Starting phenix.real_space_refine on Sun Sep 13 13:45:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5vn3_8713/09_2026/5vn3_8713.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vn3_8713/09_2026/5vn3_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_8713/09_2026/5vn3_8713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vn3_8713/09_2026/5vn3_8713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vn3_8713/09_2026/5vn3_8713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vn3_8713/09_2026/5vn3_8713.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5vn3_8713/09_2026/5vn3_8713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5vn3_8713/09_2026/5vn3_8713.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 4.93, per 1000 atoms: 0.21 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: 2.13 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: 0.61 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: 3.93 Time building geometry restraints manager: 2.78 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 - 15.57: 12883 15.57 - 31.14: 491 31.14 - 46.71: 159 46.71 - 62.28: 15 62.28 - 77.85: 24 Dihedral angle restraints: 13572 sinusoidal: 5490 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 13569 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: 0.04 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.710 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 9.332 71.386 8226 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/Z covalent geometry : bond 0.00987 / 0.44 (24162) covalent geometry : angle 1.23431 / 0.66 (32790) SS BOND : bond 0.01450 / 0.91 ( 42) SS BOND : angle 2.21844 / 1.38 ( 84) hydrogen bonds : bond 0.29037 / 19.67 ( 564) hydrogen bonds : angle 10.41193 / 7.04 ( 1566) Misc. bond : bond 0.00465 / 0.22 ( 7) link_ALPHA1-2 : bond 0.00429 / 0.22 ( 6) link_ALPHA1-2 : angle 2.68058 / 1.41 ( 18) link_ALPHA1-3 : bond 0.00567 / 0.25 ( 6) link_ALPHA1-3 : angle 1.59041 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00429 / 0.19 ( 6) link_ALPHA1-6 : angle 1.71947 / 0.85 ( 18) link_BETA1-4 : bond 0.00663 / 0.44 ( 54) link_BETA1-4 : angle 2.84408 / 1.77 ( 162) link_NAG-ASN : bond 0.01048 / 0.62 ( 57) link_NAG-ASN : angle 4.29129 / 2.88 ( 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 : 0.747 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: 0.7554 (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: 0.8409 (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: 0.1794 time to fit residues: 137.5062 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 : 0.705 ------------------------------------------------------------------------------- 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... ** 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 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 377 ASN I 422 GLN E 25 GLN E 163 GLN O 92 ASN J 103 GLN J 197 ASN J 377 ASN J 422 GLN F 25 GLN F 163 GLN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074986 restraints weight = 68905.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075849 restraints weight = 43119.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.076120 restraints weight = 33042.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.076442 restraints weight = 30009.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076541 restraints weight = 27564.119| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24340 Z= 0.147 Angle : 0.748 9.712 33261 Z= 0.366 Chirality : 0.045 0.202 4092 Planarity : 0.005 0.041 4011 Dihedral : 4.832 64.818 2988 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.37 % Favored : 91.41 % Rotamer: Outliers : 1.67 % Allowed : 7.96 % Favored : 90.37 % 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: -3.96 (0.14), residues: 2760 helix: -2.13 (0.20), residues: 438 sheet: -2.05 (0.18), residues: 753 loop : -3.18 (0.13), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 61 TYR 0.019 0.002 TYR H 79 PHE 0.015 0.001 PHE G 382 TRP 0.022 0.002 TRP K 36 HIS 0.006 0.001 HIS G 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (24162) covalent geometry : angle 0.70670 / 0.36 (32790) SS BOND : bond 0.00282 / 0.17 ( 42) SS BOND : angle 1.88906 / 1.01 ( 84) hydrogen bonds : bond 0.05250 / 3.58 ( 564) hydrogen bonds : angle 6.94742 / 4.75 ( 1566) Misc. bond : bond 0.00125 / 0.06 ( 7) link_ALPHA1-2 : bond 0.00115 / 0.06 ( 6) link_ALPHA1-2 : angle 2.12484 / 1.10 ( 18) link_ALPHA1-3 : bond 0.01032 / 0.49 ( 6) link_ALPHA1-3 : angle 1.53942 / 0.70 ( 18) link_ALPHA1-6 : bond 0.00662 / 0.36 ( 6) link_ALPHA1-6 : angle 1.72901 / 0.84 ( 18) link_BETA1-4 : bond 0.00479 / 0.30 ( 54) link_BETA1-4 : angle 1.77542 / 1.17 ( 162) link_NAG-ASN : bond 0.00453 / 0.28 ( 57) link_NAG-ASN : angle 2.70216 / 1.77 ( 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 400 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 0.747 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 92 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8519 (t0) REVERT: A 629 MET cc_start: 0.8390 (mmm) cc_final: 0.7957 (mtp) REVERT: G 61 TYR cc_start: 0.8404 (p90) cc_final: 0.8180 (p90) REVERT: G 376 PHE cc_start: 0.8309 (p90) cc_final: 0.8068 (p90) REVERT: G 457 ASP cc_start: 0.7533 (t0) cc_final: 0.7238 (t0) REVERT: C 10 ASP cc_start: 0.8124 (m-30) cc_final: 0.7695 (p0) REVERT: C 169 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6946 (mm-30) REVERT: H 1 GLN cc_start: 0.6731 (mt0) cc_final: 0.6302 (pt0) REVERT: H 13 LYS cc_start: 0.7571 (mmtt) cc_final: 0.6831 (ptmm) REVERT: H 73 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (mttt) REVERT: N 33 LEU cc_start: 0.7501 (tp) cc_final: 0.7249 (tp) REVERT: N 92 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8500 (t0) REVERT: B 566 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 624 ASP cc_start: 0.7154 (m-30) cc_final: 0.6895 (m-30) REVERT: B 629 MET cc_start: 0.8257 (mmm) cc_final: 0.7789 (mmm) REVERT: B 657 GLU cc_start: 0.7899 (tp30) cc_final: 0.7654 (tm-30) REVERT: I 61 TYR cc_start: 0.8385 (p90) cc_final: 0.8150 (p90) REVERT: E 20 GLN cc_start: 0.7189 (tp40) cc_final: 0.6978 (tm-30) REVERT: E 53 ASP cc_start: 0.7815 (m-30) cc_final: 0.7487 (m-30) REVERT: E 74 LEU cc_start: 0.8337 (mt) cc_final: 0.8033 (mt) REVERT: E 77 GLU cc_start: 0.7686 (mp0) cc_final: 0.7464 (pm20) REVERT: E 130 CYS cc_start: 0.3871 (m) cc_final: 0.3468 (t) REVERT: E 137 ASN cc_start: 0.7230 (m-40) cc_final: 0.6535 (t0) REVERT: E 138 ILE cc_start: 0.4945 (mt) cc_final: 0.4731 (mp) REVERT: K 13 LYS cc_start: 0.7238 (mmtt) cc_final: 0.6641 (ptmm) REVERT: K 23 LYS cc_start: 0.8848 (tppt) cc_final: 0.8587 (tppt) REVERT: K 81 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7620 (tm-30) REVERT: K 83 ARG cc_start: 0.7175 (mtp-110) cc_final: 0.6948 (mmt180) REVERT: K 100 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6531 (mt-10) REVERT: O 92 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8478 (t0) REVERT: D 629 MET cc_start: 0.8345 (mmm) cc_final: 0.8017 (mmm) REVERT: F 169 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7390 (mm-30) REVERT: M 13 LYS cc_start: 0.7478 (mmtt) cc_final: 0.7146 (ptmm) REVERT: M 25 SER cc_start: 0.8548 (t) cc_final: 0.8337 (m) REVERT: M 73 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8710 (mttt) REVERT: M 81 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7881 (tm-30) REVERT: M 100 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6468 (mt-10) REVERT: M 101 LYS cc_start: 0.8451 (tttm) cc_final: 0.8194 (tptt) outliers start: 41 outliers final: 16 residues processed: 384 average time/residue: 0.1466 time to fit residues: 90.4318 Evaluate side-chains 292 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 I residue 401 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 25 SER 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 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: 4.9990 chunk 91 optimal weight: 9.9990 chunk 265 optimal weight: 0.0670 chunk 86 optimal weight: 0.0770 chunk 9 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 197 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 478 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 = 0.3723 r_free = 0.3723 target = 0.097542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073535 restraints weight = 69158.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074134 restraints weight = 43294.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074358 restraints weight = 35063.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074823 restraints weight = 32285.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074874 restraints weight = 29194.913| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24340 Z= 0.163 Angle : 0.722 11.811 33261 Z= 0.346 Chirality : 0.045 0.331 4092 Planarity : 0.004 0.035 4011 Dihedral : 4.903 59.661 2988 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.77 % Favored : 91.01 % Rotamer: Outliers : 2.45 % Allowed : 9.38 % Favored : 88.17 % 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: -1.20 (0.23), residues: 453 sheet: -1.75 (0.19), residues: 681 loop : -2.85 (0.13), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 419 TYR 0.020 0.002 TYR N 91 PHE 0.014 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/Z covalent geometry : bond 0.00367 / 0.16 (24162) covalent geometry : angle 0.67703 / 0.34 (32790) SS BOND : bond 0.00287 / 0.17 ( 42) SS BOND : angle 1.47534 / 0.82 ( 84) hydrogen bonds : bond 0.04265 / 2.88 ( 564) hydrogen bonds : angle 6.32328 / 4.34 ( 1566) Misc. bond : bond 0.00120 / 0.05 ( 7) link_ALPHA1-2 : bond 0.00149 / 0.10 ( 6) link_ALPHA1-2 : angle 1.87802 / 0.95 ( 18) link_ALPHA1-3 : bond 0.01122 / 0.54 ( 6) link_ALPHA1-3 : angle 1.56685 / 0.74 ( 18) link_ALPHA1-6 : bond 0.00579 / 0.31 ( 6) link_ALPHA1-6 : angle 1.74516 / 0.85 ( 18) link_BETA1-4 : bond 0.00428 / 0.27 ( 54) link_BETA1-4 : angle 1.69885 / 1.13 ( 162) link_NAG-ASN : bond 0.00793 / 0.55 ( 57) link_NAG-ASN : angle 2.93909 / 1.92 ( 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 345 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 285 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 629 MET cc_start: 0.8476 (mmm) cc_final: 0.7983 (mtp) REVERT: G 61 TYR cc_start: 0.8401 (p90) cc_final: 0.8144 (p90) REVERT: G 377 ASN cc_start: 0.8583 (m-40) cc_final: 0.8330 (t0) REVERT: G 457 ASP cc_start: 0.7617 (t0) cc_final: 0.7224 (t0) REVERT: C 10 ASP cc_start: 0.8100 (m-30) cc_final: 0.7717 (p0) REVERT: C 85 GLU cc_start: 0.7210 (mp0) cc_final: 0.6276 (mp0) REVERT: H 1 GLN cc_start: 0.6739 (mt0) cc_final: 0.6235 (pt0) REVERT: H 13 LYS cc_start: 0.7601 (mmtt) cc_final: 0.6862 (ptmm) REVERT: H 99 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7286 (mm-30) REVERT: N 33 LEU cc_start: 0.7456 (tp) cc_final: 0.7211 (tp) REVERT: B 624 ASP cc_start: 0.7551 (m-30) cc_final: 0.7235 (m-30) REVERT: B 629 MET cc_start: 0.8297 (mmm) cc_final: 0.7862 (mmm) REVERT: I 61 TYR cc_start: 0.8424 (p90) cc_final: 0.8174 (p90) REVERT: E 20 GLN cc_start: 0.7282 (tp40) cc_final: 0.7022 (tm-30) REVERT: E 137 ASN cc_start: 0.7247 (m-40) cc_final: 0.6536 (t0) REVERT: K 13 LYS cc_start: 0.7311 (mmtt) cc_final: 0.6681 (ptmm) REVERT: K 19 LYS cc_start: 0.8818 (tptt) cc_final: 0.8410 (tptt) REVERT: K 23 LYS cc_start: 0.8960 (tppt) cc_final: 0.8748 (tppt) REVERT: K 81 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7782 (tm-30) REVERT: K 83 ARG cc_start: 0.7401 (mtp-110) cc_final: 0.7024 (mmt90) REVERT: D 624 ASP cc_start: 0.7486 (m-30) cc_final: 0.7104 (m-30) REVERT: D 629 MET cc_start: 0.8340 (mmm) cc_final: 0.8095 (mmm) REVERT: J 95 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7861 (ttp) REVERT: F 10 ASP cc_start: 0.6769 (p0) cc_final: 0.6522 (p0) REVERT: M 13 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7145 (ptmm) REVERT: M 25 SER cc_start: 0.8595 (t) cc_final: 0.8331 (m) REVERT: M 46 GLU cc_start: 0.6938 (tt0) cc_final: 0.6661 (tt0) REVERT: M 81 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7760 (tm-30) outliers start: 60 outliers final: 37 residues processed: 323 average time/residue: 0.1385 time to fit residues: 73.7976 Evaluate side-chains 294 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 208 VAL 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 84 SER 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 44 VAL Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 24 ILE 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 28 THR 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 208 VAL 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: 0.8980 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 267 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN G 301 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 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 = 0.096517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071798 restraints weight = 69720.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.072361 restraints weight = 42602.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072660 restraints weight = 32318.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073108 restraints weight = 29173.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073163 restraints weight = 26796.423| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24340 Z= 0.135 Angle : 0.680 11.662 33261 Z= 0.323 Chirality : 0.044 0.445 4092 Planarity : 0.004 0.039 4011 Dihedral : 4.865 54.646 2988 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.93 % Favored : 91.85 % Rotamer: Outliers : 2.28 % Allowed : 10.36 % Favored : 87.35 % 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: -2.89 (0.15), residues: 2760 helix: -0.67 (0.24), residues: 459 sheet: -1.44 (0.19), residues: 681 loop : -2.62 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 273 TYR 0.022 0.001 TYR B 638 PHE 0.024 0.001 PHE G 233 TRP 0.014 0.001 TRP M 36 HIS 0.005 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24162) covalent geometry : angle 0.64313 / 0.31 (32790) SS BOND : bond 0.00260 / 0.15 ( 42) SS BOND : angle 1.48830 / 0.97 ( 84) hydrogen bonds : bond 0.03611 / 2.44 ( 564) hydrogen bonds : angle 5.77087 / 3.96 ( 1566) Misc. bond : bond 0.00093 / 0.04 ( 7) link_ALPHA1-2 : bond 0.00136 / 0.08 ( 6) link_ALPHA1-2 : angle 1.70373 / 0.86 ( 18) link_ALPHA1-3 : bond 0.00859 / 0.42 ( 6) link_ALPHA1-3 : angle 1.45838 / 0.69 ( 18) link_ALPHA1-6 : bond 0.00579 / 0.31 ( 6) link_ALPHA1-6 : angle 1.67463 / 0.81 ( 18) link_BETA1-4 : bond 0.00419 / 0.26 ( 54) link_BETA1-4 : angle 1.55598 / 1.03 ( 162) link_NAG-ASN : bond 0.00739 / 0.50 ( 57) link_NAG-ASN : angle 2.52485 / 1.63 ( 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 343 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8177 (tm-30) REVERT: L 92 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8258 (t0) REVERT: A 629 MET cc_start: 0.8480 (mmm) cc_final: 0.7976 (mtp) REVERT: G 61 TYR cc_start: 0.8437 (p90) cc_final: 0.8171 (p90) REVERT: G 377 ASN cc_start: 0.8529 (m-40) cc_final: 0.8304 (t0) REVERT: G 457 ASP cc_start: 0.7749 (t0) cc_final: 0.7336 (t0) REVERT: C 10 ASP cc_start: 0.8226 (m-30) cc_final: 0.7709 (p0) REVERT: C 85 GLU cc_start: 0.7254 (mp0) cc_final: 0.6838 (mp0) REVERT: H 1 GLN cc_start: 0.6750 (mt0) cc_final: 0.5415 (pm20) REVERT: H 13 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6760 (ptmm) REVERT: N 33 LEU cc_start: 0.7549 (tp) cc_final: 0.7325 (tp) REVERT: N 92 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8562 (t0) REVERT: B 566 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8039 (tt) REVERT: B 624 ASP cc_start: 0.7630 (m-30) cc_final: 0.7294 (m-30) REVERT: B 629 MET cc_start: 0.8369 (mmm) cc_final: 0.7958 (mmm) REVERT: I 49 THR cc_start: 0.7404 (p) cc_final: 0.7074 (p) REVERT: I 61 TYR cc_start: 0.8423 (p90) cc_final: 0.8214 (p90) REVERT: E 10 ASP cc_start: 0.6888 (p0) cc_final: 0.6507 (p0) REVERT: E 74 LEU cc_start: 0.8465 (mt) cc_final: 0.8235 (mt) REVERT: E 137 ASN cc_start: 0.7288 (m-40) cc_final: 0.6609 (t0) REVERT: E 138 ILE cc_start: 0.5190 (mp) cc_final: 0.4943 (mp) REVERT: K 1 GLN cc_start: 0.6645 (mt0) cc_final: 0.6123 (pm20) REVERT: K 13 LYS cc_start: 0.7307 (mmtt) cc_final: 0.6619 (ptmm) REVERT: K 38 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6227 (ttm170) REVERT: K 46 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7154 (pt0) REVERT: K 81 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7742 (tm-30) REVERT: K 99 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7379 (mm-30) REVERT: O 92 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8192 (t0) REVERT: D 565 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4594 (mmm) REVERT: D 624 ASP cc_start: 0.7460 (m-30) cc_final: 0.7051 (m-30) REVERT: D 629 MET cc_start: 0.8315 (mmm) cc_final: 0.8038 (mmm) REVERT: J 95 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7712 (ttp) REVERT: F 136 LYS cc_start: 0.5493 (OUTLIER) cc_final: 0.5064 (ttpp) REVERT: F 169 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7479 (mm-30) REVERT: M 13 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7193 (ptmm) REVERT: M 25 SER cc_start: 0.8481 (t) cc_final: 0.8259 (m) REVERT: M 81 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7339 (tm-30) outliers start: 56 outliers final: 38 residues processed: 325 average time/residue: 0.1419 time to fit residues: 75.4313 Evaluate side-chains 303 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 ASN 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 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 I residue 44 VAL Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 401 THR 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 28 THR Chi-restraints excluded: chain K residue 38 ARG 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 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 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 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: 1.9990 chunk 20 optimal weight: 0.6980 chunk 226 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 112 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** 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 = 0.3712 r_free = 0.3712 target = 0.096984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.072626 restraints weight = 69234.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073244 restraints weight = 41223.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073402 restraints weight = 32718.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074591 restraints weight = 28996.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074471 restraints weight = 24288.069| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24340 Z= 0.116 Angle : 0.646 10.139 33261 Z= 0.308 Chirality : 0.044 0.410 4092 Planarity : 0.003 0.038 4011 Dihedral : 4.753 53.562 2988 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.61 % Favored : 92.17 % Rotamer: Outliers : 2.04 % Allowed : 11.71 % Favored : 86.25 % 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: -2.59 (0.15), residues: 2760 helix: -0.33 (0.25), residues: 459 sheet: -1.25 (0.19), residues: 681 loop : -2.45 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.022 0.001 TYR B 638 PHE 0.012 0.001 PHE I 382 TRP 0.010 0.001 TRP I 96 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (24162) covalent geometry : angle 0.61255 / 0.30 (32790) SS BOND : bond 0.00279 / 0.17 ( 42) SS BOND : angle 1.33248 / 0.84 ( 84) hydrogen bonds : bond 0.03335 / 2.23 ( 564) hydrogen bonds : angle 5.47623 / 3.77 ( 1566) Misc. bond : bond 0.00109 / 0.05 ( 7) link_ALPHA1-2 : bond 0.00151 / 0.08 ( 6) link_ALPHA1-2 : angle 1.61455 / 0.81 ( 18) link_ALPHA1-3 : bond 0.00837 / 0.42 ( 6) link_ALPHA1-3 : angle 1.44670 / 0.69 ( 18) link_ALPHA1-6 : bond 0.00590 / 0.32 ( 6) link_ALPHA1-6 : angle 1.61144 / 0.78 ( 18) link_BETA1-4 : bond 0.00426 / 0.27 ( 54) link_BETA1-4 : angle 1.48531 / 0.99 ( 162) link_NAG-ASN : bond 0.00571 / 0.39 ( 57) link_NAG-ASN : angle 2.33812 / 1.51 ( 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 323 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8185 (tm-30) REVERT: L 92 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8397 (t0) REVERT: A 629 MET cc_start: 0.8445 (mmm) cc_final: 0.7955 (mtp) REVERT: G 61 TYR cc_start: 0.8393 (p90) cc_final: 0.8142 (p90) REVERT: G 457 ASP cc_start: 0.7682 (t0) cc_final: 0.7254 (t0) REVERT: C 10 ASP cc_start: 0.8127 (m-30) cc_final: 0.7688 (p0) REVERT: C 85 GLU cc_start: 0.7115 (mp0) cc_final: 0.6656 (mp0) REVERT: H 1 GLN cc_start: 0.6892 (mt0) cc_final: 0.5412 (pm20) REVERT: H 13 LYS cc_start: 0.7608 (mmtt) cc_final: 0.6801 (ptmm) REVERT: H 81 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7619 (tm-30) REVERT: H 99 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7285 (mm-30) REVERT: H 100 TYR cc_start: 0.7064 (t80) cc_final: 0.6827 (t80) REVERT: N 33 LEU cc_start: 0.7521 (tp) cc_final: 0.7321 (tp) REVERT: N 46 LEU cc_start: 0.8420 (tp) cc_final: 0.8206 (tt) REVERT: B 624 ASP cc_start: 0.7611 (m-30) cc_final: 0.7278 (m-30) REVERT: B 629 MET cc_start: 0.8368 (mmm) cc_final: 0.7929 (mmm) REVERT: I 49 THR cc_start: 0.7410 (p) cc_final: 0.7082 (p) REVERT: E 10 ASP cc_start: 0.6952 (p0) cc_final: 0.6402 (p0) REVERT: E 74 LEU cc_start: 0.8388 (mt) cc_final: 0.8056 (mt) REVERT: K 1 GLN cc_start: 0.6648 (mt0) cc_final: 0.6175 (pm20) REVERT: K 13 LYS cc_start: 0.7299 (mmtt) cc_final: 0.6639 (ptmm) REVERT: K 38 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6241 (ttm170) REVERT: K 46 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7171 (pt0) REVERT: K 81 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7715 (tm-30) REVERT: O 92 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8426 (t0) REVERT: D 624 ASP cc_start: 0.7335 (m-30) cc_final: 0.7010 (m-30) REVERT: D 629 MET cc_start: 0.8301 (mmm) cc_final: 0.8031 (mmm) REVERT: D 647 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7642 (tm-30) REVERT: J 95 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7778 (ttp) REVERT: F 136 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.5194 (ttpt) REVERT: F 169 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7334 (mm-30) REVERT: M 13 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7372 (ptmm) REVERT: M 25 SER cc_start: 0.8552 (t) cc_final: 0.8317 (m) REVERT: M 81 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7478 (tm-30) outliers start: 50 outliers final: 40 residues processed: 307 average time/residue: 0.1353 time to fit residues: 69.2538 Evaluate side-chains 303 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 92 ASN 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 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 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 B residue 615 SER 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 309 ILE Chi-restraints excluded: chain I residue 401 THR 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 28 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 78 VAL 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 649 SER Chi-restraints excluded: chain J residue 95 MET 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 F residue 136 LYS 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: 0.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 0.0570 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN N 92 ASN I 72 HIS O 92 ASN ** 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 = 0.3706 r_free = 0.3706 target = 0.096599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072051 restraints weight = 69910.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072655 restraints weight = 42119.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.072930 restraints weight = 33100.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073489 restraints weight = 29144.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073509 restraints weight = 26314.764| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3356 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= 0.131 Angle : 0.638 10.089 33261 Z= 0.305 Chirality : 0.044 0.406 4092 Planarity : 0.003 0.037 4011 Dihedral : 4.726 52.895 2988 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.04 % Favored : 91.74 % Rotamer: Outliers : 2.57 % Allowed : 11.55 % Favored : 85.88 % 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: -2.41 (0.15), residues: 2760 helix: -0.16 (0.25), residues: 459 sheet: -1.13 (0.19), residues: 681 loop : -2.35 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 83 TYR 0.021 0.001 TYR B 638 PHE 0.014 0.001 PHE G 382 TRP 0.022 0.001 TRP M 36 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (24162) covalent geometry : angle 0.60592 / 0.30 (32790) SS BOND : bond 0.00274 / 0.17 ( 42) SS BOND : angle 1.25278 / 0.78 ( 84) hydrogen bonds : bond 0.03210 / 2.14 ( 564) hydrogen bonds : angle 5.32163 / 3.67 ( 1566) Misc. bond : bond 0.00118 / 0.05 ( 7) link_ALPHA1-2 : bond 0.00157 / 0.09 ( 6) link_ALPHA1-2 : angle 1.58780 / 0.80 ( 18) link_ALPHA1-3 : bond 0.00863 / 0.43 ( 6) link_ALPHA1-3 : angle 1.50142 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00557 / 0.30 ( 6) link_ALPHA1-6 : angle 1.62230 / 0.78 ( 18) link_BETA1-4 : bond 0.00395 / 0.25 ( 54) link_BETA1-4 : angle 1.47896 / 0.98 ( 162) link_NAG-ASN : bond 0.00557 / 0.39 ( 57) link_NAG-ASN : angle 2.28904 / 1.47 ( 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 341 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8140 (tm-30) REVERT: L 92 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8419 (t0) REVERT: A 629 MET cc_start: 0.8493 (mmm) cc_final: 0.8033 (mtp) REVERT: G 61 TYR cc_start: 0.8434 (p90) cc_final: 0.8169 (p90) REVERT: G 377 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8152 (t0) REVERT: G 457 ASP cc_start: 0.7745 (t0) cc_final: 0.7332 (t0) REVERT: C 10 ASP cc_start: 0.8134 (m-30) cc_final: 0.7702 (p0) REVERT: C 85 GLU cc_start: 0.7300 (mp0) cc_final: 0.6516 (mp0) REVERT: H 1 GLN cc_start: 0.6840 (mt0) cc_final: 0.5461 (pm20) REVERT: H 13 LYS cc_start: 0.7543 (mmtt) cc_final: 0.6734 (ptmm) REVERT: H 81 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7611 (tm-30) REVERT: H 82 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7410 (mt) REVERT: H 99 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7422 (mm-30) REVERT: H 100 TYR cc_start: 0.7250 (t80) cc_final: 0.7023 (t80) REVERT: N 1 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7040 (mm-30) REVERT: N 92 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8584 (t0) REVERT: B 624 ASP cc_start: 0.7638 (m-30) cc_final: 0.7300 (m-30) REVERT: B 629 MET cc_start: 0.8420 (mmm) cc_final: 0.7983 (mmm) REVERT: I 49 THR cc_start: 0.7511 (p) cc_final: 0.7180 (p) REVERT: E 10 ASP cc_start: 0.6817 (p0) cc_final: 0.6196 (p0) REVERT: E 74 LEU cc_start: 0.8464 (mt) cc_final: 0.8092 (mt) REVERT: K 1 GLN cc_start: 0.6613 (mt0) cc_final: 0.6104 (pm20) REVERT: K 13 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6689 (ptmm) REVERT: K 38 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6181 (ttm170) REVERT: K 81 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7714 (tm-30) REVERT: K 99 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7212 (mm-30) REVERT: O 92 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8388 (t0) REVERT: D 624 ASP cc_start: 0.7225 (m-30) cc_final: 0.6849 (m-30) REVERT: D 629 MET cc_start: 0.8350 (mmm) cc_final: 0.8011 (mmm) REVERT: D 647 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7652 (tm-30) REVERT: J 95 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7822 (ttp) REVERT: F 136 LYS cc_start: 0.5417 (OUTLIER) cc_final: 0.5153 (ttpt) REVERT: F 169 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7427 (mm-30) REVERT: M 13 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7380 (ptmm) REVERT: M 25 SER cc_start: 0.8599 (t) cc_final: 0.8389 (m) REVERT: M 81 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7512 (tm-30) outliers start: 63 outliers final: 47 residues processed: 322 average time/residue: 0.1425 time to fit residues: 76.0867 Evaluate side-chains 308 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 92 ASN 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 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 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 N residue 92 ASN Chi-restraints excluded: chain B residue 615 SER 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 309 ILE Chi-restraints excluded: chain I residue 401 THR 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 28 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 78 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 99 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 167 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN G 72 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.096274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072111 restraints weight = 68720.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072737 restraints weight = 42637.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072998 restraints weight = 34600.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073302 restraints weight = 31959.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073453 restraints weight = 29104.003| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24340 Z= 0.197 Angle : 0.695 10.915 33261 Z= 0.330 Chirality : 0.045 0.413 4092 Planarity : 0.004 0.034 4011 Dihedral : 4.861 51.510 2988 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.02 % Favored : 90.76 % Rotamer: Outliers : 3.02 % Allowed : 11.63 % Favored : 85.35 % 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: -2.43 (0.15), residues: 2760 helix: -0.33 (0.24), residues: 468 sheet: -1.06 (0.19), residues: 693 loop : -2.36 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 83 TYR 0.020 0.002 TYR B 638 PHE 0.017 0.002 PHE G 382 TRP 0.015 0.002 TRP M 36 HIS 0.004 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (24162) covalent geometry : angle 0.65953 / 0.32 (32790) SS BOND : bond 0.00432 / 0.25 ( 42) SS BOND : angle 1.82846 / 0.96 ( 84) hydrogen bonds : bond 0.03467 / 2.29 ( 564) hydrogen bonds : angle 5.43412 / 3.75 ( 1566) Misc. bond : bond 0.00136 / 0.06 ( 7) link_ALPHA1-2 : bond 0.00103 / 0.04 ( 6) link_ALPHA1-2 : angle 1.58849 / 0.80 ( 18) link_ALPHA1-3 : bond 0.00709 / 0.35 ( 6) link_ALPHA1-3 : angle 1.56249 / 0.73 ( 18) link_ALPHA1-6 : bond 0.00516 / 0.27 ( 6) link_ALPHA1-6 : angle 1.73016 / 0.84 ( 18) link_BETA1-4 : bond 0.00381 / 0.24 ( 54) link_BETA1-4 : angle 1.57984 / 1.05 ( 162) link_NAG-ASN : bond 0.00605 / 0.41 ( 57) link_NAG-ASN : angle 2.39381 / 1.53 ( 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 340 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8124 (tm-30) REVERT: G 61 TYR cc_start: 0.8449 (p90) cc_final: 0.8161 (p90) REVERT: G 72 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.7150 (t-90) REVERT: G 377 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8321 (t0) REVERT: G 457 ASP cc_start: 0.7818 (t0) cc_final: 0.7457 (t0) REVERT: C 10 ASP cc_start: 0.8060 (m-30) cc_final: 0.7692 (p0) REVERT: C 85 GLU cc_start: 0.7399 (mp0) cc_final: 0.6441 (mp0) REVERT: H 1 GLN cc_start: 0.6868 (mt0) cc_final: 0.5454 (pm20) REVERT: H 13 LYS cc_start: 0.7650 (mmtt) cc_final: 0.6821 (ptmm) REVERT: H 81 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7683 (tm-30) REVERT: H 99 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7319 (mm-30) REVERT: N 46 LEU cc_start: 0.8557 (tp) cc_final: 0.8319 (tt) REVERT: B 624 ASP cc_start: 0.7625 (m-30) cc_final: 0.7325 (m-30) REVERT: B 629 MET cc_start: 0.8378 (mmm) cc_final: 0.8013 (mmm) REVERT: I 49 THR cc_start: 0.7803 (p) cc_final: 0.7468 (p) REVERT: I 440 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7520 (mmm160) REVERT: E 10 ASP cc_start: 0.6738 (p0) cc_final: 0.6154 (p0) REVERT: E 74 LEU cc_start: 0.8450 (mt) cc_final: 0.8081 (mt) REVERT: K 1 GLN cc_start: 0.6465 (mt0) cc_final: 0.6233 (pm20) REVERT: K 13 LYS cc_start: 0.7356 (mmtt) cc_final: 0.6679 (ptmm) REVERT: K 81 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 624 ASP cc_start: 0.7131 (m-30) cc_final: 0.6895 (m-30) REVERT: D 629 MET cc_start: 0.8365 (mmm) cc_final: 0.7937 (mmm) REVERT: J 95 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8024 (ttp) REVERT: F 136 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5318 (ttpt) REVERT: M 13 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7413 (ptmm) REVERT: M 81 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7579 (tm-30) outliers start: 74 outliers final: 55 residues processed: 315 average time/residue: 0.1491 time to fit residues: 77.5149 Evaluate side-chains 306 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 72 HIS 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 25 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 88 CYS 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 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 28 THR Chi-restraints excluded: chain K residue 78 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 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 74 CYS Chi-restraints excluded: chain J residue 95 MET 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 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: 4.9990 chunk 180 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 28 optimal weight: 0.0010 chunk 148 optimal weight: 0.9990 chunk 72 optimal weight: 0.0170 chunk 49 optimal weight: 0.9980 overall best weight: 0.6028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 377 ASN N 92 ASN B 591 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.097010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072173 restraints weight = 69208.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072653 restraints weight = 43043.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073024 restraints weight = 32436.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073436 restraints weight = 29208.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073502 restraints weight = 26904.518| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24340 Z= 0.113 Angle : 0.643 11.881 33261 Z= 0.307 Chirality : 0.043 0.393 4092 Planarity : 0.003 0.036 4011 Dihedral : 4.715 53.591 2988 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.96 % Favored : 92.83 % Rotamer: Outliers : 2.08 % Allowed : 12.93 % Favored : 84.99 % 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: -2.17 (0.15), residues: 2760 helix: 0.05 (0.25), residues: 468 sheet: -0.94 (0.19), residues: 696 loop : -2.22 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 83 TYR 0.017 0.001 TYR D 638 PHE 0.048 0.001 PHE K 29 TRP 0.016 0.001 TRP M 36 HIS 0.015 0.001 HIS G 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (24162) covalent geometry : angle 0.61364 / 0.30 (32790) SS BOND : bond 0.00278 / 0.17 ( 42) SS BOND : angle 1.36979 / 0.78 ( 84) hydrogen bonds : bond 0.03086 / 2.05 ( 564) hydrogen bonds : angle 5.13057 / 3.54 ( 1566) Misc. bond : bond 0.00112 / 0.05 ( 7) link_ALPHA1-2 : bond 0.00212 / 0.10 ( 6) link_ALPHA1-2 : angle 1.51750 / 0.76 ( 18) link_ALPHA1-3 : bond 0.00877 / 0.43 ( 6) link_ALPHA1-3 : angle 1.47419 / 0.70 ( 18) link_ALPHA1-6 : bond 0.00579 / 0.31 ( 6) link_ALPHA1-6 : angle 1.55909 / 0.75 ( 18) link_BETA1-4 : bond 0.00423 / 0.27 ( 54) link_BETA1-4 : angle 1.40725 / 0.94 ( 162) link_NAG-ASN : bond 0.00513 / 0.36 ( 57) link_NAG-ASN : angle 2.17993 / 1.39 ( 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 322 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7280 (mm-30) REVERT: L 70 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 61 TYR cc_start: 0.8431 (p90) cc_final: 0.8153 (p90) REVERT: G 377 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8310 (t0) REVERT: G 457 ASP cc_start: 0.7822 (t0) cc_final: 0.7439 (t0) REVERT: C 10 ASP cc_start: 0.8209 (m-30) cc_final: 0.7716 (p0) REVERT: C 85 GLU cc_start: 0.7282 (mp0) cc_final: 0.6568 (mp0) REVERT: H 1 GLN cc_start: 0.6856 (mt0) cc_final: 0.5496 (pm20) REVERT: H 13 LYS cc_start: 0.7579 (mmtt) cc_final: 0.6719 (ptmm) REVERT: H 81 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7534 (tm-30) REVERT: H 82 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7393 (mt) REVERT: H 99 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7158 (mm-30) REVERT: N 1 GLU cc_start: 0.7767 (mt-10) cc_final: 0.6961 (mm-30) REVERT: N 92 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8592 (t0) REVERT: B 624 ASP cc_start: 0.7602 (m-30) cc_final: 0.7239 (m-30) REVERT: B 629 MET cc_start: 0.8409 (mmm) cc_final: 0.7998 (mmm) REVERT: I 49 THR cc_start: 0.7418 (p) cc_final: 0.7074 (p) REVERT: I 440 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7483 (mmm160) REVERT: E 10 ASP cc_start: 0.6753 (p0) cc_final: 0.6095 (p0) REVERT: E 39 ASN cc_start: 0.8363 (t0) cc_final: 0.8163 (t0) REVERT: E 74 LEU cc_start: 0.8466 (mt) cc_final: 0.8104 (mt) REVERT: E 85 GLU cc_start: 0.7565 (mp0) cc_final: 0.7327 (mp0) REVERT: K 13 LYS cc_start: 0.7538 (mmtt) cc_final: 0.6695 (ptmm) REVERT: K 23 LYS cc_start: 0.9074 (tppp) cc_final: 0.8690 (tppt) REVERT: K 29 PHE cc_start: 0.8134 (t80) cc_final: 0.7806 (t80) REVERT: K 81 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 624 ASP cc_start: 0.7084 (m-30) cc_final: 0.6696 (m-30) REVERT: D 629 MET cc_start: 0.8287 (mmm) cc_final: 0.8046 (mmm) REVERT: D 647 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7582 (tm-30) REVERT: J 95 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7980 (ptt) REVERT: F 85 GLU cc_start: 0.7573 (mp0) cc_final: 0.7349 (mp0) REVERT: F 136 LYS cc_start: 0.5472 (OUTLIER) cc_final: 0.5181 (ttpt) REVERT: M 13 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7365 (ptmm) REVERT: M 81 GLU cc_start: 0.8431 (tm-30) cc_final: 0.6859 (tm-30) REVERT: M 99 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6372 (mm-30) outliers start: 51 outliers final: 40 residues processed: 305 average time/residue: 0.1490 time to fit residues: 74.7117 Evaluate side-chains 300 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain G residue 49 THR 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 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 N residue 92 ASN Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS 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 76 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 28 THR Chi-restraints excluded: chain K residue 67 VAL 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 J residue 74 CYS 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 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 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: 0.5980 chunk 35 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 163 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 chunk 272 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 72 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** I 374 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.095987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071759 restraints weight = 68814.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072304 restraints weight = 43242.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072503 restraints weight = 36226.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073001 restraints weight = 32438.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073036 restraints weight = 29336.451| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24340 Z= 0.201 Angle : 0.713 12.058 33261 Z= 0.338 Chirality : 0.045 0.403 4092 Planarity : 0.004 0.032 4011 Dihedral : 4.867 51.543 2988 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.31 % Favored : 90.47 % Rotamer: Outliers : 2.53 % Allowed : 12.89 % Favored : 84.58 % 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: -2.27 (0.15), residues: 2760 helix: -0.18 (0.24), residues: 468 sheet: -1.09 (0.19), residues: 744 loop : -2.21 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 38 TYR 0.025 0.002 TYR A 638 PHE 0.040 0.002 PHE K 29 TRP 0.028 0.002 TRP M 36 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (24162) covalent geometry : angle 0.68188 / 0.33 (32790) SS BOND : bond 0.00440 / 0.26 ( 42) SS BOND : angle 1.36851 / 0.81 ( 84) hydrogen bonds : bond 0.03411 / 2.26 ( 564) hydrogen bonds : angle 5.31653 / 3.67 ( 1566) Misc. bond : bond 0.00142 / 0.06 ( 7) link_ALPHA1-2 : bond 0.00095 / 0.04 ( 6) link_ALPHA1-2 : angle 1.59162 / 0.79 ( 18) link_ALPHA1-3 : bond 0.00775 / 0.36 ( 6) link_ALPHA1-3 : angle 1.57037 / 0.73 ( 18) link_ALPHA1-6 : bond 0.00504 / 0.27 ( 6) link_ALPHA1-6 : angle 1.74503 / 0.85 ( 18) link_BETA1-4 : bond 0.00377 / 0.23 ( 54) link_BETA1-4 : angle 1.57418 / 1.05 ( 162) link_NAG-ASN : bond 0.00591 / 0.40 ( 57) link_NAG-ASN : angle 2.36806 / 1.51 ( 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 312 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8069 (tm-30) REVERT: L 81 GLU cc_start: 0.8389 (pt0) cc_final: 0.7628 (pm20) REVERT: G 61 TYR cc_start: 0.8518 (p90) cc_final: 0.8262 (p90) REVERT: G 377 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8360 (t0) REVERT: G 457 ASP cc_start: 0.7896 (t0) cc_final: 0.7569 (t0) REVERT: C 10 ASP cc_start: 0.8155 (m-30) cc_final: 0.7715 (p0) REVERT: C 85 GLU cc_start: 0.7526 (mp0) cc_final: 0.6553 (mp0) REVERT: H 1 GLN cc_start: 0.7052 (mt0) cc_final: 0.5873 (pm20) REVERT: H 13 LYS cc_start: 0.7757 (mmtt) cc_final: 0.6928 (ptmm) REVERT: H 81 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7668 (tm-30) REVERT: H 82 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7290 (mt) REVERT: N 1 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7044 (mm-30) REVERT: N 92 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8287 (t0) REVERT: B 624 ASP cc_start: 0.7627 (m-30) cc_final: 0.7256 (m-30) REVERT: B 629 MET cc_start: 0.8474 (mmm) cc_final: 0.8111 (mmm) REVERT: I 440 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7627 (mmm160) REVERT: E 10 ASP cc_start: 0.6755 (p0) cc_final: 0.6249 (p0) REVERT: E 74 LEU cc_start: 0.8471 (mt) cc_final: 0.8098 (mt) REVERT: K 13 LYS cc_start: 0.7607 (mmtt) cc_final: 0.6775 (ptmm) REVERT: K 29 PHE cc_start: 0.8145 (t80) cc_final: 0.7909 (t80) REVERT: K 81 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7894 (tm-30) REVERT: O 92 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8376 (t0) REVERT: D 565 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.4649 (mmm) REVERT: D 624 ASP cc_start: 0.7120 (m-30) cc_final: 0.6878 (m-30) REVERT: D 629 MET cc_start: 0.8370 (mmm) cc_final: 0.7996 (mmm) REVERT: J 95 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8012 (ttp) REVERT: F 136 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.5065 (ttpt) REVERT: M 13 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7336 (ptmm) REVERT: M 81 GLU cc_start: 0.8392 (tm-30) cc_final: 0.6897 (tm-30) REVERT: M 99 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6722 (mm-30) outliers start: 62 outliers final: 48 residues processed: 292 average time/residue: 0.1420 time to fit residues: 68.4679 Evaluate side-chains 299 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 76 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 92 ASN 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 J residue 74 CYS Chi-restraints excluded: chain J residue 95 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 216 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN N 92 ASN D 591 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN F 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071651 restraints weight = 69409.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072177 restraints weight = 42942.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072531 restraints weight = 32251.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072902 restraints weight = 29137.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072992 restraints weight = 26893.436| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24340 Z= 0.117 Angle : 0.656 13.132 33261 Z= 0.312 Chirality : 0.044 0.384 4092 Planarity : 0.003 0.035 4011 Dihedral : 4.740 53.990 2988 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.25 % Favored : 92.57 % Rotamer: Outliers : 2.12 % Allowed : 13.26 % Favored : 84.62 % 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: -2.01 (0.16), residues: 2760 helix: 0.20 (0.25), residues: 468 sheet: -0.95 (0.19), residues: 714 loop : -2.07 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 24 TYR 0.026 0.001 TYR A 638 PHE 0.036 0.001 PHE K 29 TRP 0.027 0.001 TRP M 36 HIS 0.016 0.001 HIS J 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (24162) covalent geometry : angle 0.62847 / 0.31 (32790) SS BOND : bond 0.00287 / 0.17 ( 42) SS BOND : angle 1.25166 / 0.74 ( 84) hydrogen bonds : bond 0.03061 / 2.05 ( 564) hydrogen bonds : angle 5.02217 / 3.47 ( 1566) Misc. bond : bond 0.00113 / 0.05 ( 7) link_ALPHA1-2 : bond 0.00222 / 0.11 ( 6) link_ALPHA1-2 : angle 1.50607 / 0.75 ( 18) link_ALPHA1-3 : bond 0.00786 / 0.40 ( 6) link_ALPHA1-3 : angle 1.47147 / 0.70 ( 18) link_ALPHA1-6 : bond 0.00581 / 0.31 ( 6) link_ALPHA1-6 : angle 1.55361 / 0.75 ( 18) link_BETA1-4 : bond 0.00411 / 0.26 ( 54) link_BETA1-4 : angle 1.39175 / 0.93 ( 162) link_NAG-ASN : bond 0.00489 / 0.34 ( 57) link_NAG-ASN : angle 2.17670 / 1.39 ( 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 307 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7285 (mm-30) REVERT: L 70 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8034 (tm-30) REVERT: G 61 TYR cc_start: 0.8489 (p90) cc_final: 0.8211 (p90) REVERT: G 377 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8280 (t0) REVERT: G 457 ASP cc_start: 0.7903 (t0) cc_final: 0.7554 (t0) REVERT: C 85 GLU cc_start: 0.7300 (mp0) cc_final: 0.6565 (mp0) REVERT: H 1 GLN cc_start: 0.7025 (mt0) cc_final: 0.5850 (pm20) REVERT: H 13 LYS cc_start: 0.7704 (mmtt) cc_final: 0.6854 (ptmm) REVERT: H 81 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7565 (tm-30) REVERT: H 82 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7336 (mt) REVERT: H 99 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7043 (mm-30) REVERT: N 33 LEU cc_start: 0.7630 (tp) cc_final: 0.7401 (tp) REVERT: N 92 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8176 (t0) REVERT: B 624 ASP cc_start: 0.7598 (m-30) cc_final: 0.7216 (m-30) REVERT: B 629 MET cc_start: 0.8450 (mmm) cc_final: 0.8054 (mmm) REVERT: I 440 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7611 (mmm160) REVERT: E 10 ASP cc_start: 0.6667 (p0) cc_final: 0.6058 (p0) REVERT: E 74 LEU cc_start: 0.8475 (mt) cc_final: 0.8096 (mt) REVERT: E 85 GLU cc_start: 0.7605 (mp0) cc_final: 0.7016 (mp0) REVERT: K 13 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6657 (ptmm) REVERT: K 29 PHE cc_start: 0.8077 (t80) cc_final: 0.7720 (t80) REVERT: K 81 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7842 (tm-30) REVERT: K 100 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6388 (tp30) REVERT: O 92 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8447 (t0) REVERT: D 624 ASP cc_start: 0.7022 (m-30) cc_final: 0.6711 (m-30) REVERT: D 629 MET cc_start: 0.8367 (mmm) cc_final: 0.8047 (mmm) REVERT: J 95 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8034 (ptt) REVERT: F 85 GLU cc_start: 0.7575 (mp0) cc_final: 0.7347 (mp0) REVERT: F 136 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.5035 (ttpt) REVERT: M 13 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7210 (ptmm) REVERT: M 81 GLU cc_start: 0.8173 (tm-30) cc_final: 0.6739 (tm-30) REVERT: M 82 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7327 (mt) REVERT: M 99 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6853 (mm-30) outliers start: 52 outliers final: 39 residues processed: 286 average time/residue: 0.1487 time to fit residues: 70.3824 Evaluate side-chains 292 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 SER 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 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 N residue 92 ASN Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS 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 76 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG 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 J residue 49 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 158 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 377 ASN N 92 ASN D 658 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071673 restraints weight = 69223.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072149 restraints weight = 43381.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072500 restraints weight = 32456.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072939 restraints weight = 29314.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073003 restraints weight = 26981.325| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24340 Z= 0.118 Angle : 0.644 13.102 33261 Z= 0.307 Chirality : 0.044 0.379 4092 Planarity : 0.003 0.036 4011 Dihedral : 4.678 56.614 2988 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.72 % Favored : 92.10 % Rotamer: Outliers : 2.12 % Allowed : 13.38 % Favored : 84.50 % 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: -1.92 (0.16), residues: 2760 helix: 0.32 (0.25), residues: 468 sheet: -0.90 (0.20), residues: 681 loop : -2.01 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 24 TYR 0.027 0.001 TYR A 638 PHE 0.049 0.001 PHE M 29 TRP 0.024 0.001 TRP M 36 HIS 0.015 0.001 HIS J 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24162) covalent geometry : angle 0.61653 / 0.30 (32790) SS BOND : bond 0.00288 / 0.16 ( 42) SS BOND : angle 1.15637 / 0.65 ( 84) hydrogen bonds : bond 0.03002 / 2.01 ( 564) hydrogen bonds : angle 4.96754 / 3.43 ( 1566) Misc. bond : bond 0.00117 / 0.05 ( 7) link_ALPHA1-2 : bond 0.00172 / 0.08 ( 6) link_ALPHA1-2 : angle 1.53207 / 0.76 ( 18) link_ALPHA1-3 : bond 0.00763 / 0.38 ( 6) link_ALPHA1-3 : angle 1.50030 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00565 / 0.31 ( 6) link_ALPHA1-6 : angle 1.55447 / 0.75 ( 18) link_BETA1-4 : bond 0.00406 / 0.26 ( 54) link_BETA1-4 : angle 1.39158 / 0.93 ( 162) link_NAG-ASN : bond 0.00480 / 0.34 ( 57) link_NAG-ASN : angle 2.13631 / 1.36 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3789.19 seconds wall clock time: 66 minutes 34.27 seconds (3994.27 seconds total)