Starting phenix.real_space_refine on Thu Mar 5 23:02:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugq_26496/03_2026/7ugq_26496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugq_26496/03_2026/7ugq_26496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ugq_26496/03_2026/7ugq_26496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugq_26496/03_2026/7ugq_26496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ugq_26496/03_2026/7ugq_26496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugq_26496/03_2026/7ugq_26496.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 150 5.16 5 C 16269 2.51 5 N 4374 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.03s 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: 26113 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3498 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3498 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 3 Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3498 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Chain: "H" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 758 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 758 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 758 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "0" 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: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.26, per 1000 atoms: 0.24 Number of scatterers: 26113 At special positions: 0 Unit cell: (152.075, 158.158, 150.337, 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 150 16.00 O 5320 8.00 N 4374 7.00 C 16269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 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 331 " - pdb=" SG CYS A 385 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.05 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 385 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 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 331 " - pdb=" SG CYS C 385 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 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=1, symmetry=0 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN d 4 " - " MAN d 5 " " MAN d 5 " - " MAN d 6 " " MAN p 4 " - " MAN p 5 " " MAN p 5 " - " MAN p 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA W 3 " - " MAN W 4 " " BMA d 3 " - " MAN d 4 " " MAN d 7 " - " MAN d 8 " " BMA i 3 " - " MAN i 4 " " BMA p 3 " - " MAN p 4 " " MAN p 7 " - " MAN p 8 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA W 3 " - " MAN W 5 " " BMA d 3 " - " MAN d 7 " " MAN d 7 " - " MAN d 9 " " BMA i 3 " - " MAN i 5 " " BMA p 3 " - " MAN p 7 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN C 465 " " NAG 1 1 " - " ASN C 332 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 241 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 354 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 461 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 241 " " NAG B 603 " - " ASN B 301 " " NAG B 604 " - " ASN B 354 " " NAG B 605 " - " ASN B 392 " " NAG B 606 " - " ASN B 461 " " NAG B 607 " - " ASN B 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 354 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 461 " " NAG C 607 " - " ASN C 448 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 160 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 276 " " NAG Z 1 " - " ASN A 340 " " NAG a 1 " - " ASN A 289 " " NAG b 1 " - " ASN A 386 " " NAG c 1 " - " ASN A 465 " " NAG d 1 " - " ASN A 332 " " NAG e 1 " - " ASN B 156 " " NAG f 1 " - " ASN B 160 " " NAG g 1 " - " ASN B 197 " " NAG h 1 " - " ASN B 234 " " NAG i 1 " - " ASN B 262 " " NAG j 1 " - " ASN B 295 " " NAG k 1 " - " ASN B 276 " " NAG l 1 " - " ASN B 340 " " NAG m 1 " - " ASN B 289 " " NAG n 1 " - " ASN B 386 " " NAG o 1 " - " ASN B 465 " " NAG p 1 " - " ASN B 332 " " NAG q 1 " - " ASN C 156 " " NAG r 1 " - " ASN C 160 " " NAG s 1 " - " ASN C 197 " " NAG t 1 " - " ASN C 234 " " NAG u 1 " - " ASN C 262 " " NAG v 1 " - " ASN C 295 " " NAG w 1 " - " ASN C 276 " " NAG x 1 " - " ASN C 340 " " NAG y 1 " - " ASN C 289 " " NAG z 1 " - " ASN C 386 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 75 sheets defined 12.7% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.819A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.532A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.723A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 334 through 354 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.536A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.806A pdb=" N SER C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.536A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 541 through 545 removed outlier: 3.731A pdb=" N LEU D 544 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 545 " --> pdb=" O ARG D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 545' Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 664 removed outlier: 4.114A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 535 through 537 No H-bonds generated for 'chain 'E' and resid 535 through 537' Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 535 through 537 No H-bonds generated for 'chain 'F' and resid 535 through 537' Processing helix chain 'F' and resid 541 through 545 removed outlier: 3.738A pdb=" N LEU F 544 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU F 545 " --> pdb=" O ARG F 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 541 through 545' Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 removed outlier: 4.180A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.638A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.594A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.828A pdb=" N GLN I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.617A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.983A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 3.531A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 37 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.826A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.958A pdb=" N HIS A 66 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.604A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.571A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AB1, first strand: chain 'A' and resid 330 through 333 removed outlier: 3.828A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS A 385 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 396 removed outlier: 6.889A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'B' and resid 494 through 495 removed outlier: 5.232A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.819A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 66 through 67 removed outlier: 7.303A pdb=" N HIS B 66 " --> pdb=" O THR B 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.585A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 154 through 162 Processing sheet with id=AC1, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.650A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.952A pdb=" N THR B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE B 468 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AC5, first strand: chain 'B' and resid 330 through 333 removed outlier: 3.804A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 385 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 423 through 425 Processing sheet with id=AC7, first strand: chain 'C' and resid 494 through 495 Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 495 removed outlier: 5.054A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.448A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 66 through 67 removed outlier: 7.039A pdb=" N HIS C 66 " --> pdb=" O THR C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.585A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AD5, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AD6, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.520A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.880A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=AD9, first strand: chain 'C' and resid 329 through 333 removed outlier: 4.155A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AE3, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AE4, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.549A pdb=" N GLY G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP G 50 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.549A pdb=" N GLY G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP G 50 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE7, first strand: chain 'H' and resid 22 through 23 Processing sheet with id=AE8, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.514A pdb=" N GLY H 56 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP H 50 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.514A pdb=" N GLY H 56 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP H 50 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 18 through 19 Processing sheet with id=AF2, first strand: chain 'I' and resid 22 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.590A pdb=" N GLY I 56 " --> pdb=" O ASN I 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP I 50 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.590A pdb=" N GLY I 56 " --> pdb=" O ASN I 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP I 50 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.068A pdb=" N VAL J 10 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA J 86 " --> pdb=" O LEU J 102 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'J' and resid 47 through 49 removed outlier: 4.202A pdb=" N TRP J 37 " --> pdb=" O ILE J 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.597A pdb=" N THR K 103 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA K 86 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 18 through 22 Processing sheet with id=AG1, first strand: chain 'K' and resid 47 through 49 removed outlier: 4.232A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.101A pdb=" N VAL L 10 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA L 86 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AG4, first strand: chain 'L' and resid 47 through 49 removed outlier: 4.184A pdb=" N TRP L 37 " --> pdb=" O ILE L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP M 72 " --> pdb=" O GLN M 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.693A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR M 58 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 97 through 100A Processing sheet with id=AG8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.568A pdb=" N GLN N 77 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP N 72 " --> pdb=" O GLN N 77 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'N' and resid 58 through 59 removed outlier: 3.964A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 97 through 100A Processing sheet with id=AH3, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.620A pdb=" N GLN O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP O 72 " --> pdb=" O GLN O 77 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.509A pdb=" N TYR O 33 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 97 through 100A Processing sheet with id=AH6, first strand: chain 'P' and resid 11 through 14 removed outlier: 5.625A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU P 107 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL P 13 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=AH8, first strand: chain 'Q' and resid 12 through 14 removed outlier: 6.670A pdb=" N VAL Q 13 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AI1, first strand: chain 'Q' and resid 44 through 48 removed outlier: 6.693A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.943A pdb=" N LEU R 11 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 19 through 22 754 hydrogen bonds defined for protein. 1965 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: 6.36 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7895 1.34 - 1.47: 7159 1.47 - 1.60: 11377 1.60 - 1.73: 3 1.73 - 1.86: 210 Bond restraints: 26644 Sorted by residual: bond pdb=" C1 NAG c 1 " pdb=" C2 NAG c 1 " ideal model delta sigma weight residual 1.532 1.636 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 NAG o 1 " pdb=" C2 NAG o 1 " ideal model delta sigma weight residual 1.532 1.635 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 NAG 0 1 " pdb=" C2 NAG 0 1 " ideal model delta sigma weight residual 1.532 1.632 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 MAN 1 7 " pdb=" O5 MAN 1 7 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1 MAN d 7 " pdb=" O5 MAN d 7 " ideal model delta sigma weight residual 1.399 1.482 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 26639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 34503 2.26 - 4.52: 1373 4.52 - 6.78: 243 6.78 - 9.04: 70 9.04 - 11.30: 21 Bond angle restraints: 36210 Sorted by residual: angle pdb=" C ARG R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta sigma weight residual 119.85 127.66 -7.81 1.01e+00 9.80e-01 5.98e+01 angle pdb=" C ASP C 460 " pdb=" N ASN C 461 " pdb=" CA ASN C 461 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C ILE E 642 " pdb=" CA ILE E 642 " pdb=" CB ILE E 642 " ideal model delta sigma weight residual 111.97 105.08 6.89 1.28e+00 6.10e-01 2.90e+01 angle pdb=" C ILE Q 66B" pdb=" N ASN Q 66C" pdb=" CA ASN Q 66C" ideal model delta sigma weight residual 120.79 127.65 -6.86 1.39e+00 5.18e-01 2.43e+01 angle pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" C ILE A 68 " ideal model delta sigma weight residual 110.05 104.83 5.22 1.09e+00 8.42e-01 2.29e+01 ... (remaining 36205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 15804 21.79 - 43.58: 1301 43.58 - 65.38: 311 65.38 - 87.17: 111 87.17 - 108.96: 61 Dihedral angle restraints: 17588 sinusoidal: 8582 harmonic: 9006 Sorted by residual: dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " pdb=" CB CYS Q 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.02 -82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.77 80.77 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -5.49 -80.51 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 17585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.495: 4421 0.495 - 0.990: 5 0.990 - 1.486: 0 1.486 - 1.981: 0 1.981 - 2.476: 3 Chirality restraints: 4429 Sorted by residual: chirality pdb=" C1 BMA 0 3 " pdb=" O4 NAG 0 2 " pdb=" C2 BMA 0 3 " pdb=" O5 BMA 0 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.59e+02 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN C 465 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 0.08 -2.48 2.00e-01 2.50e+01 1.53e+02 chirality pdb=" C1 NAG o 1 " pdb=" ND2 ASN B 465 " pdb=" C2 NAG o 1 " pdb=" O5 NAG o 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.05 -2.35 2.00e-01 2.50e+01 1.38e+02 ... (remaining 4426 not shown) Planarity restraints: 4506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " -0.289 2.00e-02 2.50e+03 2.43e-01 7.39e+02 pdb=" C7 NAG c 2 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " 0.225 2.00e-02 2.50e+03 1.97e-01 4.85e+02 pdb=" C7 NAG c 1 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " -0.011 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " -0.335 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG o 1 " -0.203 2.00e-02 2.50e+03 1.74e-01 3.76e+02 pdb=" C7 NAG o 1 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG o 1 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG o 1 " 0.286 2.00e-02 2.50e+03 pdb=" O7 NAG o 1 " -0.158 2.00e-02 2.50e+03 ... (remaining 4503 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.71: 4 1.71 - 2.51: 185 2.51 - 3.31: 25664 3.31 - 4.10: 64273 4.10 - 4.90: 114338 Warning: very small nonbonded interaction distances. Nonbonded interactions: 204464 Sorted by model distance: nonbonded pdb=" CG1 ILE E 595 " pdb=" OE2 GLU E 647 " model vdw 0.915 3.440 nonbonded pdb=" CB ILE E 595 " pdb=" OE2 GLU E 647 " model vdw 1.293 3.470 nonbonded pdb=" CB SER B 463 " pdb=" C8 NAG o 1 " model vdw 1.482 3.860 nonbonded pdb=" CD1 ILE E 595 " pdb=" OE1 GLU E 647 " model vdw 1.572 3.460 nonbonded pdb=" CG1 ILE E 595 " pdb=" CD GLU E 647 " model vdw 1.716 3.670 ... (remaining 204459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'S' selection = chain 'V' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'o' selection = chain 'q' selection = chain 't' } ncs_group { reference = (chain '1' and (resid 2 or resid 5 through 9)) selection = (chain 'd' and (resid 2 or resid 5 through 9)) selection = (chain 'p' and (resid 1 or resid 4 through 8)) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'W' selection = chain 'i' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.930 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 0.607 26826 Z= 0.516 Angle : 1.218 47.414 36706 Z= 0.577 Chirality : 0.096 2.476 4429 Planarity : 0.010 0.243 4446 Dihedral : 18.240 108.960 11669 Min Nonbonded Distance : 0.915 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 7.30 % Allowed : 17.70 % Favored : 75.01 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.27 % 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: -4.58 (0.12), residues: 3078 helix: -3.58 (0.15), residues: 411 sheet: -2.53 (0.15), residues: 855 loop : -3.29 (0.11), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 71 TYR 0.019 0.002 TYR L 51 PHE 0.019 0.002 PHE A 53 TRP 0.018 0.002 TRP I 50 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00703 (26644) covalent geometry : angle 1.07509 (36210) SS BOND : bond 0.00704 ( 47) SS BOND : angle 1.89617 ( 94) hydrogen bonds : bond 0.21546 ( 717) hydrogen bonds : angle 9.30384 ( 1965) Misc. bond : bond 0.60742 ( 1) link_ALPHA1-2 : bond 0.00193 ( 6) link_ALPHA1-2 : angle 1.66699 ( 18) link_ALPHA1-3 : bond 0.00581 ( 9) link_ALPHA1-3 : angle 3.13790 ( 27) link_ALPHA1-6 : bond 0.01349 ( 8) link_ALPHA1-6 : angle 2.01100 ( 24) link_BETA1-4 : bond 0.01074 ( 51) link_BETA1-4 : angle 4.18182 ( 153) link_NAG-ASN : bond 0.02641 ( 60) link_NAG-ASN : angle 7.13768 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 431 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 114 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 169 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8625 (mt0) REVERT: B 192 MET cc_start: 0.8202 (ptt) cc_final: 0.7997 (ptt) REVERT: C 169 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: D 651 ASN cc_start: 0.4831 (OUTLIER) cc_final: 0.4532 (t0) REVERT: D 655 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7558 (mptt) REVERT: E 650 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7240 (mm110) REVERT: E 655 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7682 (mmtp) REVERT: H 18 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7590 (p) REVERT: I 18 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7505 (p) REVERT: M 100 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8345 (m) outliers start: 195 outliers final: 119 residues processed: 600 average time/residue: 0.1781 time to fit residues: 165.1199 Evaluate side-chains 449 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 323 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 169 GLN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 54 ASN Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 105 HIS A 130 GLN A 169 GLN A 232 GLN A 408 ASN B 105 HIS B 130 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN C 67 ASN C 80 ASN C 105 HIS C 130 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN D 651 ASN F 651 ASN G 6 GLN G 43 GLN H 6 GLN H 43 GLN H 82AASN I 6 GLN I 43 GLN I 82AASN J 16 GLN J 41 HIS K 16 GLN K 41 HIS L 16 GLN L 41 HIS L 54 ASN M 39 GLN N 30 ASN Q 51 ASN Q 66CASN R 51 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139701 restraints weight = 36198.439| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.79 r_work: 0.3285 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 26826 Z= 0.268 Angle : 0.877 17.708 36706 Z= 0.398 Chirality : 0.053 0.417 4429 Planarity : 0.005 0.055 4446 Dihedral : 13.810 86.377 6313 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 6.51 % Allowed : 19.15 % Favored : 74.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.27 % 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: -3.75 (0.13), residues: 3078 helix: -1.87 (0.21), residues: 429 sheet: -2.08 (0.17), residues: 813 loop : -2.97 (0.12), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 53 TYR 0.020 0.002 TYR K 51 PHE 0.014 0.002 PHE C 159 TRP 0.015 0.002 TRP D 623 HIS 0.005 0.001 HIS B 464 Details of bonding type rmsd covalent geometry : bond 0.00627 (26644) covalent geometry : angle 0.81734 (36210) SS BOND : bond 0.01006 ( 47) SS BOND : angle 2.05134 ( 94) hydrogen bonds : bond 0.04379 ( 717) hydrogen bonds : angle 6.56851 ( 1965) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-2 : bond 0.00251 ( 6) link_ALPHA1-2 : angle 1.91522 ( 18) link_ALPHA1-3 : bond 0.01045 ( 9) link_ALPHA1-3 : angle 1.72576 ( 27) link_ALPHA1-6 : bond 0.00829 ( 8) link_ALPHA1-6 : angle 1.54420 ( 24) link_BETA1-4 : bond 0.00793 ( 51) link_BETA1-4 : angle 2.91663 ( 153) link_NAG-ASN : bond 0.00661 ( 60) link_NAG-ASN : angle 3.43415 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 336 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8173 (tt0) REVERT: A 169 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: A 341 MET cc_start: 0.8827 (tmm) cc_final: 0.8495 (tmm) REVERT: A 452 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8800 (mt) REVERT: B 114 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 452 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8604 (mt) REVERT: C 452 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8674 (mt) REVERT: C 503 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8230 (ttm110) REVERT: D 655 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7751 (mmtp) REVERT: E 609 PRO cc_start: 0.8066 (Cg_endo) cc_final: 0.7854 (Cg_exo) REVERT: G 71 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8208 (pmt-80) REVERT: I 71 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8676 (pmt-80) REVERT: M 100 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8838 (m) outliers start: 174 outliers final: 116 residues processed: 479 average time/residue: 0.1705 time to fit residues: 128.4295 Evaluate side-chains 415 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 292 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 169 GLN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 219 optimal weight: 0.4980 chunk 254 optimal weight: 9.9990 chunk 81 optimal weight: 0.0870 chunk 144 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN I 43 GLN J 41 HIS K 41 HIS L 41 HIS M 39 GLN Q 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142346 restraints weight = 36060.901| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.45 r_work: 0.3373 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26826 Z= 0.149 Angle : 0.764 15.540 36706 Z= 0.340 Chirality : 0.050 0.351 4429 Planarity : 0.004 0.050 4446 Dihedral : 11.978 87.514 6244 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.46 % Allowed : 20.95 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.30 (0.13), residues: 3078 helix: -1.02 (0.24), residues: 426 sheet: -1.87 (0.17), residues: 828 loop : -2.75 (0.12), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 31 TYR 0.023 0.001 TYR M 50 PHE 0.009 0.001 PHE C 53 TRP 0.012 0.001 TRP C 35 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00338 (26644) covalent geometry : angle 0.70717 (36210) SS BOND : bond 0.00556 ( 47) SS BOND : angle 1.76570 ( 94) hydrogen bonds : bond 0.03681 ( 717) hydrogen bonds : angle 6.09380 ( 1965) Misc. bond : bond 0.00068 ( 1) link_ALPHA1-2 : bond 0.00344 ( 6) link_ALPHA1-2 : angle 1.70064 ( 18) link_ALPHA1-3 : bond 0.01075 ( 9) link_ALPHA1-3 : angle 1.64064 ( 27) link_ALPHA1-6 : bond 0.00581 ( 8) link_ALPHA1-6 : angle 1.58396 ( 24) link_BETA1-4 : bond 0.00599 ( 51) link_BETA1-4 : angle 2.58052 ( 153) link_NAG-ASN : bond 0.00450 ( 60) link_NAG-ASN : angle 3.19520 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 321 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8160 (tt0) REVERT: A 341 MET cc_start: 0.8713 (tmm) cc_final: 0.8418 (tmm) REVERT: A 398 MET cc_start: 0.6648 (ppp) cc_final: 0.5891 (ptt) REVERT: A 452 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8782 (mt) REVERT: B 114 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 341 MET cc_start: 0.8731 (tmm) cc_final: 0.8456 (tmm) REVERT: B 452 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8590 (mt) REVERT: C 80 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.7188 (p0) REVERT: C 229 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7499 (mtt180) REVERT: C 452 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8697 (mt) REVERT: D 655 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7645 (mmtp) REVERT: E 643 TYR cc_start: 0.8235 (m-10) cc_final: 0.7929 (m-10) REVERT: E 655 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7684 (mmtp) REVERT: F 633 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7638 (mmtp) REVERT: I 71 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8582 (pmt-80) REVERT: K 94 GLU cc_start: 0.8471 (pt0) cc_final: 0.8265 (pt0) REVERT: M 100 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8165 (t) REVERT: N 34 TRP cc_start: 0.7663 (m100) cc_final: 0.7381 (m100) REVERT: N 100 MET cc_start: 0.8081 (mpp) cc_final: 0.7794 (mtm) REVERT: Q 73 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7354 (mt) REVERT: R 54 ARG cc_start: 0.8170 (ptp-170) cc_final: 0.7765 (ptp-170) outliers start: 146 outliers final: 103 residues processed: 440 average time/residue: 0.1718 time to fit residues: 119.6405 Evaluate side-chains 403 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 293 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 169 GLN Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 18 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 261 optimal weight: 0.0770 chunk 249 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN J 41 HIS K 41 HIS L 41 HIS M 39 GLN Q 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.159539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141816 restraints weight = 35861.210| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.38 r_work: 0.3376 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26826 Z= 0.175 Angle : 0.768 15.483 36706 Z= 0.343 Chirality : 0.050 0.358 4429 Planarity : 0.004 0.046 4446 Dihedral : 10.737 79.360 6226 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 6.73 % Allowed : 21.06 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.01 (0.14), residues: 3078 helix: -0.66 (0.25), residues: 426 sheet: -1.76 (0.17), residues: 798 loop : -2.54 (0.12), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 96 TYR 0.024 0.001 TYR M 50 PHE 0.015 0.001 PHE P 62 TRP 0.016 0.001 TRP C 35 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00404 (26644) covalent geometry : angle 0.71241 (36210) SS BOND : bond 0.00558 ( 47) SS BOND : angle 1.75161 ( 94) hydrogen bonds : bond 0.03438 ( 717) hydrogen bonds : angle 5.75767 ( 1965) Misc. bond : bond 0.00041 ( 1) link_ALPHA1-2 : bond 0.00256 ( 6) link_ALPHA1-2 : angle 1.77901 ( 18) link_ALPHA1-3 : bond 0.01006 ( 9) link_ALPHA1-3 : angle 1.62112 ( 27) link_ALPHA1-6 : bond 0.00509 ( 8) link_ALPHA1-6 : angle 1.58396 ( 24) link_BETA1-4 : bond 0.00566 ( 51) link_BETA1-4 : angle 2.49361 ( 153) link_NAG-ASN : bond 0.00514 ( 60) link_NAG-ASN : angle 3.22114 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 318 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8193 (tt0) REVERT: A 321 ARG cc_start: 0.7903 (ttt180) cc_final: 0.7341 (ttm-80) REVERT: A 341 MET cc_start: 0.8797 (tmm) cc_final: 0.8508 (tmm) REVERT: A 398 MET cc_start: 0.6706 (ppp) cc_final: 0.5939 (ptt) REVERT: A 452 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8779 (mt) REVERT: B 114 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8106 (tt0) REVERT: B 169 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: B 341 MET cc_start: 0.8773 (tmm) cc_final: 0.8537 (tmm) REVERT: C 80 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7115 (p0) REVERT: C 229 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7526 (mtt180) REVERT: D 655 LYS cc_start: 0.7968 (mmtp) cc_final: 0.7674 (mmtp) REVERT: E 633 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7702 (mmtt) REVERT: E 643 TYR cc_start: 0.8254 (m-10) cc_final: 0.8014 (m-10) REVERT: E 655 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7742 (mmtp) REVERT: F 633 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7716 (mmtp) REVERT: G 71 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8263 (pmt-80) REVERT: K 94 GLU cc_start: 0.8496 (pt0) cc_final: 0.8275 (pt0) REVERT: N 100 MET cc_start: 0.8165 (mpp) cc_final: 0.7905 (mtm) REVERT: Q 73 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7312 (mt) REVERT: R 54 ARG cc_start: 0.8180 (ptp-170) cc_final: 0.7782 (ptp-170) outliers start: 180 outliers final: 132 residues processed: 463 average time/residue: 0.1915 time to fit residues: 140.0184 Evaluate side-chains 436 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 299 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 54 ASN Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 227 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 GLN H 61 GLN J 41 HIS K 41 HIS L 41 HIS M 39 GLN R 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138617 restraints weight = 35917.264| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.78 r_work: 0.3292 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26826 Z= 0.202 Angle : 0.783 15.316 36706 Z= 0.350 Chirality : 0.050 0.369 4429 Planarity : 0.004 0.042 4446 Dihedral : 10.143 80.865 6211 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 6.47 % Allowed : 21.59 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.14), residues: 3078 helix: -0.69 (0.25), residues: 438 sheet: -1.67 (0.17), residues: 804 loop : -2.45 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 31 TYR 0.023 0.001 TYR M 50 PHE 0.009 0.001 PHE C 382 TRP 0.017 0.001 TRP C 35 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00475 (26644) covalent geometry : angle 0.72617 (36210) SS BOND : bond 0.00659 ( 47) SS BOND : angle 1.95856 ( 94) hydrogen bonds : bond 0.03471 ( 717) hydrogen bonds : angle 5.66035 ( 1965) Misc. bond : bond 0.00052 ( 1) link_ALPHA1-2 : bond 0.00232 ( 6) link_ALPHA1-2 : angle 1.77238 ( 18) link_ALPHA1-3 : bond 0.01108 ( 9) link_ALPHA1-3 : angle 1.68507 ( 27) link_ALPHA1-6 : bond 0.00543 ( 8) link_ALPHA1-6 : angle 1.61442 ( 24) link_BETA1-4 : bond 0.00545 ( 51) link_BETA1-4 : angle 2.44381 ( 153) link_NAG-ASN : bond 0.00515 ( 60) link_NAG-ASN : angle 3.26919 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 322 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8286 (tt0) REVERT: A 135 LYS cc_start: 0.8056 (tppt) cc_final: 0.7362 (tmtt) REVERT: A 169 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: A 321 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7514 (ttm-80) REVERT: A 341 MET cc_start: 0.8872 (tmm) cc_final: 0.8574 (tmm) REVERT: A 398 MET cc_start: 0.6773 (ppp) cc_final: 0.6077 (ptt) REVERT: A 452 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8803 (mt) REVERT: B 114 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8188 (tt0) REVERT: B 211 GLU cc_start: 0.8785 (pt0) cc_final: 0.8554 (mt-10) REVERT: B 341 MET cc_start: 0.8845 (tmm) cc_final: 0.8626 (tmm) REVERT: B 398 MET cc_start: 0.6498 (ppp) cc_final: 0.5759 (ptt) REVERT: C 80 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7214 (p0) REVERT: C 135 LYS cc_start: 0.7950 (tppt) cc_final: 0.7274 (tmtt) REVERT: C 229 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7611 (mtt180) REVERT: D 655 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7694 (mmtp) REVERT: E 643 TYR cc_start: 0.8343 (m-10) cc_final: 0.8114 (m-10) REVERT: E 655 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7723 (mmtp) REVERT: F 633 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7714 (mmtp) REVERT: G 71 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8220 (pmt-80) REVERT: H 51 MET cc_start: 0.9112 (tmm) cc_final: 0.8697 (tmm) REVERT: H 71 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7554 (pmt-80) REVERT: K 94 GLU cc_start: 0.8639 (pt0) cc_final: 0.8410 (pt0) REVERT: Q 73 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7449 (mt) REVERT: R 54 ARG cc_start: 0.8222 (ptp-170) cc_final: 0.7724 (ptp-170) REVERT: R 94 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7623 (mtm180) outliers start: 173 outliers final: 141 residues processed: 456 average time/residue: 0.1752 time to fit residues: 123.7652 Evaluate side-chains 455 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 308 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 32 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 263 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN H 61 GLN J 41 HIS K 41 HIS L 41 HIS M 39 GLN Q 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142821 restraints weight = 35965.522| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.44 r_work: 0.3368 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26826 Z= 0.136 Angle : 0.734 15.704 36706 Z= 0.325 Chirality : 0.049 0.342 4429 Planarity : 0.004 0.041 4446 Dihedral : 9.545 79.298 6208 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.72 % Allowed : 22.60 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.14), residues: 3078 helix: -0.51 (0.26), residues: 435 sheet: -1.58 (0.17), residues: 798 loop : -2.33 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 53 TYR 0.024 0.001 TYR M 50 PHE 0.011 0.001 PHE Q 62 TRP 0.020 0.001 TRP A 35 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00310 (26644) covalent geometry : angle 0.68428 (36210) SS BOND : bond 0.00531 ( 47) SS BOND : angle 1.60879 ( 94) hydrogen bonds : bond 0.03181 ( 717) hydrogen bonds : angle 5.49324 ( 1965) Misc. bond : bond 0.00058 ( 1) link_ALPHA1-2 : bond 0.00339 ( 6) link_ALPHA1-2 : angle 1.66955 ( 18) link_ALPHA1-3 : bond 0.01021 ( 9) link_ALPHA1-3 : angle 1.60259 ( 27) link_ALPHA1-6 : bond 0.00496 ( 8) link_ALPHA1-6 : angle 1.57232 ( 24) link_BETA1-4 : bond 0.00496 ( 51) link_BETA1-4 : angle 2.28899 ( 153) link_NAG-ASN : bond 0.00425 ( 60) link_NAG-ASN : angle 2.95723 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 321 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8159 (tt0) REVERT: A 135 LYS cc_start: 0.8028 (tppt) cc_final: 0.7403 (tmtt) REVERT: A 321 ARG cc_start: 0.7885 (ttt180) cc_final: 0.7397 (ttm-80) REVERT: A 341 MET cc_start: 0.8782 (tmm) cc_final: 0.8518 (tmm) REVERT: A 398 MET cc_start: 0.6676 (ppp) cc_final: 0.5937 (ptt) REVERT: A 452 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8798 (mt) REVERT: B 114 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8130 (tt0) REVERT: B 398 MET cc_start: 0.6507 (ppp) cc_final: 0.5771 (ptt) REVERT: C 80 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7005 (p0) REVERT: C 135 LYS cc_start: 0.7894 (tppt) cc_final: 0.7259 (tmtt) REVERT: C 229 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7511 (mtt180) REVERT: D 655 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7646 (mmtp) REVERT: E 655 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7655 (mmtm) REVERT: G 71 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8168 (pmt-80) REVERT: H 71 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.6964 (pmt-80) REVERT: J 54 ASN cc_start: 0.6549 (OUTLIER) cc_final: 0.6210 (p0) REVERT: N 54 ARG cc_start: 0.7129 (mmp80) cc_final: 0.6825 (mmm-85) REVERT: Q 73 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7534 (mt) REVERT: R 54 ARG cc_start: 0.8165 (ptp-170) cc_final: 0.7707 (ptp-170) outliers start: 153 outliers final: 124 residues processed: 444 average time/residue: 0.1734 time to fit residues: 121.0940 Evaluate side-chains 436 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 306 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 286 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 128 optimal weight: 2.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN I 61 GLN J 41 HIS K 41 HIS L 41 HIS M 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.156977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140143 restraints weight = 35910.661| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.48 r_work: 0.3308 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26826 Z= 0.241 Angle : 0.805 15.545 36706 Z= 0.363 Chirality : 0.051 0.384 4429 Planarity : 0.004 0.037 4446 Dihedral : 9.545 82.207 6201 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 6.77 % Allowed : 21.62 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.14), residues: 3078 helix: -0.63 (0.25), residues: 438 sheet: -1.63 (0.17), residues: 822 loop : -2.34 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 53 TYR 0.022 0.001 TYR M 50 PHE 0.024 0.002 PHE Q 62 TRP 0.017 0.002 TRP N 34 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00569 (26644) covalent geometry : angle 0.75290 (36210) SS BOND : bond 0.00859 ( 47) SS BOND : angle 2.00434 ( 94) hydrogen bonds : bond 0.03509 ( 717) hydrogen bonds : angle 5.57210 ( 1965) Misc. bond : bond 0.00070 ( 1) link_ALPHA1-2 : bond 0.00196 ( 6) link_ALPHA1-2 : angle 1.83218 ( 18) link_ALPHA1-3 : bond 0.01142 ( 9) link_ALPHA1-3 : angle 1.74110 ( 27) link_ALPHA1-6 : bond 0.00450 ( 8) link_ALPHA1-6 : angle 1.76656 ( 24) link_BETA1-4 : bond 0.00568 ( 51) link_BETA1-4 : angle 2.42301 ( 153) link_NAG-ASN : bond 0.00560 ( 60) link_NAG-ASN : angle 3.15008 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 307 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8239 (tt0) REVERT: A 135 LYS cc_start: 0.8072 (tppt) cc_final: 0.7419 (tmtt) REVERT: A 169 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: A 184 ILE cc_start: 0.8979 (tt) cc_final: 0.8686 (tt) REVERT: A 341 MET cc_start: 0.8886 (tmm) cc_final: 0.8586 (tmm) REVERT: A 398 MET cc_start: 0.6677 (ppp) cc_final: 0.5974 (ptt) REVERT: A 452 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 114 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8198 (tt0) REVERT: B 135 LYS cc_start: 0.8133 (tppt) cc_final: 0.7465 (tmtt) REVERT: B 398 MET cc_start: 0.6536 (ppp) cc_final: 0.5797 (ptt) REVERT: C 80 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7105 (p0) REVERT: C 135 LYS cc_start: 0.8030 (tppt) cc_final: 0.7368 (tmtt) REVERT: D 646 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7878 (tp) REVERT: D 655 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7798 (mmtp) REVERT: G 71 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8125 (pmt-80) REVERT: H 71 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7318 (pmt-80) REVERT: J 68 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5531 (mmmt) REVERT: M 36 TRP cc_start: 0.7515 (m100) cc_final: 0.7073 (m100) REVERT: N 54 ARG cc_start: 0.7120 (mmp80) cc_final: 0.6838 (mmm-85) REVERT: Q 63 SER cc_start: 0.7688 (t) cc_final: 0.7165 (t) REVERT: Q 73 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7522 (mt) outliers start: 181 outliers final: 145 residues processed: 461 average time/residue: 0.1743 time to fit residues: 126.3901 Evaluate side-chains 451 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 298 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 43 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 290 optimal weight: 0.0270 chunk 283 optimal weight: 20.0000 chunk 173 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 GLN J 41 HIS K 41 HIS L 41 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.160903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.140347 restraints weight = 35857.743| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.79 r_work: 0.3332 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26826 Z= 0.115 Angle : 0.724 15.237 36706 Z= 0.321 Chirality : 0.049 0.423 4429 Planarity : 0.004 0.043 4446 Dihedral : 9.056 80.320 6198 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.01 % Allowed : 23.19 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.14), residues: 3078 helix: -0.37 (0.26), residues: 435 sheet: -1.47 (0.17), residues: 798 loop : -2.21 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 31 TYR 0.024 0.001 TYR M 50 PHE 0.014 0.001 PHE C 382 TRP 0.019 0.001 TRP C 35 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00254 (26644) covalent geometry : angle 0.67551 (36210) SS BOND : bond 0.00523 ( 47) SS BOND : angle 1.41352 ( 94) hydrogen bonds : bond 0.03067 ( 717) hydrogen bonds : angle 5.35170 ( 1965) Misc. bond : bond 0.00040 ( 1) link_ALPHA1-2 : bond 0.00405 ( 6) link_ALPHA1-2 : angle 1.60658 ( 18) link_ALPHA1-3 : bond 0.00958 ( 9) link_ALPHA1-3 : angle 1.61409 ( 27) link_ALPHA1-6 : bond 0.00470 ( 8) link_ALPHA1-6 : angle 1.57372 ( 24) link_BETA1-4 : bond 0.00490 ( 51) link_BETA1-4 : angle 2.18807 ( 153) link_NAG-ASN : bond 0.00395 ( 60) link_NAG-ASN : angle 2.97839 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 308 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.9040 (m-80) cc_final: 0.8790 (m-80) REVERT: A 114 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8190 (tt0) REVERT: A 135 LYS cc_start: 0.8031 (tppt) cc_final: 0.7393 (tmtt) REVERT: A 184 ILE cc_start: 0.8925 (tt) cc_final: 0.8651 (tt) REVERT: A 341 MET cc_start: 0.8784 (tmm) cc_final: 0.8550 (tmm) REVERT: A 398 MET cc_start: 0.6629 (ppp) cc_final: 0.5912 (ptt) REVERT: A 452 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8817 (mt) REVERT: B 114 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8189 (tt0) REVERT: B 173 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8191 (m-70) REVERT: B 398 MET cc_start: 0.6520 (ppp) cc_final: 0.5816 (ptt) REVERT: C 135 LYS cc_start: 0.7923 (tppt) cc_final: 0.7242 (tmtt) REVERT: C 229 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7587 (mtt180) REVERT: D 655 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7735 (mmtp) REVERT: E 542 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7932 (mtm180) REVERT: H 71 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.6726 (pmt-80) REVERT: H 108 MET cc_start: 0.8152 (tmm) cc_final: 0.7834 (tmm) REVERT: M 105 LYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5720 (mmmt) REVERT: N 54 ARG cc_start: 0.7110 (mmp80) cc_final: 0.6823 (mmm-85) REVERT: N 100 MET cc_start: 0.8039 (mtm) cc_final: 0.7838 (mpp) REVERT: Q 63 SER cc_start: 0.7702 (t) cc_final: 0.7194 (t) REVERT: Q 73 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7556 (mt) REVERT: R 54 ARG cc_start: 0.7990 (ptp-170) cc_final: 0.7675 (ptp-170) outliers start: 134 outliers final: 113 residues processed: 421 average time/residue: 0.1777 time to fit residues: 116.5506 Evaluate side-chains 409 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 291 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 14 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN H 61 GLN J 41 HIS J 54 ASN K 41 HIS L 41 HIS R 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132703 restraints weight = 35969.635| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.10 r_work: 0.3218 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26826 Z= 0.152 Angle : 0.736 15.250 36706 Z= 0.327 Chirality : 0.049 0.345 4429 Planarity : 0.004 0.041 4446 Dihedral : 8.892 81.336 6192 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.35 % Allowed : 22.86 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.14), residues: 3078 helix: -0.31 (0.26), residues: 429 sheet: -1.46 (0.18), residues: 816 loop : -2.19 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 31 TYR 0.022 0.001 TYR M 50 PHE 0.014 0.001 PHE C 382 TRP 0.017 0.001 TRP N 34 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00353 (26644) covalent geometry : angle 0.68846 (36210) SS BOND : bond 0.00551 ( 47) SS BOND : angle 1.56867 ( 94) hydrogen bonds : bond 0.03147 ( 717) hydrogen bonds : angle 5.30522 ( 1965) Misc. bond : bond 0.00062 ( 1) link_ALPHA1-2 : bond 0.00332 ( 6) link_ALPHA1-2 : angle 1.66968 ( 18) link_ALPHA1-3 : bond 0.01002 ( 9) link_ALPHA1-3 : angle 1.66800 ( 27) link_ALPHA1-6 : bond 0.00412 ( 8) link_ALPHA1-6 : angle 1.63259 ( 24) link_BETA1-4 : bond 0.00502 ( 51) link_BETA1-4 : angle 2.23061 ( 153) link_NAG-ASN : bond 0.00460 ( 60) link_NAG-ASN : angle 2.94024 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 303 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.9030 (m-80) cc_final: 0.8802 (m-80) REVERT: A 114 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8207 (tt0) REVERT: A 135 LYS cc_start: 0.8026 (tppt) cc_final: 0.7388 (tmtt) REVERT: A 184 ILE cc_start: 0.8879 (tt) cc_final: 0.8600 (tt) REVERT: A 341 MET cc_start: 0.8805 (tmm) cc_final: 0.8556 (tmm) REVERT: A 398 MET cc_start: 0.6603 (ppp) cc_final: 0.5897 (ptt) REVERT: A 452 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8805 (mt) REVERT: B 114 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8202 (tt0) REVERT: B 135 LYS cc_start: 0.7999 (tppt) cc_final: 0.7349 (tmtt) REVERT: B 269 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7040 (t70) REVERT: B 398 MET cc_start: 0.6498 (ppp) cc_final: 0.5794 (ptt) REVERT: C 135 LYS cc_start: 0.7927 (tppt) cc_final: 0.7280 (tmtt) REVERT: D 655 LYS cc_start: 0.8039 (mmtp) cc_final: 0.7704 (mmtp) REVERT: E 542 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7922 (mtm180) REVERT: G 71 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8124 (pmt-80) REVERT: H 71 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7047 (pmt-80) REVERT: H 108 MET cc_start: 0.8195 (tmm) cc_final: 0.7864 (tmm) REVERT: K 64 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6120 (p90) REVERT: M 36 TRP cc_start: 0.7465 (m100) cc_final: 0.6403 (m-90) REVERT: M 100 MET cc_start: 0.8310 (mmt) cc_final: 0.7785 (mmt) REVERT: N 54 ARG cc_start: 0.7105 (mmp80) cc_final: 0.6829 (mmm-85) REVERT: N 100 MET cc_start: 0.8018 (mtm) cc_final: 0.7816 (mpp) REVERT: Q 63 SER cc_start: 0.7727 (t) cc_final: 0.7226 (t) REVERT: Q 73 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7544 (mt) REVERT: R 54 ARG cc_start: 0.7985 (ptp-170) cc_final: 0.7672 (ptp-170) outliers start: 143 outliers final: 120 residues processed: 425 average time/residue: 0.1768 time to fit residues: 117.5958 Evaluate side-chains 426 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 300 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 143 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 284 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 184 optimal weight: 0.1980 chunk 255 optimal weight: 0.0470 chunk 28 optimal weight: 0.8980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 41 HIS J 54 ASN K 41 HIS L 41 HIS Q 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139079 restraints weight = 35852.380| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.82 r_work: 0.3310 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 26826 Z= 0.160 Angle : 0.844 59.197 36706 Z= 0.415 Chirality : 0.050 0.820 4429 Planarity : 0.004 0.107 4446 Dihedral : 8.865 81.340 6190 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.05 % Favored : 92.92 % Rotamer: Outliers : 5.01 % Allowed : 23.08 % Favored : 71.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.14), residues: 3078 helix: -0.28 (0.26), residues: 429 sheet: -1.45 (0.18), residues: 816 loop : -2.19 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 31 TYR 0.021 0.001 TYR M 50 PHE 0.014 0.001 PHE C 382 TRP 0.023 0.001 TRP E 628 HIS 0.005 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00344 (26644) covalent geometry : angle 0.80214 (36210) SS BOND : bond 0.00508 ( 47) SS BOND : angle 2.04879 ( 94) hydrogen bonds : bond 0.03134 ( 717) hydrogen bonds : angle 5.30761 ( 1965) Misc. bond : bond 0.00059 ( 1) link_ALPHA1-2 : bond 0.00339 ( 6) link_ALPHA1-2 : angle 1.67436 ( 18) link_ALPHA1-3 : bond 0.00863 ( 9) link_ALPHA1-3 : angle 1.70203 ( 27) link_ALPHA1-6 : bond 0.00380 ( 8) link_ALPHA1-6 : angle 1.62118 ( 24) link_BETA1-4 : bond 0.00493 ( 51) link_BETA1-4 : angle 2.21585 ( 153) link_NAG-ASN : bond 0.00518 ( 60) link_NAG-ASN : angle 2.90845 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 300 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.9045 (m-80) cc_final: 0.8823 (m-80) REVERT: A 114 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8268 (tt0) REVERT: A 135 LYS cc_start: 0.8034 (tppt) cc_final: 0.7398 (tmtt) REVERT: A 184 ILE cc_start: 0.8913 (tt) cc_final: 0.8642 (tt) REVERT: A 341 MET cc_start: 0.8856 (tmm) cc_final: 0.8610 (tmm) REVERT: A 398 MET cc_start: 0.6655 (ppp) cc_final: 0.5926 (ptt) REVERT: A 452 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8804 (mt) REVERT: B 114 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8255 (tt0) REVERT: B 135 LYS cc_start: 0.8022 (tppt) cc_final: 0.7362 (tmtt) REVERT: B 269 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7155 (t70) REVERT: B 398 MET cc_start: 0.6530 (ppp) cc_final: 0.5805 (ptt) REVERT: C 135 LYS cc_start: 0.7947 (tppt) cc_final: 0.7277 (tmtt) REVERT: D 655 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7771 (mmtp) REVERT: E 542 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7954 (mtm180) REVERT: H 71 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7052 (pmt-80) REVERT: H 108 MET cc_start: 0.8187 (tmm) cc_final: 0.7846 (tmm) REVERT: J 77 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6313 (tp) REVERT: K 64 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6219 (p90) REVERT: M 36 TRP cc_start: 0.7495 (m100) cc_final: 0.6410 (m-90) REVERT: M 100 MET cc_start: 0.8339 (mmt) cc_final: 0.7813 (mmt) REVERT: N 54 ARG cc_start: 0.7107 (mmp80) cc_final: 0.6838 (mmm-85) REVERT: Q 63 SER cc_start: 0.7721 (t) cc_final: 0.7201 (t) REVERT: Q 73 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7566 (mt) REVERT: R 54 ARG cc_start: 0.8023 (ptp-170) cc_final: 0.7724 (ptp-170) outliers start: 134 outliers final: 123 residues processed: 413 average time/residue: 0.1702 time to fit residues: 110.5034 Evaluate side-chains 429 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 300 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 149 optimal weight: 0.3980 chunk 138 optimal weight: 0.0070 chunk 206 optimal weight: 30.0000 chunk 234 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 300 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS J 54 ASN K 41 HIS L 41 HIS Q 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.159822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137809 restraints weight = 35833.999| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.04 r_work: 0.3287 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 26826 Z= 0.160 Angle : 0.844 59.197 36706 Z= 0.415 Chirality : 0.050 0.820 4429 Planarity : 0.004 0.107 4446 Dihedral : 8.865 81.340 6190 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.05 % Favored : 92.92 % Rotamer: Outliers : 4.86 % Allowed : 23.19 % Favored : 71.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.14), residues: 3078 helix: -0.28 (0.26), residues: 429 sheet: -1.45 (0.18), residues: 816 loop : -2.19 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 31 TYR 0.021 0.001 TYR M 50 PHE 0.014 0.001 PHE C 382 TRP 0.023 0.001 TRP E 628 HIS 0.005 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00344 (26644) covalent geometry : angle 0.80214 (36210) SS BOND : bond 0.00508 ( 47) SS BOND : angle 2.04879 ( 94) hydrogen bonds : bond 0.03134 ( 717) hydrogen bonds : angle 5.30761 ( 1965) Misc. bond : bond 0.00059 ( 1) link_ALPHA1-2 : bond 0.00339 ( 6) link_ALPHA1-2 : angle 1.67436 ( 18) link_ALPHA1-3 : bond 0.00863 ( 9) link_ALPHA1-3 : angle 1.70203 ( 27) link_ALPHA1-6 : bond 0.00380 ( 8) link_ALPHA1-6 : angle 1.62118 ( 24) link_BETA1-4 : bond 0.00493 ( 51) link_BETA1-4 : angle 2.21585 ( 153) link_NAG-ASN : bond 0.00518 ( 60) link_NAG-ASN : angle 2.90845 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6557.14 seconds wall clock time: 113 minutes 0.16 seconds (6780.16 seconds total)