 173 TYR cc_start: 0.7454 (m-80) cc_final: 0.6274 (t80) REVERT: I 45 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7788 (ttp80) REVERT: O 43 LYS cc_start: 0.7618 (ptmt) cc_final: 0.7027 (mptt) REVERT: O 81 LYS cc_start: 0.7475 (mmmm) cc_final: 0.7251 (mmmm) REVERT: O 100 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8568 (mtpp) REVERT: N 48 MET cc_start: 0.9059 (mtp) cc_final: 0.8857 (mtm) REVERT: F 161 MET cc_start: 0.7701 (tpt) cc_final: 0.7472 (tpt) REVERT: F 173 TYR cc_start: 0.7428 (m-80) cc_final: 0.6552 (t80) REVERT: F 308 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7423 (mtp-110) REVERT: D 626 MET cc_start: 0.8738 (mtm) cc_final: 0.8519 (mtp) outliers start: 43 outliers final: 28 residues processed: 278 average time/residue: 0.1741 time to fit residues: 75.2996 Evaluate side-chains 252 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 97 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 52 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 GLN J 64 GLN M 100FGLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN N 3 GLN K 92 ASN P 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089938 restraints weight = 39782.750| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.88 r_work: 0.3099 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 26250 Z= 0.343 Angle : 0.753 11.872 35859 Z= 0.365 Chirality : 0.050 0.213 4215 Planarity : 0.005 0.047 4401 Dihedral : 6.864 49.126 5496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 2.03 % Allowed : 9.12 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3021 helix: 1.06 (0.26), residues: 402 sheet: -0.15 (0.16), residues: 1014 loop : -0.48 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 45 TYR 0.018 0.002 TYR E 217 PHE 0.023 0.003 PHE P 100C TRP 0.014 0.002 TRP B 69 HIS 0.006 0.002 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00818 (26100) covalent geometry : angle 0.71968 (35454) SS BOND : bond 0.00558 ( 45) SS BOND : angle 1.34372 ( 90) hydrogen bonds : bond 0.04542 ( 983) hydrogen bonds : angle 5.78030 ( 2610) link_ALPHA1-2 : bond 0.00416 ( 3) link_ALPHA1-2 : angle 1.43521 ( 9) link_ALPHA1-3 : bond 0.01354 ( 3) link_ALPHA1-3 : angle 1.44577 ( 9) link_ALPHA1-6 : bond 0.02659 ( 3) link_ALPHA1-6 : angle 4.05409 ( 9) link_BETA1-4 : bond 0.00595 ( 42) link_BETA1-4 : angle 2.31024 ( 126) link_NAG-ASN : bond 0.00494 ( 54) link_NAG-ASN : angle 2.41006 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.783 Fit side-chains REVERT: L 54 ARG cc_start: 0.8265 (ttm170) cc_final: 0.8002 (mtt90) REVERT: H 23 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: H 80 MET cc_start: 0.8825 (ttp) cc_final: 0.8541 (ptm) REVERT: H 97 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: B 161 MET cc_start: 0.7485 (tpt) cc_final: 0.6439 (tpp) REVERT: B 173 TYR cc_start: 0.7627 (m-80) cc_final: 0.6203 (t80) REVERT: J 27 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: J 47 TRP cc_start: 0.7509 (t-100) cc_final: 0.6893 (t-100) REVERT: J 101 ASP cc_start: 0.9126 (p0) cc_final: 0.8920 (p0) REVERT: Q 27 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7755 (tt0) REVERT: M 81 GLU cc_start: 0.8681 (tt0) cc_final: 0.8415 (tt0) REVERT: M 97 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: O 27 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: O 100 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8651 (mtpp) REVERT: N 97 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8459 (m-10) REVERT: F 161 MET cc_start: 0.7807 (tpt) cc_final: 0.7567 (tpt) outliers start: 54 outliers final: 41 residues processed: 246 average time/residue: 0.1757 time to fit residues: 67.7243 Evaluate side-chains 238 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 97 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain C residue 607 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 18 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN C 607 ASN N 3 GLN F 280 ASN K 92 ASN P 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.134494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095149 restraints weight = 39804.158| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.00 r_work: 0.3159 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26250 Z= 0.133 Angle : 0.616 10.393 35859 Z= 0.297 Chirality : 0.045 0.189 4215 Planarity : 0.004 0.045 4401 Dihedral : 6.345 47.061 5496 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 1.73 % Allowed : 9.72 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3021 helix: 1.26 (0.26), residues: 420 sheet: -0.03 (0.16), residues: 999 loop : -0.34 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 45 TYR 0.011 0.001 TYR O 50 PHE 0.010 0.001 PHE Q 83 TRP 0.019 0.001 TRP I 94 HIS 0.003 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00300 (26100) covalent geometry : angle 0.58231 (35454) SS BOND : bond 0.00270 ( 45) SS BOND : angle 1.01763 ( 90) hydrogen bonds : bond 0.03626 ( 983) hydrogen bonds : angle 5.50499 ( 2610) link_ALPHA1-2 : bond 0.00451 ( 3) link_ALPHA1-2 : angle 1.67337 ( 9) link_ALPHA1-3 : bond 0.01491 ( 3) link_ALPHA1-3 : angle 0.84122 ( 9) link_ALPHA1-6 : bond 0.02927 ( 3) link_ALPHA1-6 : angle 4.62662 ( 9) link_BETA1-4 : bond 0.00621 ( 42) link_BETA1-4 : angle 2.02748 ( 126) link_NAG-ASN : bond 0.00322 ( 54) link_NAG-ASN : angle 2.13119 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.972 Fit side-chains REVERT: H 23 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: H 72 ASP cc_start: 0.8714 (t0) cc_final: 0.8480 (t0) REVERT: H 80 MET cc_start: 0.8733 (ttp) cc_final: 0.8431 (ptm) REVERT: H 97 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: B 161 MET cc_start: 0.7543 (tpt) cc_final: 0.6463 (tpp) REVERT: J 27 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: J 47 TRP cc_start: 0.7356 (t-100) cc_final: 0.6765 (t-100) REVERT: Q 27 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7761 (tt0) REVERT: M 81 GLU cc_start: 0.8628 (tt0) cc_final: 0.8361 (tt0) REVERT: M 97 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: E 173 TYR cc_start: 0.7524 (m-80) cc_final: 0.6259 (t80) REVERT: E 308 ARG cc_start: 0.7596 (mmm160) cc_final: 0.7362 (mmm-85) REVERT: I 45 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7656 (ttp80) REVERT: I 103 LYS cc_start: 0.7610 (tttt) cc_final: 0.7122 (tttp) REVERT: O 27 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: O 100 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8596 (mtpp) REVERT: R 27 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7527 (tm-30) REVERT: N 97 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8208 (m-10) REVERT: F 161 MET cc_start: 0.7766 (tpt) cc_final: 0.7498 (tpt) REVERT: F 173 TYR cc_start: 0.7467 (m-80) cc_final: 0.6569 (t80) REVERT: F 308 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7458 (mtp-110) REVERT: K 103 LYS cc_start: 0.7596 (tttt) cc_final: 0.7251 (tttp) outliers start: 46 outliers final: 35 residues processed: 254 average time/residue: 0.1687 time to fit residues: 67.3957 Evaluate side-chains 249 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 97 PHE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 607 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 225 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN N 3 GLN K 92 ASN P 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092222 restraints weight = 39986.978| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.88 r_work: 0.3130 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 26250 Z= 0.238 Angle : 0.673 11.180 35859 Z= 0.324 Chirality : 0.047 0.197 4215 Planarity : 0.004 0.046 4401 Dihedral : 6.485 46.252 5496 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 1.91 % Allowed : 9.87 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3021 helix: 1.36 (0.27), residues: 402 sheet: -0.08 (0.16), residues: 999 loop : -0.44 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.013 0.001 TYR E 217 PHE 0.015 0.002 PHE P 100C TRP 0.016 0.002 TRP B 479 HIS 0.004 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00567 (26100) covalent geometry : angle 0.64026 (35454) SS BOND : bond 0.00405 ( 45) SS BOND : angle 1.04082 ( 90) hydrogen bonds : bond 0.04028 ( 983) hydrogen bonds : angle 5.58816 ( 2610) link_ALPHA1-2 : bond 0.00411 ( 3) link_ALPHA1-2 : angle 1.55021 ( 9) link_ALPHA1-3 : bond 0.01413 ( 3) link_ALPHA1-3 : angle 1.20703 ( 9) link_ALPHA1-6 : bond 0.02833 ( 3) link_ALPHA1-6 : angle 4.37991 ( 9) link_BETA1-4 : bond 0.00596 ( 42) link_BETA1-4 : angle 2.15701 ( 126) link_NAG-ASN : bond 0.00394 ( 54) link_NAG-ASN : angle 2.23616 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.824 Fit side-chains REVERT: H 23 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: H 72 ASP cc_start: 0.8712 (t0) cc_final: 0.8482 (t0) REVERT: H 80 MET cc_start: 0.8719 (ttp) cc_final: 0.8395 (ptm) REVERT: H 97 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: B 161 MET cc_start: 0.7506 (tpt) cc_final: 0.6396 (tpp) REVERT: B 173 TYR cc_start: 0.7484 (m-80) cc_final: 0.6137 (t80) REVERT: B 308 ARG cc_start: 0.7530 (mtp180) cc_final: 0.7272 (mtp-110) REVERT: J 27 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: J 47 TRP cc_start: 0.7388 (t-100) cc_final: 0.6807 (t-100) REVERT: Q 27 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7788 (tt0) REVERT: M 81 GLU cc_start: 0.8633 (tt0) cc_final: 0.8369 (tt0) REVERT: M 97 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: E 173 TYR cc_start: 0.7532 (m-80) cc_final: 0.6310 (t80) REVERT: I 45 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7692 (ttp80) REVERT: I 103 LYS cc_start: 0.7694 (tttt) cc_final: 0.7216 (tttp) REVERT: O 27 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: O 100 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8636 (mtpp) REVERT: N 97 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8321 (m-10) REVERT: F 161 MET cc_start: 0.7784 (tpt) cc_final: 0.7533 (tpt) REVERT: F 173 TYR cc_start: 0.7518 (m-80) cc_final: 0.6614 (t80) REVERT: K 103 LYS cc_start: 0.7581 (tttt) cc_final: 0.7206 (tttp) REVERT: P 27 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7206 (m-30) outliers start: 51 outliers final: 37 residues processed: 248 average time/residue: 0.1738 time to fit residues: 67.1640 Evaluate side-chains 243 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 97 PHE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 116 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN G 37 GLN J 64 GLN E 280 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN N 3 GLN K 92 ASN P 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095477 restraints weight = 39503.149| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.92 r_work: 0.3173 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26250 Z= 0.122 Angle : 0.605 11.473 35859 Z= 0.291 Chirality : 0.044 0.185 4215 Planarity : 0.004 0.044 4401 Dihedral : 6.056 44.386 5496 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 1.58 % Allowed : 10.14 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3021 helix: 1.50 (0.27), residues: 420 sheet: -0.03 (0.16), residues: 1017 loop : -0.33 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 308 TYR 0.011 0.001 TYR O 50 PHE 0.011 0.001 PHE Q 83 TRP 0.019 0.001 TRP B 479 HIS 0.003 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00272 (26100) covalent geometry : angle 0.57245 (35454) SS BOND : bond 0.00264 ( 45) SS BOND : angle 0.88497 ( 90) hydrogen bonds : bond 0.03460 ( 983) hydrogen bonds : angle 5.39731 ( 2610) link_ALPHA1-2 : bond 0.00467 ( 3) link_ALPHA1-2 : angle 1.70524 ( 9) link_ALPHA1-3 : bond 0.01504 ( 3) link_ALPHA1-3 : angle 0.82862 ( 9) link_ALPHA1-6 : bond 0.03048 ( 3) link_ALPHA1-6 : angle 4.78478 ( 9) link_BETA1-4 : bond 0.00633 ( 42) link_BETA1-4 : angle 1.98344 ( 126) link_NAG-ASN : bond 0.00305 ( 54) link_NAG-ASN : angle 2.07247 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: H 72 ASP cc_start: 0.8737 (t0) cc_final: 0.8503 (t0) REVERT: H 97 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.7843 (m-10) REVERT: B 161 MET cc_start: 0.7569 (tpt) cc_final: 0.6478 (tpp) REVERT: B 173 TYR cc_start: 0.7420 (m-80) cc_final: 0.6224 (t80) REVERT: B 308 ARG cc_start: 0.7362 (mtp180) cc_final: 0.7149 (mtp-110) REVERT: G 37 GLN cc_start: 0.8652 (tt0) cc_final: 0.7385 (tt0) REVERT: J 27 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: J 47 TRP cc_start: 0.7252 (t-100) cc_final: 0.6769 (t-100) REVERT: Q 27 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7825 (tt0) REVERT: M 97 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: E 173 TYR cc_start: 0.7467 (m-80) cc_final: 0.6349 (t80) REVERT: I 45 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7669 (ttp80) REVERT: I 103 LYS cc_start: 0.7702 (tttt) cc_final: 0.7218 (tttp) REVERT: O 27 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: O 100 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8610 (mtpp) REVERT: N 97 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8307 (m-10) REVERT: F 173 TYR cc_start: 0.7406 (m-80) cc_final: 0.6699 (t80) REVERT: K 103 LYS cc_start: 0.7555 (tttt) cc_final: 0.7173 (tttp) outliers start: 42 outliers final: 28 residues processed: 254 average time/residue: 0.1773 time to fit residues: 69.7382 Evaluate side-chains 247 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 97 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 198 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 260 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN N 3 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094883 restraints weight = 39562.622| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.88 r_work: 0.3161 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26250 Z= 0.178 Angle : 0.631 11.256 35859 Z= 0.304 Chirality : 0.045 0.186 4215 Planarity : 0.004 0.044 4401 Dihedral : 6.061 43.126 5496 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 1.43 % Allowed : 10.55 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 3021 helix: 1.67 (0.27), residues: 402 sheet: 0.06 (0.16), residues: 993 loop : -0.41 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 45 TYR 0.012 0.001 TYR O 50 PHE 0.014 0.002 PHE Q 83 TRP 0.018 0.001 TRP B 479 HIS 0.004 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00417 (26100) covalent geometry : angle 0.59875 (35454) SS BOND : bond 0.00332 ( 45) SS BOND : angle 0.88700 ( 90) hydrogen bonds : bond 0.03703 ( 983) hydrogen bonds : angle 5.42526 ( 2610) link_ALPHA1-2 : bond 0.00419 ( 3) link_ALPHA1-2 : angle 1.64197 ( 9) link_ALPHA1-3 : bond 0.01441 ( 3) link_ALPHA1-3 : angle 1.08056 ( 9) link_ALPHA1-6 : bond 0.02969 ( 3) link_ALPHA1-6 : angle 4.60681 ( 9) link_BETA1-4 : bond 0.00608 ( 42) link_BETA1-4 : angle 2.06706 ( 126) link_NAG-ASN : bond 0.00345 ( 54) link_NAG-ASN : angle 2.10032 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6969.00 seconds wall clock time: 120 minutes 6.43 seconds (7206.43 seconds total)