Starting phenix.real_space_refine on Thu Mar 5 08:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rai_24362/03_2026/7rai_24362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rai_24362/03_2026/7rai_24362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rai_24362/03_2026/7rai_24362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rai_24362/03_2026/7rai_24362.map" model { file = "/net/cci-nas-00/data/ceres_data/7rai_24362/03_2026/7rai_24362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rai_24362/03_2026/7rai_24362.cif" } resolution = 3.24 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= 0.006 sd= 0.103 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 153 5.16 5 C 12840 2.51 5 N 3429 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20652 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "M" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "J" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 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: "T" 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: "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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: "f" 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.78, per 1000 atoms: 0.23 Number of scatterers: 20652 At special positions: 0 Unit cell: (135.192, 134.144, 132.048, 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 153 16.00 O 4230 8.00 N 3429 7.00 C 12840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 97 " - pdb=" SG CYS I 100B" distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " 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=2.04 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 201 " - pdb=" SG CYS E 433 " 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 F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 97 " - pdb=" SG CYS J 100B" distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 4 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA P 3 " - " MAN P 7 " " BMA Y 3 " - " MAN Y 5 " " BMA b 3 " - " MAN b 7 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 7 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 355 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 355 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 339 " " NAG E 606 " - " ASN E 355 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG L1001 " - " ASN L 18 " " NAG M1001 " - " ASN M 18 " " NAG N1001 " - " ASN N 18 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 197 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 295 " " NAG e 1 " - " ASN C 301 " " NAG f 1 " - " ASN C 332 " " NAG g 1 " - " ASN C 363 " " NAG h 1 " - " ASN C 386 " " NAG i 1 " - " ASN C 392 " " NAG j 1 " - " ASN C 448 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 262 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 295 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 916.0 milliseconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 50 sheets defined 15.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.577A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.802A pdb=" N THR A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.800A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.803A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.822A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.693A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.627A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 663 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.327A pdb=" N ALA H 65 " --> pdb=" O LYS H 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.603A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 removed outlier: 3.804A pdb=" N THR C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.808A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.779A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.833A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 583 Processing helix chain 'D' and resid 583 through 596 removed outlier: 3.691A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.597A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 663 Processing helix chain 'I' and resid 61 through 65 removed outlier: 4.373A pdb=" N ALA I 65 " --> pdb=" O LYS I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.064A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 114 removed outlier: 3.543A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.806A pdb=" N THR E 341 " --> pdb=" O THR E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.837A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.788A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.882A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 583 Processing helix chain 'F' and resid 583 through 596 removed outlier: 3.699A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.603A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 663 Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.348A pdb=" N ALA J 65 " --> pdb=" O LYS J 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.152A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.430A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.065A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.648A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 333 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 320 removed outlier: 7.047A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER H 100A" --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.662A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.034A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.034A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.009A pdb=" N ILE L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR L 72 " --> pdb=" O GLY L 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L 86 " --> pdb=" O SER L 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.151A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.433A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.071A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.622A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 315 through 320 removed outlier: 7.042A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER I 100A" --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.627A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.023A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.023A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'M' and resid 4 through 6 removed outlier: 4.005A pdb=" N ILE M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR M 72 " --> pdb=" O GLY M 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.513A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.157A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.436A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.120A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AE3, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.623A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 333 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 315 through 320 removed outlier: 7.052A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER J 100A" --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.610A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AE8, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.028A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.028A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AF4, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.524A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.524A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE N 86 " --> pdb=" O SER N 102 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.89 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: 6407 1.34 - 1.46: 5219 1.46 - 1.58: 9203 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 21045 Sorted by residual: bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C5 MAN P 7 " pdb=" O5 MAN P 7 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C5 MAN b 7 " pdb=" O5 MAN b 7 " ideal model delta sigma weight residual 1.418 1.451 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 21040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 26815 1.62 - 3.24: 1352 3.24 - 4.86: 247 4.86 - 6.48: 72 6.48 - 8.10: 23 Bond angle restraints: 28509 Sorted by residual: angle pdb=" N LEU B 545 " pdb=" CA LEU B 545 " pdb=" C LEU B 545 " ideal model delta sigma weight residual 114.62 110.64 3.98 1.14e+00 7.69e-01 1.22e+01 angle pdb=" N LEU D 545 " pdb=" CA LEU D 545 " pdb=" C LEU D 545 " ideal model delta sigma weight residual 114.62 110.66 3.96 1.14e+00 7.69e-01 1.20e+01 angle pdb=" C CYS E 119 " pdb=" N VAL E 120 " pdb=" CA VAL E 120 " ideal model delta sigma weight residual 120.35 124.55 -4.20 1.39e+00 5.18e-01 9.14e+00 angle pdb=" C CYS C 119 " pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta sigma weight residual 120.35 124.39 -4.04 1.39e+00 5.18e-01 8.43e+00 angle pdb=" CA LEU D 545 " pdb=" C LEU D 545 " pdb=" N SER D 546 " ideal model delta sigma weight residual 119.71 116.41 3.30 1.17e+00 7.31e-01 7.98e+00 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 12930 21.85 - 43.70: 904 43.70 - 65.56: 244 65.56 - 87.41: 150 87.41 - 109.26: 94 Dihedral angle restraints: 14322 sinusoidal: 7407 harmonic: 6915 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -121.00 35.00 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -120.95 34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -120.81 34.81 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 14319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2736 0.059 - 0.117: 659 0.117 - 0.175: 111 0.175 - 0.234: 16 0.234 - 0.292: 24 Chirality restraints: 3546 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.36e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3543 not shown) Planarity restraints: 3531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 42 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 43 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 42 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO E 43 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 42 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO C 43 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.022 5.00e-02 4.00e+02 ... (remaining 3528 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2485 2.74 - 3.28: 19799 3.28 - 3.82: 32058 3.82 - 4.36: 39270 4.36 - 4.90: 69655 Nonbonded interactions: 163267 Sorted by model distance: nonbonded pdb=" N ASP A 167 " pdb=" OD1 ASP A 167 " model vdw 2.199 3.120 nonbonded pdb=" N ASP E 167 " pdb=" OD1 ASP E 167 " model vdw 2.200 3.120 nonbonded pdb=" NE2 GLN C 258 " pdb=" OG1 THR C 387 " model vdw 2.201 3.120 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.209 3.120 nonbonded pdb=" NE2 GLN A 258 " pdb=" OG1 THR A 387 " model vdw 2.210 3.120 ... (remaining 163262 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 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'P' selection = chain 'b' selection = chain 'n' } 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.160 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.008 0.064 21219 Z= 0.364 Angle : 0.932 11.271 28989 Z= 0.432 Chirality : 0.056 0.292 3546 Planarity : 0.004 0.040 3474 Dihedral : 19.829 109.262 9744 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 7.69 % Allowed : 12.27 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.14), residues: 2376 helix: -2.98 (0.20), residues: 432 sheet: -2.86 (0.16), residues: 750 loop : -3.38 (0.14), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 166 TYR 0.024 0.002 TYR L 91 PHE 0.015 0.002 PHE M 98 TRP 0.018 0.002 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00818 (21045) covalent geometry : angle 0.87835 (28509) SS BOND : bond 0.00443 ( 42) SS BOND : angle 1.40502 ( 84) hydrogen bonds : bond 0.22749 ( 557) hydrogen bonds : angle 10.24541 ( 1557) link_ALPHA1-2 : bond 0.00296 ( 6) link_ALPHA1-2 : angle 2.49024 ( 18) link_ALPHA1-3 : bond 0.00523 ( 6) link_ALPHA1-3 : angle 1.69153 ( 18) link_ALPHA1-6 : bond 0.00261 ( 6) link_ALPHA1-6 : angle 1.93175 ( 18) link_BETA1-4 : bond 0.00772 ( 57) link_BETA1-4 : angle 2.06271 ( 171) link_NAG-ASN : bond 0.00638 ( 57) link_NAG-ASN : angle 3.49249 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 331 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.7346 (ptmt) REVERT: A 271 MET cc_start: 0.7651 (tpt) cc_final: 0.7364 (tpp) REVERT: A 469 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6588 (mtp85) REVERT: A 475 MET cc_start: 0.8024 (mmm) cc_final: 0.7689 (mmm) REVERT: B 543 ASN cc_start: 0.8804 (m110) cc_final: 0.8444 (m110) REVERT: B 619 LEU cc_start: 0.7980 (mt) cc_final: 0.7763 (mt) REVERT: H 19 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7955 (ttm170) REVERT: H 24 ASP cc_start: 0.8673 (p0) cc_final: 0.8297 (p0) REVERT: H 46 GLU cc_start: 0.8169 (tt0) cc_final: 0.7931 (tt0) REVERT: L 3 GLN cc_start: 0.8094 (mm110) cc_final: 0.7851 (mm-40) REVERT: L 81 ASP cc_start: 0.8002 (t0) cc_final: 0.7739 (t0) REVERT: L 91 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8795 (p90) REVERT: L 100 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: C 91 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: C 155 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.7471 (ptmt) REVERT: C 271 MET cc_start: 0.7760 (tpt) cc_final: 0.7499 (tpp) REVERT: C 305 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: C 475 MET cc_start: 0.8120 (mmm) cc_final: 0.7673 (mmm) REVERT: D 543 ASN cc_start: 0.8847 (m110) cc_final: 0.8469 (m110) REVERT: D 544 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8896 (tt) REVERT: D 654 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7200 (mt-10) REVERT: I 24 ASP cc_start: 0.8753 (p0) cc_final: 0.8503 (p0) REVERT: M 50 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7978 (mtp85) REVERT: M 100 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: E 155 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7455 (ptmt) REVERT: E 271 MET cc_start: 0.7691 (tpt) cc_final: 0.7335 (mmp) REVERT: E 475 MET cc_start: 0.8034 (mmm) cc_final: 0.7399 (mmm) REVERT: F 543 ASN cc_start: 0.8888 (m110) cc_final: 0.8504 (m110) REVERT: F 601 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8210 (mtpp) REVERT: F 632 ASP cc_start: 0.8944 (t0) cc_final: 0.8717 (t0) REVERT: F 654 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7105 (mt-10) REVERT: J 23 LYS cc_start: 0.9294 (tttm) cc_final: 0.9041 (tttt) REVERT: J 24 ASP cc_start: 0.8719 (p0) cc_final: 0.8345 (p0) REVERT: J 67 MET cc_start: 0.8695 (ptm) cc_final: 0.8241 (ptm) REVERT: N 61 ARG cc_start: 0.8507 (ptp90) cc_final: 0.8304 (ptt-90) REVERT: N 79 GLN cc_start: 0.8176 (mt0) cc_final: 0.7947 (mt0) outliers start: 161 outliers final: 83 residues processed: 464 average time/residue: 0.1708 time to fit residues: 116.7302 Evaluate side-chains 349 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 256 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 249 HIS A 293 GLN A 302 ASN B 540 GLN B 607 ASN B 618 ASN H 3 GLN H 6 GLN H 108 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN C 66 HIS C 114 GLN C 249 HIS C 302 ASN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 607 ASN D 618 ASN I 3 GLN I 6 GLN I 108 GLN M 6 GLN M 79 GLN M 89 GLN E 66 HIS E 114 GLN E 249 HIS E 302 ASN F 540 GLN F 607 ASN F 618 ASN J 3 GLN J 6 GLN N 6 GLN N 79 GLN N 89 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.081259 restraints weight = 35018.753| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.50 r_work: 0.2947 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21219 Z= 0.146 Angle : 0.770 10.327 28989 Z= 0.348 Chirality : 0.048 0.241 3546 Planarity : 0.004 0.045 3474 Dihedral : 14.934 74.575 5469 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.97 % Allowed : 15.09 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.15), residues: 2376 helix: -2.01 (0.24), residues: 408 sheet: -1.98 (0.17), residues: 735 loop : -2.71 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 24 TYR 0.017 0.001 TYR L 91 PHE 0.015 0.001 PHE E 382 TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00339 (21045) covalent geometry : angle 0.71381 (28509) SS BOND : bond 0.00376 ( 42) SS BOND : angle 0.92251 ( 84) hydrogen bonds : bond 0.04165 ( 557) hydrogen bonds : angle 6.27907 ( 1557) link_ALPHA1-2 : bond 0.00334 ( 6) link_ALPHA1-2 : angle 2.32649 ( 18) link_ALPHA1-3 : bond 0.01268 ( 6) link_ALPHA1-3 : angle 1.69393 ( 18) link_ALPHA1-6 : bond 0.00333 ( 6) link_ALPHA1-6 : angle 1.98895 ( 18) link_BETA1-4 : bond 0.00586 ( 57) link_BETA1-4 : angle 2.11762 ( 171) link_NAG-ASN : bond 0.00379 ( 57) link_NAG-ASN : angle 3.06188 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 310 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8539 (mmtp) cc_final: 0.7753 (mmtm) REVERT: A 91 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: A 244 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8971 (t) REVERT: A 271 MET cc_start: 0.8211 (tpt) cc_final: 0.7928 (mmm) REVERT: A 434 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8292 (ttp) REVERT: A 469 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7159 (mtp85) REVERT: A 475 MET cc_start: 0.8128 (mmm) cc_final: 0.7506 (mmm) REVERT: B 543 ASN cc_start: 0.8794 (m110) cc_final: 0.8434 (m-40) REVERT: B 626 MET cc_start: 0.7447 (mtp) cc_final: 0.6486 (ttm) REVERT: B 654 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6738 (mt-10) REVERT: H 19 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7964 (ttm170) REVERT: H 24 ASP cc_start: 0.8551 (p0) cc_final: 0.8280 (p0) REVERT: H 46 GLU cc_start: 0.8488 (tt0) cc_final: 0.8240 (tt0) REVERT: L 81 ASP cc_start: 0.8498 (t0) cc_final: 0.8169 (t70) REVERT: L 100 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: C 195 ASN cc_start: 0.8868 (p0) cc_final: 0.8566 (p0) REVERT: C 244 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8922 (t) REVERT: C 271 MET cc_start: 0.8168 (tpt) cc_final: 0.7613 (tpp) REVERT: C 475 MET cc_start: 0.8177 (mmm) cc_final: 0.7591 (mmm) REVERT: D 535 MET cc_start: 0.8291 (mmt) cc_final: 0.7984 (ttp) REVERT: D 543 ASN cc_start: 0.8779 (m110) cc_final: 0.8431 (m110) REVERT: D 574 LYS cc_start: 0.8172 (mttt) cc_final: 0.7941 (mttt) REVERT: D 654 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7029 (mt-10) REVERT: D 659 ASP cc_start: 0.6860 (m-30) cc_final: 0.6656 (m-30) REVERT: I 19 ARG cc_start: 0.8314 (ttm170) cc_final: 0.8022 (ttm170) REVERT: I 43 GLN cc_start: 0.7699 (pm20) cc_final: 0.7387 (pm20) REVERT: I 100 GLU cc_start: 0.8415 (mp0) cc_final: 0.8201 (mm-30) REVERT: M 50 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8246 (mtp85) REVERT: M 100 GLN cc_start: 0.8855 (pm20) cc_final: 0.8612 (pm20) REVERT: E 46 LYS cc_start: 0.8537 (mmtp) cc_final: 0.7923 (mttp) REVERT: E 161 MET cc_start: 0.8792 (tpt) cc_final: 0.8469 (tpt) REVERT: E 166 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8416 (mmt180) REVERT: E 244 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8880 (t) REVERT: E 271 MET cc_start: 0.8016 (tpt) cc_final: 0.7516 (mmp) REVERT: E 305 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: E 370 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: E 373 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.9007 (m) REVERT: E 469 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6336 (ptp90) REVERT: E 475 MET cc_start: 0.8086 (mmm) cc_final: 0.7198 (mmm) REVERT: F 542 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8374 (ttm110) REVERT: F 543 ASN cc_start: 0.8823 (m110) cc_final: 0.8397 (m110) REVERT: F 588 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7686 (ttm-80) REVERT: F 601 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8147 (mtpp) REVERT: F 654 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6945 (mt-10) REVERT: J 24 ASP cc_start: 0.8656 (p0) cc_final: 0.8452 (p0) REVERT: J 100 GLU cc_start: 0.8406 (mp0) cc_final: 0.8064 (mt-10) REVERT: N 24 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.7537 (ttm110) REVERT: N 81 ASP cc_start: 0.8563 (t0) cc_final: 0.8246 (t0) outliers start: 104 outliers final: 46 residues processed: 393 average time/residue: 0.1529 time to fit residues: 90.8511 Evaluate side-chains 327 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain N residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 213 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN B 618 ASN B 625 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 293 GLN D 618 ASN M 6 GLN M 37 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 293 GLN E 328 GLN F 618 ASN N 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078941 restraints weight = 35512.532| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.50 r_work: 0.2908 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21219 Z= 0.237 Angle : 0.833 17.586 28989 Z= 0.367 Chirality : 0.055 0.869 3546 Planarity : 0.004 0.047 3474 Dihedral : 12.512 68.464 5370 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.87 % Allowed : 16.95 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.16), residues: 2376 helix: -1.42 (0.26), residues: 402 sheet: -1.76 (0.18), residues: 750 loop : -2.58 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 24 TYR 0.025 0.002 TYR L 91 PHE 0.016 0.002 PHE I 91 TRP 0.014 0.001 TRP E 112 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00565 (21045) covalent geometry : angle 0.74934 (28509) SS BOND : bond 0.00479 ( 42) SS BOND : angle 1.30799 ( 84) hydrogen bonds : bond 0.04206 ( 557) hydrogen bonds : angle 5.81005 ( 1557) link_ALPHA1-2 : bond 0.00366 ( 6) link_ALPHA1-2 : angle 2.22214 ( 18) link_ALPHA1-3 : bond 0.01176 ( 6) link_ALPHA1-3 : angle 1.25417 ( 18) link_ALPHA1-6 : bond 0.00326 ( 6) link_ALPHA1-6 : angle 1.79782 ( 18) link_BETA1-4 : bond 0.00526 ( 57) link_BETA1-4 : angle 2.12003 ( 171) link_NAG-ASN : bond 0.00531 ( 57) link_NAG-ASN : angle 4.18936 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 281 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8498 (mmtp) cc_final: 0.7674 (mttm) REVERT: A 244 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9056 (t) REVERT: A 246 GLN cc_start: 0.8093 (tp40) cc_final: 0.7664 (pm20) REVERT: A 271 MET cc_start: 0.8238 (tpt) cc_final: 0.7922 (mmm) REVERT: A 426 MET cc_start: 0.8995 (mmm) cc_final: 0.8729 (mmm) REVERT: A 469 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7231 (mtp85) REVERT: A 475 MET cc_start: 0.8175 (mmm) cc_final: 0.7564 (mmm) REVERT: B 543 ASN cc_start: 0.8920 (m110) cc_final: 0.8449 (m110) REVERT: B 588 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7806 (ttm-80) REVERT: B 626 MET cc_start: 0.7174 (mtp) cc_final: 0.6753 (mtp) REVERT: B 654 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6723 (mt-10) REVERT: H 24 ASP cc_start: 0.8699 (p0) cc_final: 0.8454 (p0) REVERT: H 46 GLU cc_start: 0.8502 (tt0) cc_final: 0.8232 (tt0) REVERT: H 64 GLN cc_start: 0.8858 (tp40) cc_final: 0.8574 (tp40) REVERT: L 74 THR cc_start: 0.8572 (p) cc_final: 0.8321 (t) REVERT: L 81 ASP cc_start: 0.8573 (t0) cc_final: 0.8242 (t70) REVERT: L 100 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: L 105 MET cc_start: 0.7965 (mtm) cc_final: 0.7687 (mpp) REVERT: C 211 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8754 (tp30) REVERT: C 244 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9020 (t) REVERT: C 246 GLN cc_start: 0.8055 (tp40) cc_final: 0.7657 (pm20) REVERT: C 271 MET cc_start: 0.8202 (tpt) cc_final: 0.7634 (tpp) REVERT: C 428 GLN cc_start: 0.8574 (mt0) cc_final: 0.7975 (mm-40) REVERT: C 475 MET cc_start: 0.8260 (mmm) cc_final: 0.7611 (mmm) REVERT: D 574 LYS cc_start: 0.8101 (mttt) cc_final: 0.7871 (mttt) REVERT: D 654 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6958 (mt-10) REVERT: D 659 ASP cc_start: 0.6866 (m-30) cc_final: 0.6647 (m-30) REVERT: I 43 GLN cc_start: 0.7673 (pm20) cc_final: 0.7259 (pm20) REVERT: I 100 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: M 50 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8274 (mtp85) REVERT: E 153 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8043 (tp30) REVERT: E 211 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8626 (tp30) REVERT: E 271 MET cc_start: 0.8055 (tpt) cc_final: 0.7497 (mmp) REVERT: E 305 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: E 370 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8557 (mp0) REVERT: E 434 MET cc_start: 0.8834 (ttp) cc_final: 0.8622 (ttt) REVERT: E 469 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6610 (ptp90) REVERT: E 475 MET cc_start: 0.8225 (mmm) cc_final: 0.7371 (mmm) REVERT: F 543 ASN cc_start: 0.8826 (m110) cc_final: 0.8376 (m110) REVERT: F 626 MET cc_start: 0.7298 (mtp) cc_final: 0.6356 (ttm) REVERT: F 654 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6969 (mt-10) REVERT: J 24 ASP cc_start: 0.8710 (p0) cc_final: 0.8484 (p0) REVERT: J 81 GLU cc_start: 0.7554 (tt0) cc_final: 0.6960 (mp0) REVERT: J 100 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: N 81 ASP cc_start: 0.8642 (t0) cc_final: 0.8296 (t0) outliers start: 123 outliers final: 69 residues processed: 375 average time/residue: 0.1593 time to fit residues: 89.7643 Evaluate side-chains 344 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 143 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 37 GLN F 625 ASN N 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079392 restraints weight = 35347.350| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.50 r_work: 0.2914 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21219 Z= 0.208 Angle : 0.794 16.728 28989 Z= 0.350 Chirality : 0.054 0.758 3546 Planarity : 0.004 0.036 3474 Dihedral : 11.118 63.010 5356 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.87 % Allowed : 18.48 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 2376 helix: -1.27 (0.26), residues: 408 sheet: -1.57 (0.18), residues: 750 loop : -2.46 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 500 TYR 0.020 0.002 TYR L 91 PHE 0.014 0.002 PHE C 382 TRP 0.015 0.001 TRP A 112 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00493 (21045) covalent geometry : angle 0.71455 (28509) SS BOND : bond 0.00437 ( 42) SS BOND : angle 1.10523 ( 84) hydrogen bonds : bond 0.03789 ( 557) hydrogen bonds : angle 5.52134 ( 1557) link_ALPHA1-2 : bond 0.00395 ( 6) link_ALPHA1-2 : angle 2.18357 ( 18) link_ALPHA1-3 : bond 0.01256 ( 6) link_ALPHA1-3 : angle 1.20158 ( 18) link_ALPHA1-6 : bond 0.00341 ( 6) link_ALPHA1-6 : angle 1.74579 ( 18) link_BETA1-4 : bond 0.00500 ( 57) link_BETA1-4 : angle 1.96001 ( 171) link_NAG-ASN : bond 0.00542 ( 57) link_NAG-ASN : angle 4.03428 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 272 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8526 (mmtp) cc_final: 0.7690 (mttm) REVERT: A 161 MET cc_start: 0.8786 (tpp) cc_final: 0.8404 (tpp) REVERT: A 211 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8690 (mm-30) REVERT: A 271 MET cc_start: 0.8227 (tpt) cc_final: 0.7921 (mmm) REVERT: A 426 MET cc_start: 0.9013 (mmm) cc_final: 0.8727 (mmm) REVERT: A 469 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7332 (mtp85) REVERT: A 475 MET cc_start: 0.8177 (mmm) cc_final: 0.7486 (mmm) REVERT: B 543 ASN cc_start: 0.8876 (m110) cc_final: 0.8478 (m110) REVERT: B 626 MET cc_start: 0.7195 (mtp) cc_final: 0.6826 (mtp) REVERT: B 654 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6742 (mt-10) REVERT: H 19 ARG cc_start: 0.8445 (ttm170) cc_final: 0.8238 (ttm170) REVERT: H 24 ASP cc_start: 0.8677 (p0) cc_final: 0.8437 (p0) REVERT: H 46 GLU cc_start: 0.8491 (tt0) cc_final: 0.8228 (tt0) REVERT: H 64 GLN cc_start: 0.8862 (tp40) cc_final: 0.8565 (tp40) REVERT: L 24 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7417 (ttm110) REVERT: L 50 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8399 (mtp85) REVERT: L 74 THR cc_start: 0.8591 (p) cc_final: 0.8375 (t) REVERT: L 81 ASP cc_start: 0.8582 (t0) cc_final: 0.8274 (t70) REVERT: C 150 MET cc_start: 0.8141 (tpt) cc_final: 0.7913 (tpp) REVERT: C 211 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8785 (tp30) REVERT: C 244 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9058 (t) REVERT: C 246 GLN cc_start: 0.8064 (tp40) cc_final: 0.7643 (pm20) REVERT: C 271 MET cc_start: 0.8179 (tpt) cc_final: 0.7646 (tpp) REVERT: C 428 GLN cc_start: 0.8602 (mt0) cc_final: 0.8001 (mm-40) REVERT: C 475 MET cc_start: 0.8257 (mmm) cc_final: 0.7658 (mmm) REVERT: D 574 LYS cc_start: 0.8091 (mttt) cc_final: 0.7867 (mttt) REVERT: D 654 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7049 (mt-10) REVERT: D 659 ASP cc_start: 0.6870 (m-30) cc_final: 0.6631 (m-30) REVERT: I 3 GLN cc_start: 0.7044 (tp-100) cc_final: 0.6656 (tp-100) REVERT: I 43 GLN cc_start: 0.7751 (pm20) cc_final: 0.7346 (pm20) REVERT: I 100 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8235 (mm-30) REVERT: M 4 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7735 (mmm) REVERT: M 33 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8411 (tp) REVERT: M 50 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8265 (mtp85) REVERT: M 100 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8527 (pm20) REVERT: E 153 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8172 (tp30) REVERT: E 211 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8641 (tp30) REVERT: E 246 GLN cc_start: 0.8148 (tp40) cc_final: 0.7752 (pm20) REVERT: E 271 MET cc_start: 0.8054 (tpt) cc_final: 0.7505 (mmp) REVERT: E 305 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8224 (ttpp) REVERT: E 370 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: E 469 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6554 (ptp90) REVERT: E 475 MET cc_start: 0.8168 (mmm) cc_final: 0.7321 (mmm) REVERT: F 543 ASN cc_start: 0.8781 (m110) cc_final: 0.8325 (m110) REVERT: F 654 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6992 (mt-10) REVERT: J 81 GLU cc_start: 0.7573 (tt0) cc_final: 0.6965 (mp0) REVERT: J 100 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: N 24 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7333 (ttm110) REVERT: N 81 ASP cc_start: 0.8637 (t0) cc_final: 0.8310 (t0) outliers start: 123 outliers final: 74 residues processed: 367 average time/residue: 0.1594 time to fit residues: 88.2409 Evaluate side-chains 350 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 262 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 145 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 183 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN M 6 GLN F 618 ASN N 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.110027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082233 restraints weight = 34935.464| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.49 r_work: 0.2967 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21219 Z= 0.125 Angle : 0.730 16.618 28989 Z= 0.320 Chirality : 0.050 0.623 3546 Planarity : 0.003 0.034 3474 Dihedral : 9.915 59.873 5350 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.63 % Allowed : 20.39 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.16), residues: 2376 helix: -1.05 (0.26), residues: 408 sheet: -1.27 (0.19), residues: 747 loop : -2.27 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 24 TYR 0.016 0.001 TYR A 486 PHE 0.012 0.001 PHE C 382 TRP 0.013 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00284 (21045) covalent geometry : angle 0.65621 (28509) SS BOND : bond 0.00436 ( 42) SS BOND : angle 1.13038 ( 84) hydrogen bonds : bond 0.03287 ( 557) hydrogen bonds : angle 5.11995 ( 1557) link_ALPHA1-2 : bond 0.00351 ( 6) link_ALPHA1-2 : angle 2.01262 ( 18) link_ALPHA1-3 : bond 0.01305 ( 6) link_ALPHA1-3 : angle 1.03437 ( 18) link_ALPHA1-6 : bond 0.00574 ( 6) link_ALPHA1-6 : angle 1.57229 ( 18) link_BETA1-4 : bond 0.00512 ( 57) link_BETA1-4 : angle 1.71906 ( 171) link_NAG-ASN : bond 0.00483 ( 57) link_NAG-ASN : angle 3.77861 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 290 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8516 (mmtp) cc_final: 0.7714 (mttm) REVERT: A 265 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8656 (mt) REVERT: A 271 MET cc_start: 0.8187 (tpt) cc_final: 0.7918 (mmm) REVERT: A 469 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7107 (mtp85) REVERT: A 475 MET cc_start: 0.8090 (mmm) cc_final: 0.7460 (mmm) REVERT: B 543 ASN cc_start: 0.8877 (m110) cc_final: 0.8481 (m110) REVERT: B 626 MET cc_start: 0.7110 (mtp) cc_final: 0.6734 (mtp) REVERT: B 654 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6556 (mt-10) REVERT: H 24 ASP cc_start: 0.8625 (p0) cc_final: 0.8415 (p0) REVERT: H 46 GLU cc_start: 0.8385 (tt0) cc_final: 0.8151 (tt0) REVERT: H 54 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8334 (t0) REVERT: H 64 GLN cc_start: 0.8860 (tp40) cc_final: 0.8534 (tp-100) REVERT: L 4 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.6980 (mmm) REVERT: L 24 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7446 (ttm110) REVERT: L 50 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8346 (mtp85) REVERT: L 74 THR cc_start: 0.8572 (p) cc_final: 0.8353 (t) REVERT: L 81 ASP cc_start: 0.8509 (t0) cc_final: 0.8174 (t70) REVERT: C 35 TRP cc_start: 0.8568 (m100) cc_final: 0.8021 (m-90) REVERT: C 46 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8163 (mmtm) REVERT: C 211 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8740 (tp30) REVERT: C 244 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9076 (t) REVERT: C 246 GLN cc_start: 0.8046 (tp40) cc_final: 0.7598 (pm20) REVERT: C 271 MET cc_start: 0.8175 (tpt) cc_final: 0.7949 (mmm) REVERT: C 428 GLN cc_start: 0.8572 (mt0) cc_final: 0.7964 (mm-40) REVERT: C 475 MET cc_start: 0.8179 (mmm) cc_final: 0.7634 (mmm) REVERT: D 626 MET cc_start: 0.7075 (mtp) cc_final: 0.6610 (ttm) REVERT: D 654 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7079 (mt-10) REVERT: D 659 ASP cc_start: 0.6990 (m-30) cc_final: 0.6739 (m-30) REVERT: I 3 GLN cc_start: 0.7122 (tp-100) cc_final: 0.6689 (tp-100) REVERT: I 19 ARG cc_start: 0.8310 (ttm170) cc_final: 0.8088 (ttm170) REVERT: I 43 GLN cc_start: 0.7687 (pm20) cc_final: 0.7304 (pm20) REVERT: I 54 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8193 (t0) REVERT: I 100 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: M 24 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7469 (ttm110) REVERT: M 33 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8332 (tp) REVERT: M 50 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8243 (mtp85) REVERT: M 76 LYS cc_start: 0.8330 (mmmm) cc_final: 0.8068 (mmmm) REVERT: E 150 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7523 (ttm) REVERT: E 153 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: E 211 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8644 (tp30) REVERT: E 246 GLN cc_start: 0.8156 (tp40) cc_final: 0.7721 (pm20) REVERT: E 271 MET cc_start: 0.8089 (tpt) cc_final: 0.7504 (mmp) REVERT: E 469 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6553 (ptp90) REVERT: E 475 MET cc_start: 0.8033 (mmm) cc_final: 0.7171 (mmm) REVERT: F 535 MET cc_start: 0.8465 (mmm) cc_final: 0.8231 (mmm) REVERT: F 543 ASN cc_start: 0.8678 (m110) cc_final: 0.8241 (m110) REVERT: F 626 MET cc_start: 0.7171 (mtp) cc_final: 0.6465 (ttm) REVERT: F 654 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7109 (mt-10) REVERT: J 24 ASP cc_start: 0.8624 (p0) cc_final: 0.8351 (p0) REVERT: J 54 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8028 (t0) REVERT: J 81 GLU cc_start: 0.7655 (tt0) cc_final: 0.6985 (mp0) REVERT: J 100 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: N 24 ARG cc_start: 0.7599 (mtp-110) cc_final: 0.7290 (ttm110) REVERT: N 76 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7904 (mmmm) REVERT: N 81 ASP cc_start: 0.8652 (t0) cc_final: 0.8335 (t0) outliers start: 97 outliers final: 52 residues processed: 363 average time/residue: 0.1601 time to fit residues: 87.7794 Evaluate side-chains 344 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 14 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 232 optimal weight: 0.0980 chunk 208 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078930 restraints weight = 35232.075| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.49 r_work: 0.2909 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21219 Z= 0.254 Angle : 0.791 16.835 28989 Z= 0.352 Chirality : 0.052 0.654 3546 Planarity : 0.004 0.038 3474 Dihedral : 9.710 59.169 5337 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.06 % Allowed : 20.06 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.16), residues: 2376 helix: -1.00 (0.27), residues: 408 sheet: -1.29 (0.19), residues: 750 loop : -2.26 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 76 TYR 0.024 0.002 TYR L 91 PHE 0.016 0.002 PHE J 91 TRP 0.013 0.001 TRP A 112 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00608 (21045) covalent geometry : angle 0.71876 (28509) SS BOND : bond 0.00551 ( 42) SS BOND : angle 1.12259 ( 84) hydrogen bonds : bond 0.03711 ( 557) hydrogen bonds : angle 5.33928 ( 1557) link_ALPHA1-2 : bond 0.00361 ( 6) link_ALPHA1-2 : angle 2.16248 ( 18) link_ALPHA1-3 : bond 0.01335 ( 6) link_ALPHA1-3 : angle 1.14640 ( 18) link_ALPHA1-6 : bond 0.00430 ( 6) link_ALPHA1-6 : angle 1.60612 ( 18) link_BETA1-4 : bond 0.00508 ( 57) link_BETA1-4 : angle 1.73940 ( 171) link_NAG-ASN : bond 0.00585 ( 57) link_NAG-ASN : angle 3.92968 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 265 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8488 (mmtp) cc_final: 0.7670 (mttm) REVERT: A 211 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: A 265 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8741 (mp) REVERT: A 271 MET cc_start: 0.8133 (tpt) cc_final: 0.7846 (mmp) REVERT: A 469 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6612 (mtp85) REVERT: A 475 MET cc_start: 0.8217 (mmm) cc_final: 0.7536 (mmm) REVERT: B 543 ASN cc_start: 0.8910 (m110) cc_final: 0.8482 (m110) REVERT: B 626 MET cc_start: 0.7237 (mtp) cc_final: 0.6837 (mtp) REVERT: B 654 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6611 (mt-10) REVERT: H 24 ASP cc_start: 0.8771 (p0) cc_final: 0.8422 (p0) REVERT: H 46 GLU cc_start: 0.8506 (tt0) cc_final: 0.8236 (tt0) REVERT: H 57 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9196 (mmtp) REVERT: H 64 GLN cc_start: 0.8877 (tp40) cc_final: 0.8563 (tp40) REVERT: L 50 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8385 (mtp85) REVERT: L 81 ASP cc_start: 0.8564 (t0) cc_final: 0.8247 (t70) REVERT: C 46 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8155 (mmtm) REVERT: C 155 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7141 (ptmt) REVERT: C 211 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8674 (tp30) REVERT: C 244 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9073 (t) REVERT: C 246 GLN cc_start: 0.7977 (tp40) cc_final: 0.7637 (pm20) REVERT: C 271 MET cc_start: 0.8182 (tpt) cc_final: 0.7722 (tpp) REVERT: C 428 GLN cc_start: 0.8601 (mt0) cc_final: 0.7965 (mm-40) REVERT: C 475 MET cc_start: 0.8309 (mmm) cc_final: 0.7640 (mmm) REVERT: D 626 MET cc_start: 0.7135 (mtp) cc_final: 0.6553 (ttm) REVERT: D 654 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7070 (mt-10) REVERT: D 659 ASP cc_start: 0.6886 (m-30) cc_final: 0.6638 (m-30) REVERT: I 3 GLN cc_start: 0.7282 (tp-100) cc_final: 0.6917 (tp-100) REVERT: I 43 GLN cc_start: 0.7775 (pm20) cc_final: 0.7361 (pm20) REVERT: I 48 MET cc_start: 0.8876 (mtp) cc_final: 0.8603 (ttm) REVERT: I 100 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8205 (mm-30) REVERT: M 4 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7498 (mmm) REVERT: M 33 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8237 (tp) REVERT: M 50 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8273 (mtp85) REVERT: M 100 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: E 153 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: E 211 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8621 (tp30) REVERT: E 246 GLN cc_start: 0.8164 (tp40) cc_final: 0.7766 (pm20) REVERT: E 271 MET cc_start: 0.7969 (tpt) cc_final: 0.7466 (mmp) REVERT: E 469 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6654 (ptp90) REVERT: E 475 MET cc_start: 0.8207 (mmm) cc_final: 0.7389 (mmm) REVERT: F 535 MET cc_start: 0.8479 (mmm) cc_final: 0.8255 (mmm) REVERT: F 543 ASN cc_start: 0.8799 (m110) cc_final: 0.8319 (m110) REVERT: F 588 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.8017 (ttm-80) REVERT: F 626 MET cc_start: 0.7215 (mtp) cc_final: 0.6399 (ttm) REVERT: F 654 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7000 (mt-10) REVERT: J 24 ASP cc_start: 0.8751 (p0) cc_final: 0.8420 (p0) REVERT: J 54 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (t0) REVERT: J 81 GLU cc_start: 0.7570 (tt0) cc_final: 0.6966 (mp0) REVERT: J 100 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: N 81 ASP cc_start: 0.8679 (t0) cc_final: 0.8354 (t0) outliers start: 106 outliers final: 67 residues processed: 347 average time/residue: 0.1501 time to fit residues: 78.8215 Evaluate side-chains 345 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 262 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085714 restraints weight = 35063.010| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.91 r_work: 0.3001 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21219 Z= 0.175 Angle : 0.760 16.279 28989 Z= 0.336 Chirality : 0.050 0.603 3546 Planarity : 0.004 0.037 3474 Dihedral : 9.360 59.977 5335 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.63 % Allowed : 20.87 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.16), residues: 2376 helix: -0.72 (0.27), residues: 390 sheet: -1.17 (0.19), residues: 750 loop : -2.16 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 24 TYR 0.016 0.001 TYR L 91 PHE 0.012 0.001 PHE J 91 TRP 0.013 0.001 TRP A 112 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00415 (21045) covalent geometry : angle 0.68710 (28509) SS BOND : bond 0.00455 ( 42) SS BOND : angle 1.57998 ( 84) hydrogen bonds : bond 0.03427 ( 557) hydrogen bonds : angle 5.15874 ( 1557) link_ALPHA1-2 : bond 0.00345 ( 6) link_ALPHA1-2 : angle 2.07202 ( 18) link_ALPHA1-3 : bond 0.01328 ( 6) link_ALPHA1-3 : angle 1.03314 ( 18) link_ALPHA1-6 : bond 0.00548 ( 6) link_ALPHA1-6 : angle 1.49768 ( 18) link_BETA1-4 : bond 0.00504 ( 57) link_BETA1-4 : angle 1.62231 ( 171) link_NAG-ASN : bond 0.00506 ( 57) link_NAG-ASN : angle 3.82349 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 265 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8616 (mmtp) cc_final: 0.7899 (mttm) REVERT: A 211 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8792 (mm-30) REVERT: A 265 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8888 (mp) REVERT: A 271 MET cc_start: 0.8209 (tpt) cc_final: 0.7967 (mmm) REVERT: A 469 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.6863 (mtp85) REVERT: A 475 MET cc_start: 0.8117 (mmm) cc_final: 0.7705 (mmm) REVERT: B 543 ASN cc_start: 0.8971 (m110) cc_final: 0.8636 (m110) REVERT: B 654 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6831 (mt-10) REVERT: H 24 ASP cc_start: 0.8520 (p0) cc_final: 0.8178 (p0) REVERT: H 64 GLN cc_start: 0.8855 (tp40) cc_final: 0.8583 (tp40) REVERT: L 24 ARG cc_start: 0.7743 (mtp-110) cc_final: 0.7493 (ttm110) REVERT: L 50 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8350 (mtp85) REVERT: L 81 ASP cc_start: 0.8293 (t0) cc_final: 0.8000 (t70) REVERT: C 46 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8310 (mmtm) REVERT: C 155 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.7699 (ptmt) REVERT: C 271 MET cc_start: 0.8261 (tpt) cc_final: 0.8035 (mmm) REVERT: C 428 GLN cc_start: 0.8543 (mt0) cc_final: 0.8099 (mm-40) REVERT: C 475 MET cc_start: 0.8222 (mmm) cc_final: 0.7892 (mmm) REVERT: D 626 MET cc_start: 0.7296 (mtp) cc_final: 0.6987 (ttm) REVERT: D 654 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7269 (mt-10) REVERT: D 659 ASP cc_start: 0.7180 (m-30) cc_final: 0.6918 (m-30) REVERT: I 3 GLN cc_start: 0.7313 (tp-100) cc_final: 0.7106 (tp-100) REVERT: I 43 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: I 100 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8226 (mm-30) REVERT: M 33 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8458 (tp) REVERT: M 50 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8253 (mtp85) REVERT: M 100 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: E 150 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7572 (ttm) REVERT: E 153 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: E 211 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8756 (tp30) REVERT: E 271 MET cc_start: 0.8079 (tpt) cc_final: 0.7569 (mmp) REVERT: E 469 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6934 (ptp90) REVERT: E 475 MET cc_start: 0.8076 (mmm) cc_final: 0.7570 (mmm) REVERT: F 535 MET cc_start: 0.8386 (mmm) cc_final: 0.8162 (mmm) REVERT: F 543 ASN cc_start: 0.8742 (m110) cc_final: 0.8360 (m110) REVERT: F 626 MET cc_start: 0.7426 (mtp) cc_final: 0.6916 (ttm) REVERT: F 654 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7292 (mt-10) REVERT: J 24 ASP cc_start: 0.8513 (p0) cc_final: 0.8295 (p0) REVERT: J 81 GLU cc_start: 0.7588 (tt0) cc_final: 0.7220 (mp0) REVERT: N 24 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7475 (ttm110) REVERT: N 81 ASP cc_start: 0.8508 (t0) cc_final: 0.8239 (t0) outliers start: 97 outliers final: 66 residues processed: 337 average time/residue: 0.1552 time to fit residues: 78.8441 Evaluate side-chains 341 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 263 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 119 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.109054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083251 restraints weight = 34964.140| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.12 r_work: 0.2986 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21219 Z= 0.155 Angle : 0.753 17.255 28989 Z= 0.333 Chirality : 0.050 0.642 3546 Planarity : 0.004 0.037 3474 Dihedral : 8.996 59.725 5329 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.35 % Allowed : 21.11 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.16), residues: 2376 helix: -0.63 (0.27), residues: 390 sheet: -1.06 (0.19), residues: 750 loop : -2.09 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 24 TYR 0.014 0.001 TYR A 486 PHE 0.011 0.001 PHE E 382 TRP 0.012 0.001 TRP A 112 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00362 (21045) covalent geometry : angle 0.68633 (28509) SS BOND : bond 0.00445 ( 42) SS BOND : angle 1.46077 ( 84) hydrogen bonds : bond 0.03312 ( 557) hydrogen bonds : angle 5.05574 ( 1557) link_ALPHA1-2 : bond 0.00307 ( 6) link_ALPHA1-2 : angle 2.02773 ( 18) link_ALPHA1-3 : bond 0.01336 ( 6) link_ALPHA1-3 : angle 1.00059 ( 18) link_ALPHA1-6 : bond 0.00631 ( 6) link_ALPHA1-6 : angle 1.41757 ( 18) link_BETA1-4 : bond 0.00512 ( 57) link_BETA1-4 : angle 1.57905 ( 171) link_NAG-ASN : bond 0.00482 ( 57) link_NAG-ASN : angle 3.65097 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 268 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8496 (mmtp) cc_final: 0.7691 (mttm) REVERT: A 211 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: A 265 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8754 (mp) REVERT: A 271 MET cc_start: 0.8100 (tpt) cc_final: 0.7537 (tpp) REVERT: A 434 MET cc_start: 0.8195 (ttt) cc_final: 0.7882 (ttt) REVERT: A 469 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6474 (mtp85) REVERT: A 475 MET cc_start: 0.8109 (mmm) cc_final: 0.7482 (mmm) REVERT: B 543 ASN cc_start: 0.8916 (m110) cc_final: 0.8496 (m110) REVERT: B 654 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6554 (mt-10) REVERT: H 24 ASP cc_start: 0.8664 (p0) cc_final: 0.8284 (p0) REVERT: H 64 GLN cc_start: 0.8862 (tp40) cc_final: 0.8503 (tp-100) REVERT: L 24 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7365 (ttm110) REVERT: L 50 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8322 (mtp85) REVERT: L 81 ASP cc_start: 0.8448 (t0) cc_final: 0.8126 (t0) REVERT: C 46 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8166 (mmtm) REVERT: C 155 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7512 (ptmt) REVERT: C 246 GLN cc_start: 0.8358 (pm20) cc_final: 0.7796 (tp-100) REVERT: C 265 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8757 (mp) REVERT: C 271 MET cc_start: 0.8216 (tpt) cc_final: 0.7941 (mmm) REVERT: C 475 MET cc_start: 0.8172 (mmm) cc_final: 0.7614 (mmm) REVERT: D 535 MET cc_start: 0.8261 (mmm) cc_final: 0.7924 (mmm) REVERT: D 626 MET cc_start: 0.7023 (mtp) cc_final: 0.6639 (ttm) REVERT: D 654 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7131 (mt-10) REVERT: D 659 ASP cc_start: 0.7080 (m-30) cc_final: 0.6830 (m-30) REVERT: I 3 GLN cc_start: 0.7228 (tp-100) cc_final: 0.7003 (tp-100) REVERT: I 43 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: I 100 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: M 24 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7446 (ttm110) REVERT: M 33 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8307 (tp) REVERT: M 50 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8179 (mtp85) REVERT: M 76 LYS cc_start: 0.8301 (mmmm) cc_final: 0.7979 (mmmm) REVERT: M 100 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: E 150 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7479 (ttm) REVERT: E 153 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: E 211 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8640 (tp30) REVERT: E 246 GLN cc_start: 0.8377 (pm20) cc_final: 0.7987 (tp-100) REVERT: E 271 MET cc_start: 0.7974 (tpt) cc_final: 0.7408 (mmp) REVERT: E 469 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6618 (ptp90) REVERT: E 475 MET cc_start: 0.8082 (mmm) cc_final: 0.7358 (mmm) REVERT: F 535 MET cc_start: 0.8402 (mmm) cc_final: 0.8171 (mmm) REVERT: F 543 ASN cc_start: 0.8716 (m110) cc_final: 0.8308 (m110) REVERT: F 626 MET cc_start: 0.7230 (mtp) cc_final: 0.6603 (ttm) REVERT: F 654 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7153 (mt-10) REVERT: J 24 ASP cc_start: 0.8699 (p0) cc_final: 0.8419 (p0) REVERT: J 81 GLU cc_start: 0.7499 (tt0) cc_final: 0.6957 (mp0) REVERT: N 24 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7287 (ttm110) REVERT: N 81 ASP cc_start: 0.8600 (t0) cc_final: 0.8300 (t0) outliers start: 91 outliers final: 63 residues processed: 337 average time/residue: 0.1634 time to fit residues: 82.3145 Evaluate side-chains 339 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 263 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 119 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 0.0070 chunk 89 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091184 restraints weight = 34859.601| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.68 r_work: 0.3089 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21219 Z= 0.137 Angle : 0.726 15.887 28989 Z= 0.322 Chirality : 0.049 0.572 3546 Planarity : 0.003 0.035 3474 Dihedral : 8.618 59.791 5328 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.20 % Allowed : 21.16 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 2376 helix: -0.45 (0.27), residues: 384 sheet: -0.96 (0.19), residues: 750 loop : -2.01 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 24 TYR 0.014 0.001 TYR A 486 PHE 0.012 0.001 PHE E 382 TRP 0.009 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00317 (21045) covalent geometry : angle 0.66137 (28509) SS BOND : bond 0.00409 ( 42) SS BOND : angle 1.18414 ( 84) hydrogen bonds : bond 0.03187 ( 557) hydrogen bonds : angle 4.94483 ( 1557) link_ALPHA1-2 : bond 0.00297 ( 6) link_ALPHA1-2 : angle 1.97703 ( 18) link_ALPHA1-3 : bond 0.01318 ( 6) link_ALPHA1-3 : angle 0.98138 ( 18) link_ALPHA1-6 : bond 0.00704 ( 6) link_ALPHA1-6 : angle 1.34171 ( 18) link_BETA1-4 : bond 0.00511 ( 57) link_BETA1-4 : angle 1.54477 ( 171) link_NAG-ASN : bond 0.00472 ( 57) link_NAG-ASN : angle 3.54819 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 276 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8184 (mmtm) REVERT: A 271 MET cc_start: 0.8550 (tpt) cc_final: 0.8157 (tpp) REVERT: A 434 MET cc_start: 0.8483 (ttt) cc_final: 0.8266 (ttt) REVERT: A 469 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7145 (mtp85) REVERT: A 475 MET cc_start: 0.8250 (mmm) cc_final: 0.7997 (mmm) REVERT: B 543 ASN cc_start: 0.8865 (m110) cc_final: 0.8609 (m110) REVERT: B 654 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6870 (mt-10) REVERT: H 24 ASP cc_start: 0.8330 (p0) cc_final: 0.8048 (p0) REVERT: H 64 GLN cc_start: 0.8824 (tp40) cc_final: 0.8593 (tp-100) REVERT: L 24 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7675 (ttm110) REVERT: L 81 ASP cc_start: 0.8138 (t0) cc_final: 0.7880 (t0) REVERT: C 35 TRP cc_start: 0.8768 (m100) cc_final: 0.8405 (m-90) REVERT: C 155 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8092 (ptmt) REVERT: C 246 GLN cc_start: 0.8465 (pm20) cc_final: 0.8057 (tp-100) REVERT: C 502 LYS cc_start: 0.8956 (tttt) cc_final: 0.8730 (tttp) REVERT: D 654 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7406 (mt-10) REVERT: D 659 ASP cc_start: 0.7375 (m-30) cc_final: 0.7116 (m-30) REVERT: M 50 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8341 (mtp85) REVERT: M 76 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8055 (mmmm) REVERT: M 100 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8537 (pm20) REVERT: E 150 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7948 (ttm) REVERT: E 211 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8935 (tp30) REVERT: E 246 GLN cc_start: 0.8414 (pm20) cc_final: 0.8070 (tp-100) REVERT: E 271 MET cc_start: 0.8279 (tpt) cc_final: 0.7922 (mmp) REVERT: E 469 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7279 (ptp90) REVERT: E 475 MET cc_start: 0.8237 (mmm) cc_final: 0.7874 (mmm) REVERT: F 543 ASN cc_start: 0.8627 (m110) cc_final: 0.8353 (m110) REVERT: F 654 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7460 (mt-10) REVERT: J 81 GLU cc_start: 0.7650 (tt0) cc_final: 0.7348 (mp0) REVERT: N 24 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7625 (ttm110) REVERT: N 81 ASP cc_start: 0.8474 (t0) cc_final: 0.8236 (t0) outliers start: 88 outliers final: 60 residues processed: 339 average time/residue: 0.1541 time to fit residues: 78.8155 Evaluate side-chains 334 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 16 optimal weight: 0.0670 chunk 218 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090693 restraints weight = 35208.950| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.65 r_work: 0.3079 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21219 Z= 0.169 Angle : 0.768 17.601 28989 Z= 0.340 Chirality : 0.050 0.702 3546 Planarity : 0.004 0.036 3474 Dihedral : 8.481 59.940 5326 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.49 % Allowed : 21.49 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2376 helix: -0.31 (0.28), residues: 378 sheet: -0.95 (0.19), residues: 750 loop : -1.96 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 24 TYR 0.019 0.001 TYR C 486 PHE 0.014 0.001 PHE E 382 TRP 0.010 0.001 TRP A 112 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00399 (21045) covalent geometry : angle 0.70039 (28509) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.52005 ( 84) hydrogen bonds : bond 0.03276 ( 557) hydrogen bonds : angle 4.99255 ( 1557) link_ALPHA1-2 : bond 0.00292 ( 6) link_ALPHA1-2 : angle 1.98142 ( 18) link_ALPHA1-3 : bond 0.01295 ( 6) link_ALPHA1-3 : angle 0.98566 ( 18) link_ALPHA1-6 : bond 0.00673 ( 6) link_ALPHA1-6 : angle 1.35424 ( 18) link_BETA1-4 : bond 0.00503 ( 57) link_BETA1-4 : angle 1.58194 ( 171) link_NAG-ASN : bond 0.00483 ( 57) link_NAG-ASN : angle 3.73257 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 261 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8224 (mmtm) REVERT: A 271 MET cc_start: 0.8539 (tpt) cc_final: 0.8176 (tpp) REVERT: A 469 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7195 (mtp85) REVERT: A 475 MET cc_start: 0.8312 (mmm) cc_final: 0.8019 (mmm) REVERT: B 543 ASN cc_start: 0.8823 (m110) cc_final: 0.8580 (m110) REVERT: H 24 ASP cc_start: 0.8289 (p0) cc_final: 0.7997 (p0) REVERT: H 64 GLN cc_start: 0.8798 (tp40) cc_final: 0.8585 (tp-100) REVERT: L 24 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7701 (ttm110) REVERT: L 81 ASP cc_start: 0.8124 (t0) cc_final: 0.7872 (t0) REVERT: C 150 MET cc_start: 0.8456 (mmm) cc_final: 0.7831 (ttm) REVERT: C 155 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.7978 (ptmt) REVERT: C 246 GLN cc_start: 0.8457 (pm20) cc_final: 0.8097 (tp-100) REVERT: C 502 LYS cc_start: 0.8989 (tttt) cc_final: 0.8776 (tttp) REVERT: D 654 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7399 (mt-10) REVERT: D 659 ASP cc_start: 0.7416 (m-30) cc_final: 0.7157 (m-30) REVERT: I 43 GLN cc_start: 0.7910 (pm20) cc_final: 0.7452 (pm20) REVERT: M 50 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8297 (mtp85) REVERT: M 76 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8066 (mmmm) REVERT: E 150 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7961 (ttm) REVERT: E 211 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8963 (tp30) REVERT: E 246 GLN cc_start: 0.8436 (pm20) cc_final: 0.8177 (tp-100) REVERT: E 271 MET cc_start: 0.8308 (tpt) cc_final: 0.7954 (mmp) REVERT: E 469 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7495 (ptp90) REVERT: E 475 MET cc_start: 0.8249 (mmm) cc_final: 0.7912 (mmm) REVERT: F 543 ASN cc_start: 0.8643 (m110) cc_final: 0.8356 (m110) REVERT: F 654 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7512 (mt-10) REVERT: J 81 GLU cc_start: 0.7668 (tt0) cc_final: 0.7386 (mp0) REVERT: N 24 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7664 (ttm110) REVERT: N 81 ASP cc_start: 0.8386 (t0) cc_final: 0.8157 (t0) outliers start: 73 outliers final: 61 residues processed: 315 average time/residue: 0.1531 time to fit residues: 72.5758 Evaluate side-chains 323 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 25 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 150 optimal weight: 0.0770 chunk 92 optimal weight: 0.0000 chunk 226 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.114472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092145 restraints weight = 35253.631| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.65 r_work: 0.3103 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21219 Z= 0.138 Angle : 0.738 17.399 28989 Z= 0.327 Chirality : 0.049 0.694 3546 Planarity : 0.003 0.037 3474 Dihedral : 8.207 59.315 5326 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.10 % Allowed : 22.06 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.17), residues: 2376 helix: -0.27 (0.28), residues: 384 sheet: -0.87 (0.19), residues: 741 loop : -1.87 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 24 TYR 0.013 0.001 TYR A 486 PHE 0.012 0.001 PHE E 382 TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00321 (21045) covalent geometry : angle 0.67390 (28509) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.37580 ( 84) hydrogen bonds : bond 0.03170 ( 557) hydrogen bonds : angle 4.85982 ( 1557) link_ALPHA1-2 : bond 0.00273 ( 6) link_ALPHA1-2 : angle 1.92156 ( 18) link_ALPHA1-3 : bond 0.01251 ( 6) link_ALPHA1-3 : angle 0.97002 ( 18) link_ALPHA1-6 : bond 0.00747 ( 6) link_ALPHA1-6 : angle 1.28338 ( 18) link_BETA1-4 : bond 0.00514 ( 57) link_BETA1-4 : angle 1.52441 ( 171) link_NAG-ASN : bond 0.00470 ( 57) link_NAG-ASN : angle 3.57829 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4573.35 seconds wall clock time: 79 minutes 16.32 seconds (4756.32 seconds total)