Starting phenix.real_space_refine on Wed Nov 19 11:35:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vn3_8713/11_2025/5vn3_8713.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vn3_8713/11_2025/5vn3_8713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5vn3_8713/11_2025/5vn3_8713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vn3_8713/11_2025/5vn3_8713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vn3_8713/11_2025/5vn3_8713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vn3_8713/11_2025/5vn3_8713.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 14808 2.51 5 N 3936 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23727 Number of models: 1 Model: "" Number of chains: 54 Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "G" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "N" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "J" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "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: 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: "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: 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: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.16, per 1000 atoms: 0.26 Number of scatterers: 23727 At special positions: 0 Unit cell: (192.57, 188.64, 146.72, 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 123 16.00 O 4860 8.00 N 3936 7.00 C 14808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS G 501 " distance=1.98 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.02 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.01 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS I 501 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.02 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.01 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 159 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS J 501 " distance=2.09 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.02 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.02 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.01 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.02 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.04 Simple disulfide: pdb=" SG CYS F 130 " - pdb=" SG CYS F 159 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 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=7, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA c 3 " - " MAN c 4 " " BMA g 3 " - " MAN g 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA R 3 " - " MAN R 7 " " BMA S 3 " - " MAN S 4 " " BMA c 3 " - " MAN c 7 " " BMA d 3 " - " MAN d 4 " " BMA n 3 " - " MAN n 7 " " BMA o 3 " - " MAN o 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 616 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 616 " " NAG D 703 " - " ASN D 625 " " NAG D 704 " - " ASN D 637 " " NAG G 601 " - " ASN G 88 " " NAG G 622 " - " ASN G 339 " " NAG G 623 " - " ASN G 355 " " NAG G 631 " - " ASN G 397 " " NAG I 601 " - " ASN I 88 " " NAG I 622 " - " ASN I 339 " " NAG I 623 " - " ASN I 355 " " NAG I 631 " - " ASN I 397 " " NAG J 601 " - " ASN J 88 " " NAG J 622 " - " ASN J 339 " " NAG J 623 " - " ASN J 355 " " NAG J 631 " - " ASN J 397 " " NAG P 1 " - " ASN G 234 " " NAG Q 1 " - " ASN G 241 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN G 276 " " NAG T 1 " - " ASN G 295 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 362 " " NAG W 1 " - " ASN G 386 " " NAG X 1 " - " ASN G 413 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 392 " " NAG a 1 " - " ASN I 234 " " NAG b 1 " - " ASN I 241 " " NAG c 1 " - " ASN I 262 " " NAG d 1 " - " ASN I 276 " " NAG e 1 " - " ASN I 295 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 362 " " NAG h 1 " - " ASN I 386 " " NAG i 1 " - " ASN I 413 " " NAG j 1 " - " ASN I 448 " " NAG k 1 " - " ASN I 392 " " NAG l 1 " - " ASN J 234 " " NAG m 1 " - " ASN J 241 " " NAG n 1 " - " ASN J 262 " " NAG o 1 " - " ASN J 276 " " NAG p 1 " - " ASN J 295 " " NAG q 1 " - " ASN J 332 " " NAG r 1 " - " ASN J 362 " " NAG s 1 " - " ASN J 386 " " NAG t 1 " - " ASN J 413 " " NAG u 1 " - " ASN J 448 " " NAG v 1 " - " ASN J 392 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 54 sheets defined 17.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 529 through 547 removed outlier: 3.820A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.718A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.733A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 662 removed outlier: 3.580A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 73 Processing helix chain 'G' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 341 " --> pdb=" O ARG G 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.821A pdb=" N THR G 373 " --> pdb=" O PRO G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE G 391 " --> pdb=" O THR G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 481 removed outlier: 3.501A pdb=" N ASN G 478 " --> pdb=" O ASN G 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 removed outlier: 3.820A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.718A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP B 623 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.734A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 662 removed outlier: 3.581A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 73 Processing helix chain 'I' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.822A pdb=" N THR I 373 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 481 removed outlier: 3.500A pdb=" N ASN I 478 " --> pdb=" O ASN I 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 547 removed outlier: 3.821A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 568 Processing helix chain 'D' and resid 569 through 593 removed outlier: 3.719A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 596 No H-bonds generated for 'chain 'D' and resid 594 through 596' Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.734A pdb=" N LYS D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 662 removed outlier: 3.581A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 662 " --> pdb=" O GLN D 658 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 Processing helix chain 'J' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR J 341 " --> pdb=" O ARG J 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA J 347 " --> pdb=" O GLY J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.821A pdb=" N THR J 373 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE J 391 " --> pdb=" O THR J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 481 removed outlier: 3.500A pdb=" N ASN J 478 " --> pdb=" O ASN J 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER J 481 " --> pdb=" O ASP J 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.585A pdb=" N ALA L 25 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL G 36 " --> pdb=" O THR G 499 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR G 499 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL G 38 " --> pdb=" O ALA G 497 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA G 497 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR G 40 " --> pdb=" O GLY G 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY G 495 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL G 44 " --> pdb=" O ILE G 491 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE G 491 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.557A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'G' and resid 374 through 378 Processing sheet with id=AB1, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.076A pdb=" N LYS C 2 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN C 40 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY C 99 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN C 112 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 148 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL C 168 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 37 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 37 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.586A pdb=" N ALA N 25 " --> pdb=" O ALA N 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL I 36 " --> pdb=" O THR I 499 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR I 499 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL I 38 " --> pdb=" O ALA I 497 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA I 497 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR I 40 " --> pdb=" O GLY I 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY I 495 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL I 44 " --> pdb=" O ILE I 491 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE I 491 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'I' and resid 84 through 85 removed outlier: 3.556A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N VAL I 292 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N SER I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 357 through 361 Processing sheet with id=AC9, first strand: chain 'I' and resid 374 through 378 Processing sheet with id=AD1, first strand: chain 'I' and resid 423 through 425 Processing sheet with id=AD2, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.076A pdb=" N LYS E 2 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AD4, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY E 99 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN E 112 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E 148 " --> pdb=" O GLN E 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL E 168 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE K 91 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE K 91 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.585A pdb=" N ALA O 25 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA O 69 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA O 34 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN O 89 " --> pdb=" O ALA O 34 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL J 36 " --> pdb=" O THR J 499 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR J 499 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL J 38 " --> pdb=" O ALA J 497 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA J 497 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR J 40 " --> pdb=" O GLY J 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY J 495 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL J 44 " --> pdb=" O ILE J 491 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE J 491 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AE5, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.557A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS J 487 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.502A pdb=" N VAL J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 295 " --> pdb=" O ASN J 332 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.502A pdb=" N VAL J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 357 through 361 Processing sheet with id=AE9, first strand: chain 'J' and resid 374 through 378 Processing sheet with id=AF1, first strand: chain 'J' and resid 423 through 425 Processing sheet with id=AF2, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.077A pdb=" N LYS F 2 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AF4, first strand: chain 'F' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN F 40 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY F 99 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN F 112 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN F 148 " --> pdb=" O GLN F 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL F 168 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL M 37 " --> pdb=" O PHE M 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL M 37 " --> pdb=" O PHE M 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1566 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: 4.27 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7422 1.34 - 1.46: 5788 1.46 - 1.58: 10792 1.58 - 1.70: 1 1.70 - 1.82: 159 Bond restraints: 24162 Sorted by residual: bond pdb=" C GLN L 38 " pdb=" N LYS L 39 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.18e+01 bond pdb=" C GLN O 38 " pdb=" N LYS O 39 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.18e+01 bond pdb=" C GLN N 38 " pdb=" N LYS N 39 " ideal model delta sigma weight residual 1.333 1.239 0.093 2.74e-02 1.33e+03 1.16e+01 bond pdb=" C1 MAN r 4 " pdb=" O5 MAN r 4 " ideal model delta sigma weight residual 1.399 1.458 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.26e+00 ... (remaining 24157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 30623 2.31 - 4.62: 1844 4.62 - 6.93: 272 6.93 - 9.23: 33 9.23 - 11.54: 18 Bond angle restraints: 32790 Sorted by residual: angle pdb=" C ASN G 300 " pdb=" N ASN G 301 " pdb=" CA ASN G 301 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C ASN J 300 " pdb=" N ASN J 301 " pdb=" CA ASN J 301 " ideal model delta sigma weight residual 121.54 133.07 -11.53 1.91e+00 2.74e-01 3.64e+01 angle pdb=" C ASN I 300 " pdb=" N ASN I 301 " pdb=" CA ASN I 301 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.62e+01 angle pdb=" N ASN I 301 " pdb=" CA ASN I 301 " pdb=" C ASN I 301 " ideal model delta sigma weight residual 110.80 120.95 -10.15 2.13e+00 2.20e-01 2.27e+01 angle pdb=" N ASN G 301 " pdb=" CA ASN G 301 " pdb=" C ASN G 301 " ideal model delta sigma weight residual 110.80 120.90 -10.10 2.13e+00 2.20e-01 2.25e+01 ... (remaining 32785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 15337 22.30 - 44.59: 572 44.59 - 66.89: 70 66.89 - 89.19: 140 89.19 - 111.48: 84 Dihedral angle restraints: 16203 sinusoidal: 8121 harmonic: 8082 Sorted by residual: dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.85 77.85 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.85 77.85 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.84 77.84 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 16200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3129 0.072 - 0.144: 809 0.144 - 0.216: 120 0.216 - 0.289: 28 0.289 - 0.361: 6 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CB ILE B 603 " pdb=" CA ILE B 603 " pdb=" CG1 ILE B 603 " pdb=" CG2 ILE B 603 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE D 603 " pdb=" CA ILE D 603 " pdb=" CG1 ILE D 603 " pdb=" CG2 ILE D 603 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE A 603 " pdb=" CA ILE A 603 " pdb=" CG1 ILE A 603 " pdb=" CG2 ILE A 603 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 4089 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 625 " 0.024 2.00e-02 2.50e+03 2.36e-02 6.97e+00 pdb=" CG ASN A 625 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 625 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 625 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 276 " 0.023 2.00e-02 2.50e+03 2.29e-02 6.55e+00 pdb=" CG ASN G 276 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN G 276 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN G 276 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 276 " 0.022 2.00e-02 2.50e+03 2.23e-02 6.24e+00 pdb=" CG ASN I 276 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN I 276 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN I 276 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG d 1 " 0.028 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4503 2.77 - 3.30: 21149 3.30 - 3.83: 37189 3.83 - 4.37: 41954 4.37 - 4.90: 73821 Nonbonded interactions: 178616 Sorted by model distance: nonbonded pdb=" O GLY J 441 " pdb=" O6 MAN n 5 " model vdw 2.235 3.040 nonbonded pdb=" O GLY I 441 " pdb=" O6 MAN c 5 " model vdw 2.247 3.040 nonbonded pdb=" O CYS D 604 " pdb=" OG1 THR J 37 " model vdw 2.256 3.040 nonbonded pdb=" NE2 GLN L 38 " pdb=" O LYS L 39 " model vdw 2.294 3.120 nonbonded pdb=" NE2 GLN O 38 " pdb=" O LYS O 39 " model vdw 2.295 3.120 ... (remaining 178611 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 'u' } ncs_group { reference = chain 'Q' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'R' selection = chain 'c' selection = chain 'n' } ncs_group { reference = chain 'S' selection = chain 'V' selection = chain 'd' selection = chain 'g' selection = chain 'o' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.470 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.010 0.094 24340 Z= 0.445 Angle : 1.287 15.109 33261 Z= 0.667 Chirality : 0.067 0.361 4092 Planarity : 0.006 0.062 4011 Dihedral : 16.113 111.482 10857 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.76 % Favored : 88.80 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -5.03 (0.12), residues: 2760 helix: -4.37 (0.10), residues: 444 sheet: -2.51 (0.18), residues: 720 loop : -3.56 (0.12), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.029 0.004 TYR I 384 PHE 0.042 0.004 PHE G 382 TRP 0.037 0.004 TRP G 45 HIS 0.009 0.003 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00987 (24162) covalent geometry : angle 1.23431 (32790) SS BOND : bond 0.01450 ( 42) SS BOND : angle 2.21844 ( 84) hydrogen bonds : bond 0.29037 ( 564) hydrogen bonds : angle 10.41193 ( 1566) Misc. bond : bond 0.00465 ( 7) link_ALPHA1-2 : bond 0.00429 ( 6) link_ALPHA1-2 : angle 2.68058 ( 18) link_ALPHA1-3 : bond 0.00567 ( 6) link_ALPHA1-3 : angle 1.59041 ( 18) link_ALPHA1-6 : bond 0.00429 ( 6) link_ALPHA1-6 : angle 1.71947 ( 18) link_BETA1-4 : bond 0.00663 ( 54) link_BETA1-4 : angle 2.84408 ( 162) link_NAG-ASN : bond 0.01048 ( 57) link_NAG-ASN : angle 4.29129 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 514 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 MET cc_start: 0.8653 (mmm) cc_final: 0.8430 (mmm) REVERT: A 657 GLU cc_start: 0.8432 (tp30) cc_final: 0.8214 (tm-30) REVERT: G 61 TYR cc_start: 0.8224 (p90) cc_final: 0.8012 (p90) REVERT: G 426 MET cc_start: 0.9157 (mtm) cc_final: 0.8664 (mtm) REVERT: H 1 GLN cc_start: 0.6871 (mt0) cc_final: 0.5321 (pm20) REVERT: H 13 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6937 (ptmm) REVERT: B 624 ASP cc_start: 0.7446 (m-30) cc_final: 0.7195 (m-30) REVERT: B 629 MET cc_start: 0.8482 (mmm) cc_final: 0.8094 (mmm) REVERT: B 657 GLU cc_start: 0.8507 (tp30) cc_final: 0.7578 (tm-30) REVERT: I 61 TYR cc_start: 0.8322 (p90) cc_final: 0.8099 (p90) REVERT: E 70 ILE cc_start: 0.9078 (mt) cc_final: 0.8369 (mt) REVERT: E 130 CYS cc_start: 0.3801 (m) cc_final: 0.3216 (t) REVERT: E 137 ASN cc_start: 0.7553 (m-40) cc_final: 0.6667 (t0) REVERT: K 1 GLN cc_start: 0.6268 (mt0) cc_final: 0.5557 (pm20) REVERT: K 13 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6696 (ptmm) REVERT: O 46 LEU cc_start: 0.8300 (tp) cc_final: 0.8085 (tt) REVERT: O 70 GLU cc_start: 0.8238 (tt0) cc_final: 0.7849 (tm-30) REVERT: D 629 MET cc_start: 0.8543 (mmm) cc_final: 0.8215 (mmm) REVERT: D 657 GLU cc_start: 0.8675 (tp30) cc_final: 0.8410 (tm-30) REVERT: J 426 MET cc_start: 0.8896 (mtm) cc_final: 0.8616 (mtm) REVERT: M 1 GLN cc_start: 0.6429 (mt0) cc_final: 0.5370 (pm20) REVERT: M 13 LYS cc_start: 0.7364 (mmtt) cc_final: 0.7153 (ptmm) REVERT: M 101 LYS cc_start: 0.8331 (tttm) cc_final: 0.8121 (tptt) outliers start: 3 outliers final: 0 residues processed: 514 average time/residue: 0.1987 time to fit residues: 150.6100 Evaluate side-chains 282 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 197 ASN G 308 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN C 25 GLN C 163 GLN H 82BASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN B 653 GLN I 103 GLN I 197 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN I 422 GLN E 25 GLN E 163 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN J 103 GLN J 197 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 ASN J 422 GLN F 25 GLN F 163 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.098857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075229 restraints weight = 68885.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.076125 restraints weight = 42874.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076488 restraints weight = 32940.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076739 restraints weight = 29982.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076847 restraints weight = 27282.931| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24340 Z= 0.143 Angle : 0.766 10.037 33261 Z= 0.367 Chirality : 0.047 0.226 4092 Planarity : 0.005 0.042 4011 Dihedral : 14.340 87.995 5619 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.88 % Rotamer: Outliers : 1.88 % Allowed : 7.83 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.94 (0.14), residues: 2760 helix: -2.18 (0.20), residues: 438 sheet: -1.98 (0.18), residues: 735 loop : -3.18 (0.13), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 61 TYR 0.020 0.002 TYR H 79 PHE 0.015 0.001 PHE G 382 TRP 0.022 0.002 TRP K 36 HIS 0.005 0.001 HIS G 308 Details of bonding type rmsd covalent geometry : bond 0.00319 (24162) covalent geometry : angle 0.72300 (32790) SS BOND : bond 0.00245 ( 42) SS BOND : angle 1.80335 ( 84) hydrogen bonds : bond 0.04783 ( 564) hydrogen bonds : angle 6.75839 ( 1566) Misc. bond : bond 0.00121 ( 7) link_ALPHA1-2 : bond 0.00173 ( 6) link_ALPHA1-2 : angle 2.34423 ( 18) link_ALPHA1-3 : bond 0.01440 ( 6) link_ALPHA1-3 : angle 1.40193 ( 18) link_ALPHA1-6 : bond 0.00823 ( 6) link_ALPHA1-6 : angle 2.40775 ( 18) link_BETA1-4 : bond 0.00477 ( 54) link_BETA1-4 : angle 2.20512 ( 162) link_NAG-ASN : bond 0.00467 ( 57) link_NAG-ASN : angle 2.52260 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 360 time to evaluate : 0.941 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: L 92 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8512 (t0) REVERT: A 629 MET cc_start: 0.8392 (mmm) cc_final: 0.7959 (mtp) REVERT: A 659 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8251 (tt0) REVERT: G 61 TYR cc_start: 0.8407 (p90) cc_final: 0.8168 (p90) REVERT: G 376 PHE cc_start: 0.8326 (p90) cc_final: 0.8063 (p90) REVERT: G 457 ASP cc_start: 0.7521 (t0) cc_final: 0.7203 (t0) REVERT: C 10 ASP cc_start: 0.8115 (m-30) cc_final: 0.7692 (p0) REVERT: C 169 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6923 (mm-30) REVERT: H 1 GLN cc_start: 0.6742 (mt0) cc_final: 0.6319 (pt0) REVERT: H 13 LYS cc_start: 0.7565 (mmtt) cc_final: 0.6829 (ptmm) REVERT: H 73 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (mttt) REVERT: N 92 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8521 (t0) REVERT: B 566 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7895 (tt) REVERT: B 624 ASP cc_start: 0.7114 (m-30) cc_final: 0.6858 (m-30) REVERT: B 629 MET cc_start: 0.8244 (mmm) cc_final: 0.7766 (mmm) REVERT: B 657 GLU cc_start: 0.7891 (tp30) cc_final: 0.7679 (tm-30) REVERT: I 61 TYR cc_start: 0.8391 (p90) cc_final: 0.8154 (p90) REVERT: E 53 ASP cc_start: 0.7821 (m-30) cc_final: 0.7497 (m-30) REVERT: E 74 LEU cc_start: 0.8337 (mt) cc_final: 0.8035 (mt) REVERT: E 130 CYS cc_start: 0.3853 (m) cc_final: 0.3458 (t) REVERT: E 137 ASN cc_start: 0.7208 (m-40) cc_final: 0.6502 (t0) REVERT: E 138 ILE cc_start: 0.4933 (mt) cc_final: 0.4717 (mp) REVERT: K 13 LYS cc_start: 0.7231 (mmtt) cc_final: 0.6631 (ptmm) REVERT: K 23 LYS cc_start: 0.8885 (tppt) cc_final: 0.8666 (tppt) REVERT: K 81 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7574 (tm-30) REVERT: K 100 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6500 (mt-10) REVERT: O 92 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8465 (t0) REVERT: D 629 MET cc_start: 0.8351 (mmm) cc_final: 0.8001 (mmm) REVERT: F 169 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7328 (mm-30) REVERT: M 13 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7159 (ptmm) REVERT: M 25 SER cc_start: 0.8565 (t) cc_final: 0.8353 (m) REVERT: M 73 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8695 (mttt) REVERT: M 81 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7900 (tm-30) REVERT: M 100 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6499 (mt-10) REVERT: M 101 LYS cc_start: 0.8428 (tttm) cc_final: 0.8171 (tptt) outliers start: 46 outliers final: 20 residues processed: 388 average time/residue: 0.1622 time to fit residues: 100.0226 Evaluate side-chains 289 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 92 ASN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 265 optimal weight: 0.0570 chunk 86 optimal weight: 0.0010 chunk 9 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 187 optimal weight: 0.0570 chunk 263 optimal weight: 9.9990 overall best weight: 1.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 197 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS E 39 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 100HASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.098118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074088 restraints weight = 68860.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074802 restraints weight = 44102.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075226 restraints weight = 33234.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.075495 restraints weight = 30088.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075585 restraints weight = 27585.253| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24340 Z= 0.150 Angle : 0.738 10.277 33261 Z= 0.347 Chirality : 0.047 0.383 4092 Planarity : 0.004 0.034 4011 Dihedral : 12.412 84.622 5619 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.51 % Favored : 91.27 % Rotamer: Outliers : 2.20 % Allowed : 9.71 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.34 (0.14), residues: 2760 helix: -1.25 (0.23), residues: 456 sheet: -1.74 (0.19), residues: 687 loop : -2.85 (0.13), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 419 TYR 0.019 0.002 TYR N 91 PHE 0.015 0.001 PHE G 382 TRP 0.023 0.001 TRP M 36 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00330 (24162) covalent geometry : angle 0.69278 (32790) SS BOND : bond 0.00262 ( 42) SS BOND : angle 1.38111 ( 84) hydrogen bonds : bond 0.04153 ( 564) hydrogen bonds : angle 6.22319 ( 1566) Misc. bond : bond 0.00110 ( 7) link_ALPHA1-2 : bond 0.00190 ( 6) link_ALPHA1-2 : angle 2.02496 ( 18) link_ALPHA1-3 : bond 0.01363 ( 6) link_ALPHA1-3 : angle 1.30243 ( 18) link_ALPHA1-6 : bond 0.00696 ( 6) link_ALPHA1-6 : angle 2.34730 ( 18) link_BETA1-4 : bond 0.00464 ( 54) link_BETA1-4 : angle 2.12061 ( 162) link_NAG-ASN : bond 0.01251 ( 57) link_NAG-ASN : angle 2.71750 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 629 MET cc_start: 0.8453 (mmm) cc_final: 0.7970 (mtp) REVERT: A 659 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8299 (tt0) REVERT: G 61 TYR cc_start: 0.8353 (p90) cc_final: 0.8126 (p90) REVERT: G 457 ASP cc_start: 0.7577 (t0) cc_final: 0.7177 (t0) REVERT: C 10 ASP cc_start: 0.8099 (m-30) cc_final: 0.7670 (p0) REVERT: C 85 GLU cc_start: 0.7136 (mp0) cc_final: 0.6230 (mp0) REVERT: H 1 GLN cc_start: 0.6720 (mt0) cc_final: 0.6228 (pt0) REVERT: H 13 LYS cc_start: 0.7577 (mmtt) cc_final: 0.6831 (ptmm) REVERT: B 624 ASP cc_start: 0.7503 (m-30) cc_final: 0.7190 (m-30) REVERT: B 629 MET cc_start: 0.8243 (mmm) cc_final: 0.7824 (mmm) REVERT: I 61 TYR cc_start: 0.8384 (p90) cc_final: 0.8155 (p90) REVERT: E 137 ASN cc_start: 0.7265 (m-40) cc_final: 0.6589 (t0) REVERT: K 13 LYS cc_start: 0.7281 (mmtt) cc_final: 0.6647 (ptmm) REVERT: K 19 LYS cc_start: 0.8931 (tptt) cc_final: 0.8275 (tptt) REVERT: K 81 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 629 MET cc_start: 0.8413 (mmm) cc_final: 0.8091 (mmm) REVERT: J 95 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7771 (ttp) REVERT: F 10 ASP cc_start: 0.6779 (p0) cc_final: 0.6485 (p0) REVERT: M 13 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7141 (ptmm) REVERT: M 25 SER cc_start: 0.8570 (t) cc_final: 0.8365 (m) REVERT: M 81 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7784 (tm-30) REVERT: M 99 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7372 (mm-30) outliers start: 54 outliers final: 31 residues processed: 311 average time/residue: 0.1480 time to fit residues: 76.7640 Evaluate side-chains 281 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 206 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN O 92 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.095484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071529 restraints weight = 68801.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071982 restraints weight = 43327.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072349 restraints weight = 35161.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072672 restraints weight = 32287.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072762 restraints weight = 29170.329| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24340 Z= 0.231 Angle : 0.792 11.849 33261 Z= 0.370 Chirality : 0.049 0.467 4092 Planarity : 0.004 0.037 4011 Dihedral : 10.414 79.251 5619 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.82 % Favored : 89.96 % Rotamer: Outliers : 2.86 % Allowed : 10.57 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.12 (0.14), residues: 2760 helix: -1.03 (0.23), residues: 468 sheet: -1.50 (0.19), residues: 708 loop : -2.78 (0.13), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 273 TYR 0.025 0.002 TYR B 638 PHE 0.021 0.002 PHE G 233 TRP 0.016 0.002 TRP G 96 HIS 0.006 0.002 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00533 (24162) covalent geometry : angle 0.74944 (32790) SS BOND : bond 0.00350 ( 42) SS BOND : angle 1.47752 ( 84) hydrogen bonds : bond 0.04097 ( 564) hydrogen bonds : angle 5.99509 ( 1566) Misc. bond : bond 0.00116 ( 7) link_ALPHA1-2 : bond 0.00039 ( 6) link_ALPHA1-2 : angle 1.91387 ( 18) link_ALPHA1-3 : bond 0.01311 ( 6) link_ALPHA1-3 : angle 1.36905 ( 18) link_ALPHA1-6 : bond 0.00691 ( 6) link_ALPHA1-6 : angle 2.48867 ( 18) link_BETA1-4 : bond 0.00424 ( 54) link_BETA1-4 : angle 2.17326 ( 162) link_NAG-ASN : bond 0.00758 ( 57) link_NAG-ASN : angle 2.73463 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8185 (tm-30) REVERT: L 92 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8350 (t0) REVERT: G 61 TYR cc_start: 0.8538 (p90) cc_final: 0.8291 (p90) REVERT: G 457 ASP cc_start: 0.7764 (t0) cc_final: 0.7384 (t0) REVERT: C 10 ASP cc_start: 0.8145 (m-30) cc_final: 0.7720 (p0) REVERT: C 85 GLU cc_start: 0.7416 (mp0) cc_final: 0.6492 (mp0) REVERT: H 1 GLN cc_start: 0.6884 (mt0) cc_final: 0.5397 (pm20) REVERT: H 13 LYS cc_start: 0.7613 (mmtt) cc_final: 0.6797 (ptmm) REVERT: H 99 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7292 (mm-30) REVERT: N 92 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8401 (t0) REVERT: B 566 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8078 (tt) REVERT: B 624 ASP cc_start: 0.7657 (m-30) cc_final: 0.7346 (m-30) REVERT: B 629 MET cc_start: 0.8380 (mmm) cc_final: 0.8043 (mmm) REVERT: I 49 THR cc_start: 0.7673 (p) cc_final: 0.7342 (p) REVERT: I 61 TYR cc_start: 0.8400 (p90) cc_final: 0.8188 (p90) REVERT: E 74 LEU cc_start: 0.8458 (mt) cc_final: 0.8244 (mt) REVERT: K 1 GLN cc_start: 0.6691 (mt0) cc_final: 0.6192 (pm20) REVERT: K 13 LYS cc_start: 0.7408 (mmtt) cc_final: 0.6715 (ptmm) REVERT: K 38 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6130 (ttm170) REVERT: K 81 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7774 (tm-30) REVERT: K 99 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7476 (mm-30) REVERT: O 92 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8283 (t0) REVERT: D 624 ASP cc_start: 0.7376 (m-30) cc_final: 0.7046 (m-30) REVERT: D 629 MET cc_start: 0.8431 (mmm) cc_final: 0.8013 (mmm) REVERT: J 95 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7873 (ttp) REVERT: F 169 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7518 (mm-30) REVERT: M 13 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7259 (ptmm) REVERT: M 25 SER cc_start: 0.8653 (t) cc_final: 0.8397 (m) REVERT: M 81 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7505 (tm-30) outliers start: 70 outliers final: 47 residues processed: 319 average time/residue: 0.1518 time to fit residues: 79.0968 Evaluate side-chains 302 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 92 ASN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain D residue 659 GLU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 257 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN E 39 ASN O 92 ASN J 308 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072679 restraints weight = 68072.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073295 restraints weight = 42099.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073587 restraints weight = 34288.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073941 restraints weight = 31457.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074067 restraints weight = 28420.330| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24340 Z= 0.145 Angle : 0.705 10.344 33261 Z= 0.331 Chirality : 0.047 0.435 4092 Planarity : 0.003 0.036 4011 Dihedral : 9.324 74.582 5619 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.12 % Favored : 91.67 % Rotamer: Outliers : 2.45 % Allowed : 11.91 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.81 (0.15), residues: 2760 helix: -0.63 (0.24), residues: 465 sheet: -1.28 (0.19), residues: 717 loop : -2.65 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 38 TYR 0.023 0.001 TYR B 638 PHE 0.016 0.001 PHE I 382 TRP 0.011 0.001 TRP A 571 HIS 0.004 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00331 (24162) covalent geometry : angle 0.66524 (32790) SS BOND : bond 0.00262 ( 42) SS BOND : angle 1.40174 ( 84) hydrogen bonds : bond 0.03630 ( 564) hydrogen bonds : angle 5.64192 ( 1566) Misc. bond : bond 0.00111 ( 7) link_ALPHA1-2 : bond 0.00164 ( 6) link_ALPHA1-2 : angle 1.83554 ( 18) link_ALPHA1-3 : bond 0.01403 ( 6) link_ALPHA1-3 : angle 1.28708 ( 18) link_ALPHA1-6 : bond 0.00791 ( 6) link_ALPHA1-6 : angle 2.34203 ( 18) link_BETA1-4 : bond 0.00447 ( 54) link_BETA1-4 : angle 1.93510 ( 162) link_NAG-ASN : bond 0.00598 ( 57) link_NAG-ASN : angle 2.48236 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8134 (tm-30) REVERT: A 647 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7798 (tm-30) REVERT: G 61 TYR cc_start: 0.8515 (p90) cc_final: 0.8262 (p90) REVERT: G 457 ASP cc_start: 0.7742 (t0) cc_final: 0.7352 (t0) REVERT: C 10 ASP cc_start: 0.8093 (m-30) cc_final: 0.7694 (p0) REVERT: C 85 GLU cc_start: 0.7293 (mp0) cc_final: 0.6478 (mp0) REVERT: H 1 GLN cc_start: 0.7010 (mt0) cc_final: 0.5472 (pm20) REVERT: H 13 LYS cc_start: 0.7605 (mmtt) cc_final: 0.6775 (ptmm) REVERT: H 81 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7682 (tm-30) REVERT: H 99 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 566 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8123 (tt) REVERT: B 624 ASP cc_start: 0.7617 (m-30) cc_final: 0.7304 (m-30) REVERT: B 629 MET cc_start: 0.8358 (mmm) cc_final: 0.8019 (mmm) REVERT: I 49 THR cc_start: 0.7544 (p) cc_final: 0.7194 (p) REVERT: I 61 TYR cc_start: 0.8410 (p90) cc_final: 0.8195 (p90) REVERT: E 74 LEU cc_start: 0.8516 (mt) cc_final: 0.8293 (mt) REVERT: K 1 GLN cc_start: 0.6617 (mt0) cc_final: 0.6027 (pm20) REVERT: K 13 LYS cc_start: 0.7384 (mmtt) cc_final: 0.6694 (ptmm) REVERT: K 81 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7745 (tm-30) REVERT: K 99 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7494 (mm-30) REVERT: D 565 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4698 (mmm) REVERT: D 624 ASP cc_start: 0.7099 (m-30) cc_final: 0.6840 (m-30) REVERT: D 629 MET cc_start: 0.8347 (mmm) cc_final: 0.8029 (mmm) REVERT: D 638 TYR cc_start: 0.8155 (m-10) cc_final: 0.7946 (m-10) REVERT: J 95 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7823 (ttp) REVERT: F 136 LYS cc_start: 0.5217 (OUTLIER) cc_final: 0.4763 (tmmt) REVERT: F 169 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7426 (mm-30) REVERT: M 13 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7405 (ptmm) REVERT: M 25 SER cc_start: 0.8602 (t) cc_final: 0.8361 (m) REVERT: M 81 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7555 (tm-30) outliers start: 60 outliers final: 44 residues processed: 308 average time/residue: 0.1523 time to fit residues: 77.0091 Evaluate side-chains 301 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 263 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 0.0060 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.096912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072837 restraints weight = 68645.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073542 restraints weight = 42034.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073790 restraints weight = 33759.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074170 restraints weight = 31280.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074232 restraints weight = 28422.467| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24340 Z= 0.139 Angle : 0.675 11.898 33261 Z= 0.317 Chirality : 0.046 0.411 4092 Planarity : 0.003 0.035 4011 Dihedral : 8.452 69.330 5619 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.30 % Favored : 91.49 % Rotamer: Outliers : 2.49 % Allowed : 12.08 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.15), residues: 2760 helix: -0.34 (0.25), residues: 465 sheet: -1.17 (0.19), residues: 726 loop : -2.47 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.026 0.001 TYR B 638 PHE 0.015 0.001 PHE G 382 TRP 0.012 0.001 TRP G 338 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00318 (24162) covalent geometry : angle 0.63902 (32790) SS BOND : bond 0.00271 ( 42) SS BOND : angle 1.29294 ( 84) hydrogen bonds : bond 0.03297 ( 564) hydrogen bonds : angle 5.34731 ( 1566) Misc. bond : bond 0.00118 ( 7) link_ALPHA1-2 : bond 0.00163 ( 6) link_ALPHA1-2 : angle 1.73344 ( 18) link_ALPHA1-3 : bond 0.01350 ( 6) link_ALPHA1-3 : angle 1.43468 ( 18) link_ALPHA1-6 : bond 0.00826 ( 6) link_ALPHA1-6 : angle 2.24431 ( 18) link_BETA1-4 : bond 0.00440 ( 54) link_BETA1-4 : angle 1.74893 ( 162) link_NAG-ASN : bond 0.00553 ( 57) link_NAG-ASN : angle 2.36992 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 647 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7773 (tm-30) REVERT: G 61 TYR cc_start: 0.8469 (p90) cc_final: 0.8186 (p90) REVERT: G 457 ASP cc_start: 0.7762 (t0) cc_final: 0.7417 (t0) REVERT: C 10 ASP cc_start: 0.7989 (m-30) cc_final: 0.7673 (p0) REVERT: C 85 GLU cc_start: 0.7375 (mp0) cc_final: 0.6603 (mp0) REVERT: H 1 GLN cc_start: 0.7080 (mt0) cc_final: 0.5541 (pm20) REVERT: H 13 LYS cc_start: 0.7691 (mmtt) cc_final: 0.6920 (ptmm) REVERT: H 81 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7690 (tm-30) REVERT: H 99 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 624 ASP cc_start: 0.7595 (m-30) cc_final: 0.7287 (m-30) REVERT: B 629 MET cc_start: 0.8333 (mmm) cc_final: 0.7986 (mmm) REVERT: I 49 THR cc_start: 0.7711 (p) cc_final: 0.7378 (p) REVERT: I 61 TYR cc_start: 0.8367 (p90) cc_final: 0.8132 (p90) REVERT: I 440 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7566 (mmm160) REVERT: K 1 GLN cc_start: 0.6629 (mt0) cc_final: 0.6207 (pm20) REVERT: K 13 LYS cc_start: 0.7349 (mmtt) cc_final: 0.6671 (ptmm) REVERT: K 81 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7724 (tm-30) REVERT: K 99 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7549 (mm-30) REVERT: D 624 ASP cc_start: 0.7019 (m-30) cc_final: 0.6772 (m-30) REVERT: D 629 MET cc_start: 0.8343 (mmm) cc_final: 0.7987 (mmm) REVERT: J 95 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7891 (ttp) REVERT: F 136 LYS cc_start: 0.5019 (OUTLIER) cc_final: 0.4712 (tmmt) REVERT: F 169 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7214 (mm-30) REVERT: M 13 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7436 (ptmm) REVERT: M 81 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7590 (tm-30) outliers start: 61 outliers final: 49 residues processed: 313 average time/residue: 0.1580 time to fit residues: 80.3122 Evaluate side-chains 303 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain D residue 659 GLU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS I 197 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.093769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069546 restraints weight = 68918.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.069834 restraints weight = 44025.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070100 restraints weight = 36572.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070555 restraints weight = 33198.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.070607 restraints weight = 30259.857| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 24340 Z= 0.302 Angle : 0.831 12.369 33261 Z= 0.390 Chirality : 0.049 0.431 4092 Planarity : 0.004 0.052 4011 Dihedral : 8.794 65.659 5619 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.98 % Favored : 88.80 % Rotamer: Outliers : 2.98 % Allowed : 12.36 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.83 (0.15), residues: 2760 helix: -0.94 (0.23), residues: 483 sheet: -1.33 (0.19), residues: 747 loop : -2.56 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 503 TYR 0.020 0.002 TYR G 39 PHE 0.020 0.002 PHE I 382 TRP 0.023 0.002 TRP M 36 HIS 0.006 0.002 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00704 (24162) covalent geometry : angle 0.79213 (32790) SS BOND : bond 0.00542 ( 42) SS BOND : angle 1.50138 ( 84) hydrogen bonds : bond 0.04117 ( 564) hydrogen bonds : angle 5.81017 ( 1566) Misc. bond : bond 0.00167 ( 7) link_ALPHA1-2 : bond 0.00106 ( 6) link_ALPHA1-2 : angle 1.80779 ( 18) link_ALPHA1-3 : bond 0.01117 ( 6) link_ALPHA1-3 : angle 1.85226 ( 18) link_ALPHA1-6 : bond 0.00878 ( 6) link_ALPHA1-6 : angle 2.28919 ( 18) link_BETA1-4 : bond 0.00418 ( 54) link_BETA1-4 : angle 2.07097 ( 162) link_NAG-ASN : bond 0.00762 ( 57) link_NAG-ASN : angle 2.74618 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 1.008 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: L 70 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8192 (tm-30) REVERT: G 61 TYR cc_start: 0.8578 (p90) cc_final: 0.8288 (p90) REVERT: G 457 ASP cc_start: 0.7921 (t0) cc_final: 0.7580 (t0) REVERT: C 85 GLU cc_start: 0.7505 (mp0) cc_final: 0.6584 (mp0) REVERT: H 1 GLN cc_start: 0.7137 (mt0) cc_final: 0.5920 (pm20) REVERT: H 13 LYS cc_start: 0.7887 (mmtt) cc_final: 0.6911 (ptmm) REVERT: H 81 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7724 (tm-30) REVERT: H 99 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 624 ASP cc_start: 0.7560 (m-30) cc_final: 0.7248 (m-30) REVERT: B 629 MET cc_start: 0.8522 (mmm) cc_final: 0.8161 (mmm) REVERT: I 61 TYR cc_start: 0.8466 (p90) cc_final: 0.8231 (p90) REVERT: I 440 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7631 (mmm160) REVERT: K 1 GLN cc_start: 0.6910 (mt0) cc_final: 0.6359 (pm20) REVERT: K 13 LYS cc_start: 0.7555 (mmtt) cc_final: 0.6898 (ptmm) REVERT: K 81 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7921 (tm-30) REVERT: D 565 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.4590 (mmm) REVERT: D 629 MET cc_start: 0.8424 (mmm) cc_final: 0.8043 (mmm) REVERT: F 136 LYS cc_start: 0.5093 (OUTLIER) cc_final: 0.4592 (ttpt) REVERT: M 13 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7299 (ptmm) REVERT: M 81 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7587 (tm-30) outliers start: 73 outliers final: 60 residues processed: 291 average time/residue: 0.1586 time to fit residues: 74.8025 Evaluate side-chains 293 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain D residue 659 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 176 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 150 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 72 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.095416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071197 restraints weight = 68274.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.071829 restraints weight = 42363.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072069 restraints weight = 34647.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.072403 restraints weight = 31820.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072537 restraints weight = 28947.686| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24340 Z= 0.168 Angle : 0.711 12.850 33261 Z= 0.335 Chirality : 0.046 0.412 4092 Planarity : 0.003 0.034 4011 Dihedral : 8.287 61.503 5619 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.44 % Favored : 91.34 % Rotamer: Outliers : 2.61 % Allowed : 13.14 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.54 (0.15), residues: 2760 helix: -0.49 (0.24), residues: 465 sheet: -1.22 (0.19), residues: 744 loop : -2.38 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.016 0.002 TYR B 638 PHE 0.018 0.002 PHE I 382 TRP 0.017 0.001 TRP M 36 HIS 0.004 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00390 (24162) covalent geometry : angle 0.67434 (32790) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.34044 ( 84) hydrogen bonds : bond 0.03525 ( 564) hydrogen bonds : angle 5.43603 ( 1566) Misc. bond : bond 0.00139 ( 7) link_ALPHA1-2 : bond 0.00158 ( 6) link_ALPHA1-2 : angle 1.72510 ( 18) link_ALPHA1-3 : bond 0.01225 ( 6) link_ALPHA1-3 : angle 1.64615 ( 18) link_ALPHA1-6 : bond 0.01032 ( 6) link_ALPHA1-6 : angle 1.90856 ( 18) link_BETA1-4 : bond 0.00431 ( 54) link_BETA1-4 : angle 1.78549 ( 162) link_NAG-ASN : bond 0.00561 ( 57) link_NAG-ASN : angle 2.48824 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 251 time to evaluate : 0.980 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: L 70 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8079 (tm-30) REVERT: L 92 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8212 (t0) REVERT: G 61 TYR cc_start: 0.8574 (p90) cc_final: 0.8251 (p90) REVERT: G 377 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8187 (t0) REVERT: G 457 ASP cc_start: 0.7852 (t0) cc_final: 0.7530 (t0) REVERT: C 85 GLU cc_start: 0.7440 (mp0) cc_final: 0.6503 (mp0) REVERT: H 1 GLN cc_start: 0.7094 (mt0) cc_final: 0.5904 (pm20) REVERT: H 13 LYS cc_start: 0.7882 (mmtt) cc_final: 0.6932 (ptmm) REVERT: H 81 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 99 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7233 (mm-30) REVERT: N 33 LEU cc_start: 0.7340 (tp) cc_final: 0.7134 (tp) REVERT: B 624 ASP cc_start: 0.7649 (m-30) cc_final: 0.7302 (m-30) REVERT: B 629 MET cc_start: 0.8386 (mmm) cc_final: 0.8075 (mmm) REVERT: I 61 TYR cc_start: 0.8436 (p90) cc_final: 0.8204 (p90) REVERT: I 440 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7580 (mmm160) REVERT: K 13 LYS cc_start: 0.7531 (mmtt) cc_final: 0.6724 (ptmm) REVERT: K 81 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 565 MET cc_start: 0.4974 (OUTLIER) cc_final: 0.4690 (mmm) REVERT: D 624 ASP cc_start: 0.7037 (m-30) cc_final: 0.6735 (m-30) REVERT: D 629 MET cc_start: 0.8245 (mmm) cc_final: 0.8039 (mmm) REVERT: D 638 TYR cc_start: 0.8170 (m-10) cc_final: 0.7941 (m-10) REVERT: F 136 LYS cc_start: 0.5152 (OUTLIER) cc_final: 0.4639 (ttpt) REVERT: M 13 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7367 (ptmm) REVERT: M 81 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7600 (tm-30) outliers start: 64 outliers final: 54 residues processed: 298 average time/residue: 0.1556 time to fit residues: 75.8656 Evaluate side-chains 294 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 147 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 75 optimal weight: 0.0000 chunk 163 optimal weight: 30.0000 chunk 179 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 265 optimal weight: 0.0980 chunk 210 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN B 591 GLN D 591 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.097604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073473 restraints weight = 68449.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074170 restraints weight = 42440.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074449 restraints weight = 33575.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074782 restraints weight = 31487.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074908 restraints weight = 28585.094| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24340 Z= 0.113 Angle : 0.664 13.000 33261 Z= 0.315 Chirality : 0.045 0.384 4092 Planarity : 0.003 0.038 4011 Dihedral : 7.416 59.313 5619 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.68 % Favored : 92.10 % Rotamer: Outliers : 1.88 % Allowed : 14.08 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.19 (0.15), residues: 2760 helix: -0.00 (0.25), residues: 465 sheet: -1.03 (0.19), residues: 744 loop : -2.20 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.016 0.001 TYR G 384 PHE 0.015 0.001 PHE I 53 TRP 0.022 0.001 TRP M 36 HIS 0.012 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00257 (24162) covalent geometry : angle 0.63267 (32790) SS BOND : bond 0.00261 ( 42) SS BOND : angle 1.22368 ( 84) hydrogen bonds : bond 0.03111 ( 564) hydrogen bonds : angle 5.01407 ( 1566) Misc. bond : bond 0.00118 ( 7) link_ALPHA1-2 : bond 0.00232 ( 6) link_ALPHA1-2 : angle 1.74840 ( 18) link_ALPHA1-3 : bond 0.01303 ( 6) link_ALPHA1-3 : angle 1.47485 ( 18) link_ALPHA1-6 : bond 0.01100 ( 6) link_ALPHA1-6 : angle 1.67407 ( 18) link_BETA1-4 : bond 0.00470 ( 54) link_BETA1-4 : angle 1.55899 ( 162) link_NAG-ASN : bond 0.00510 ( 57) link_NAG-ASN : angle 2.24836 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7934 (tm-30) REVERT: L 81 GLU cc_start: 0.8143 (pt0) cc_final: 0.7524 (pm20) REVERT: L 92 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8456 (t0) REVERT: A 647 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7835 (tm-30) REVERT: G 61 TYR cc_start: 0.8461 (p90) cc_final: 0.8171 (p90) REVERT: G 457 ASP cc_start: 0.7787 (t0) cc_final: 0.7489 (t0) REVERT: C 10 ASP cc_start: 0.7998 (m-30) cc_final: 0.7645 (p0) REVERT: H 1 GLN cc_start: 0.7026 (mt0) cc_final: 0.5852 (pm20) REVERT: H 13 LYS cc_start: 0.7890 (mmtt) cc_final: 0.6952 (ptmm) REVERT: H 81 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7695 (tm-30) REVERT: H 82 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7241 (mt) REVERT: H 83 ARG cc_start: 0.6730 (mmt90) cc_final: 0.6301 (ttp-110) REVERT: H 99 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7089 (mm-30) REVERT: N 40 PRO cc_start: 0.7641 (Cg_exo) cc_final: 0.7441 (Cg_endo) REVERT: B 624 ASP cc_start: 0.7558 (m-30) cc_final: 0.7208 (m-30) REVERT: B 629 MET cc_start: 0.8281 (mmm) cc_final: 0.8004 (mmm) REVERT: I 61 TYR cc_start: 0.8341 (p90) cc_final: 0.8126 (p90) REVERT: I 440 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7677 (mmm160) REVERT: E 39 ASN cc_start: 0.8319 (t0) cc_final: 0.8115 (t0) REVERT: K 6 GLU cc_start: 0.7432 (mp0) cc_final: 0.7158 (mp0) REVERT: K 13 LYS cc_start: 0.7637 (mmtt) cc_final: 0.6783 (ptmm) REVERT: K 23 LYS cc_start: 0.9222 (tppt) cc_final: 0.9011 (tppt) REVERT: K 81 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7920 (tm-30) REVERT: O 92 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8415 (t0) REVERT: D 624 ASP cc_start: 0.7107 (m-30) cc_final: 0.6862 (m-30) REVERT: D 638 TYR cc_start: 0.8037 (m-10) cc_final: 0.7762 (m-10) REVERT: F 56 ASP cc_start: 0.7718 (m-30) cc_final: 0.7448 (m-30) REVERT: F 85 GLU cc_start: 0.7551 (mp0) cc_final: 0.7344 (mp0) REVERT: F 136 LYS cc_start: 0.5148 (OUTLIER) cc_final: 0.4636 (ttpt) REVERT: M 13 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7390 (ptmm) REVERT: M 81 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7019 (tm-30) REVERT: M 82 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7165 (mt) outliers start: 46 outliers final: 34 residues processed: 303 average time/residue: 0.1594 time to fit residues: 78.2499 Evaluate side-chains 284 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 216 optimal weight: 0.0870 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.097394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073094 restraints weight = 69024.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073779 restraints weight = 42726.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074078 restraints weight = 34908.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074398 restraints weight = 32087.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074535 restraints weight = 28951.338| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24340 Z= 0.122 Angle : 0.672 12.593 33261 Z= 0.317 Chirality : 0.045 0.378 4092 Planarity : 0.003 0.038 4011 Dihedral : 7.005 58.430 5619 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.50 % Favored : 92.32 % Rotamer: Outliers : 1.80 % Allowed : 14.61 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.02 (0.15), residues: 2760 helix: 0.12 (0.25), residues: 465 sheet: -0.91 (0.19), residues: 714 loop : -2.08 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 82A TYR 0.013 0.001 TYR B 638 PHE 0.048 0.002 PHE M 29 TRP 0.032 0.001 TRP M 36 HIS 0.011 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00283 (24162) covalent geometry : angle 0.63864 (32790) SS BOND : bond 0.00298 ( 42) SS BOND : angle 1.81808 ( 84) hydrogen bonds : bond 0.03005 ( 564) hydrogen bonds : angle 4.99969 ( 1566) Misc. bond : bond 0.00124 ( 7) link_ALPHA1-2 : bond 0.00200 ( 6) link_ALPHA1-2 : angle 1.73064 ( 18) link_ALPHA1-3 : bond 0.01132 ( 6) link_ALPHA1-3 : angle 1.48860 ( 18) link_ALPHA1-6 : bond 0.01115 ( 6) link_ALPHA1-6 : angle 1.55036 ( 18) link_BETA1-4 : bond 0.00453 ( 54) link_BETA1-4 : angle 1.55882 ( 162) link_NAG-ASN : bond 0.00476 ( 57) link_NAG-ASN : angle 2.24129 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 GLU cc_start: 0.8118 (pt0) cc_final: 0.7527 (pm20) REVERT: A 647 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7878 (tm-30) REVERT: G 61 TYR cc_start: 0.8440 (p90) cc_final: 0.8195 (p90) REVERT: G 377 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7479 (t0) REVERT: G 457 ASP cc_start: 0.7785 (t0) cc_final: 0.7515 (t0) REVERT: H 1 GLN cc_start: 0.6966 (mt0) cc_final: 0.5837 (pm20) REVERT: H 13 LYS cc_start: 0.7877 (mmtt) cc_final: 0.6881 (ptmm) REVERT: H 81 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7677 (tm-30) REVERT: H 82 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7255 (mt) REVERT: H 99 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 624 ASP cc_start: 0.7553 (m-30) cc_final: 0.7211 (m-30) REVERT: B 629 MET cc_start: 0.8347 (mmm) cc_final: 0.8037 (mmm) REVERT: I 61 TYR cc_start: 0.8302 (p90) cc_final: 0.8080 (p90) REVERT: I 440 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.7658 (mmm160) REVERT: K 13 LYS cc_start: 0.7530 (mmtt) cc_final: 0.6758 (ptmm) REVERT: K 81 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 638 TYR cc_start: 0.7988 (m-10) cc_final: 0.7734 (m-10) REVERT: F 56 ASP cc_start: 0.7774 (m-30) cc_final: 0.7502 (m-30) REVERT: M 13 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7399 (ptmm) REVERT: M 81 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7036 (tm-30) REVERT: M 82 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7162 (mt) outliers start: 44 outliers final: 39 residues processed: 279 average time/residue: 0.1575 time to fit residues: 71.5694 Evaluate side-chains 280 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 158 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 254 optimal weight: 0.4980 chunk 201 optimal weight: 2.9990 chunk 266 optimal weight: 0.0670 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.098066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073397 restraints weight = 68628.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074583 restraints weight = 42853.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074884 restraints weight = 31853.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075147 restraints weight = 29447.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075211 restraints weight = 27132.874| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24340 Z= 0.114 Angle : 0.658 12.648 33261 Z= 0.312 Chirality : 0.044 0.365 4092 Planarity : 0.003 0.038 4011 Dihedral : 6.540 58.034 5619 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.25 % Favored : 92.57 % Rotamer: Outliers : 1.88 % Allowed : 14.48 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2760 helix: 0.31 (0.25), residues: 465 sheet: -0.86 (0.19), residues: 744 loop : -2.03 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 327 TYR 0.013 0.001 TYR B 638 PHE 0.038 0.001 PHE M 29 TRP 0.027 0.001 TRP M 36 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00264 (24162) covalent geometry : angle 0.62816 (32790) SS BOND : bond 0.00286 ( 42) SS BOND : angle 1.50595 ( 84) hydrogen bonds : bond 0.02880 ( 564) hydrogen bonds : angle 4.87520 ( 1566) Misc. bond : bond 0.00115 ( 7) link_ALPHA1-2 : bond 0.00195 ( 6) link_ALPHA1-2 : angle 1.71427 ( 18) link_ALPHA1-3 : bond 0.01127 ( 6) link_ALPHA1-3 : angle 1.41427 ( 18) link_ALPHA1-6 : bond 0.01122 ( 6) link_ALPHA1-6 : angle 1.38316 ( 18) link_BETA1-4 : bond 0.00469 ( 54) link_BETA1-4 : angle 1.48265 ( 162) link_NAG-ASN : bond 0.00466 ( 57) link_NAG-ASN : angle 2.16345 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.04 seconds wall clock time: 69 minutes 13.78 seconds (4153.78 seconds total)