Starting phenix.real_space_refine on Sun Sep 13 08:24:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6opp_20152/09_2026/6opp_20152.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opp_20152/09_2026/6opp_20152.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/6opp_20152/09_2026/6opp_20152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opp_20152/09_2026/6opp_20152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6opp_20152/09_2026/6opp_20152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opp_20152/09_2026/6opp_20152.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6opp_20152/09_2026/6opp_20152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6opp_20152/09_2026/6opp_20152.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= -0.002 sd= 0.074 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 115 5.16 5 C 13657 2.51 5 N 3604 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 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: 21852 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: "B" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1071 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3051 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: "I" 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: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3051 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Chain: "E" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1101 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain breaks: 1 Chain: "G" 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: "K" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1046 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "J" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2998 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 3 Chain: "M" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "N" 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: "F" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: 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: 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: 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: "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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "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: 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: "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: 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Unusual residues: {'LMT': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: "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: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {'LMT': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 Chain: "K" 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: 5.40, per 1000 atoms: 0.25 Number of scatterers: 21852 At special positions: 0 Unit cell: (161.13, 158.51, 145.41, 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 115 16.00 O 4476 8.00 N 3604 7.00 C 13657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS A 501 " distance=2.12 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.08 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.12 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.12 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.06 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.10 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 605 " - pdb=" SG CYS J 501 " distance=2.08 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.07 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=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 16 " - pdb=" SG CYS M 84 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " 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=0, 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 " 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 c 3 " - " MAN c 7 " " BMA n 3 " - " MAN n 6 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG 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 u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 621 " - " ASN A 339 " " NAG A 622 " - " ASN A 355 " " NAG A 632 " - " ASN A 397 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 616 " " NAG B 704 " - " ASN B 625 " " NAG B 705 " - " ASN B 637 " " NAG D 601 " - " ASN D 88 " " NAG D 620 " - " ASN D 339 " " NAG D 621 " - " ASN D 355 " " NAG D 631 " - " ASN D 397 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 616 " " NAG E 703 " - " ASN E 625 " " NAG E 704 " - " ASN E 637 " " NAG J 601 " - " ASN J 88 " " NAG J 620 " - " ASN J 339 " " NAG J 621 " - " ASN J 355 " " NAG J 632 " - " ASN J 397 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 616 " " NAG K 703 " - " ASN K 625 " " NAG K 704 " - " ASN K 637 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 362 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN D 234 " " NAG b 1 " - " ASN D 241 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 276 " " NAG e 1 " - " ASN D 295 " " NAG f 1 " - " ASN D 332 " " NAG g 1 " - " ASN D 362 " " NAG h 1 " - " ASN D 386 " " NAG i 1 " - " ASN D 392 " " NAG j 1 " - " ASN D 413 " " NAG k 1 " - " ASN D 448 " " 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 392 " " NAG u 1 " - " ASN J 413 " " NAG v 1 " - " ASN J 448 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 830.4 milliseconds 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 44 sheets defined 22.1% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 568 through 593 Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.033A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 4.025A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.610A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.623A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.072A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.711A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 114 removed outlier: 4.230A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 350 removed outlier: 3.557A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.692A pdb=" N ASN D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 547 Processing helix chain 'E' and resid 567 through 593 Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 661 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 100C Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'K' and resid 529 through 547 Processing helix chain 'K' and resid 566 through 593 removed outlier: 4.249A pdb=" N VAL K 570 " --> pdb=" O LEU K 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 597 Processing helix chain 'K' and resid 618 through 626 Processing helix chain 'K' and resid 627 through 635 removed outlier: 3.888A pdb=" N LYS K 633 " --> pdb=" O MET K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 661 Processing helix chain 'J' and resid 64 through 74 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 98 through 114 removed outlier: 4.211A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 353 removed outlier: 3.836A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 476 through 484 removed outlier: 4.444A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 64 removed outlier: 4.163A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 79 Processing helix chain 'N' and resid 28 through 30 No H-bonds generated for 'chain 'N' and resid 28 through 30' Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 99 through 100C Processing helix chain 'F' and resid 58 through 64 removed outlier: 4.408A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.298A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.298A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.015A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA8, first strand: chain 'A' and resid 196 through 202 Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.805A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.329A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.524A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU C 96 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 4 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE C 26 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY C 38 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP C 28 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.557A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.557A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.663A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.239A pdb=" N VAL E 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N TYR D 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N CYS E 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 199 through 202 Processing sheet with id=AC6, first strand: chain 'D' and resid 259 through 260 removed outlier: 6.537A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.184A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.640A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.184A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.799A pdb=" N SER G 33 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AD2, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 10 through 12 removed outlier: 7.079A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N CYS O 88 " --> pdb=" O GLY O 99 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY O 101 " --> pdb=" O TYR O 86 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TYR O 86 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 603 through 609 removed outlier: 7.296A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 47 removed outlier: 4.601A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 55 removed outlier: 5.356A pdb=" N ILE J 215 " --> pdb=" O GLY J 250 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY J 250 " --> pdb=" O ILE J 215 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR J 217 " --> pdb=" O THR J 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 91 through 92 Processing sheet with id=AD8, first strand: chain 'J' and resid 197 through 202 Processing sheet with id=AD9, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.749A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY J 451 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N GLU J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU J 453 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N LEU J 288 " --> pdb=" O LEU J 453 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N ASP J 457 " --> pdb=" O ILE J 284 " (cutoff:3.500A) removed outlier: 12.349A pdb=" N ILE J 284 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER J 334 " --> pdb=" O GLU J 293 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 271 through 273 removed outlier: 12.349A pdb=" N ILE J 284 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N ASP J 457 " --> pdb=" O ILE J 284 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N LEU J 288 " --> pdb=" O LEU J 453 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU J 453 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N GLU J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY J 451 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N THR J 357 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE J 468 " --> pdb=" O THR J 357 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE J 359 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 2 through 5 removed outlier: 6.598A pdb=" N LYS M 2 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU M 96 " --> pdb=" O LYS M 2 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL M 4 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP M 28 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 12 through 17 Processing sheet with id=AE4, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AE5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.446A pdb=" N GLU N 10 " --> pdb=" O THR N 110 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.446A pdb=" N GLU N 10 " --> pdb=" O THR N 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.345A pdb=" N LYS F 2 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU F 96 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL F 4 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE F 26 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY F 38 " --> pdb=" O PHE F 26 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP F 28 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 12 through 17 879 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4013 1.31 - 1.45: 6630 1.45 - 1.58: 11450 1.58 - 1.71: 23 1.71 - 1.85: 144 Bond restraints: 22260 Sorted by residual: bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.385 0.112 1.40e-02 5.10e+03 6.42e+01 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 ... (remaining 22255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 25081 2.26 - 4.51: 4249 4.51 - 6.77: 735 6.77 - 9.02: 125 9.02 - 11.28: 11 Bond angle restraints: 30201 Sorted by residual: angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 120.03 128.37 -8.34 9.90e-01 1.02e+00 7.10e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.92 128.85 -8.93 1.07e+00 8.73e-01 6.96e+01 angle pdb=" N ARG A 440 " pdb=" CA ARG A 440 " pdb=" C ARG A 440 " ideal model delta sigma weight residual 111.28 120.31 -9.03 1.09e+00 8.42e-01 6.86e+01 angle pdb=" C ALA H 60 " pdb=" N PRO H 61 " pdb=" CA PRO H 61 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.02e+00 9.61e-01 6.03e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 120.38 128.28 -7.90 1.03e+00 9.43e-01 5.89e+01 ... (remaining 30196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11876 17.99 - 35.98: 366 35.98 - 53.97: 107 53.97 - 71.96: 49 71.96 - 89.95: 15 Dihedral angle restraints: 12413 sinusoidal: 5038 harmonic: 7375 Sorted by residual: dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual 93.00 154.83 -61.83 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 150.63 -57.63 1 1.00e+01 1.00e-02 4.46e+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 93.00 149.72 -56.72 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 12410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2900 0.115 - 0.230: 738 0.230 - 0.345: 96 0.345 - 0.460: 21 0.460 - 0.575: 15 Chirality restraints: 3770 Sorted by residual: chirality pdb=" C1 NAG o 2 " pdb=" O4 NAG o 1 " pdb=" C2 NAG o 2 " pdb=" O5 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 BMA i 3 " pdb=" O4 NAG i 2 " pdb=" C2 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.73e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.55e+01 ... (remaining 3767 not shown) Planarity restraints: 3729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.093 2.00e-02 2.50e+03 1.02e-01 1.29e+02 pdb=" CG ASN D 234 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.162 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 234 " -0.063 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN J 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN J 234 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN J 234 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 1 " 0.082 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" C7 NAG q 1 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG q 1 " 0.062 2.00e-02 2.50e+03 pdb=" N2 NAG q 1 " -0.108 2.00e-02 2.50e+03 pdb=" O7 NAG q 1 " -0.017 2.00e-02 2.50e+03 ... (remaining 3726 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5839 2.80 - 3.32: 19524 3.32 - 3.85: 37510 3.85 - 4.37: 43807 4.37 - 4.90: 71531 Nonbonded interactions: 178211 Sorted by model distance: nonbonded pdb=" N ASN A 88 " pdb=" OD1 ASN A 88 " model vdw 2.271 3.120 nonbonded pdb=" O4 NAG q 2 " pdb=" O6 NAG q 2 " model vdw 2.346 3.040 nonbonded pdb=" OG1 THR D 37 " pdb=" OG1 THR D 499 " model vdw 2.385 3.040 nonbonded pdb=" N ASP N 100A" pdb=" OD1 ASP N 100A" model vdw 2.398 3.120 nonbonded pdb=" O5 NAG W 1 " pdb=" O6 NAG W 1 " model vdw 2.404 2.432 ... (remaining 178206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 127 or resid 196 through 632)) selection = (chain 'D' and (resid 32 through 127 or resid 196 through 631)) selection = chain 'J' } ncs_group { reference = (chain 'B' and (resid 518 through 547 or resid 567 through 664 or resid 702 thro \ ugh 704)) selection = (chain 'E' and (resid 518 through 547 or resid 563 or resid 568 through 664 or r \ esid 702 through 704)) selection = (chain 'K' and (resid 518 through 547 or resid 567 through 664 or resid 702 thro \ ugh 704)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'X' selection = chain 'Y' selection = chain 'd' selection = chain 'i' selection = chain 'j' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'R' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 2 or resid 5 through 7)) selection = (chain 'n' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'V' 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: 2.150 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.340 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.023 0.144 22421 Z= 1.203 Angle : 1.825 11.280 30645 Z= 1.140 Chirality : 0.107 0.575 3770 Planarity : 0.009 0.068 3672 Dihedral : 10.915 89.955 7534 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 0.58 % Allowed : 0.49 % Favored : 98.92 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 2511 helix: 0.78 (0.23), residues: 429 sheet: 0.69 (0.18), residues: 752 loop : 0.47 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 542 TYR 0.083 0.009 TYR E 638 PHE 0.044 0.007 PHE H 29 TRP 0.065 0.010 TRP J 479 HIS 0.016 0.002 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.02272 / 1.20 (22260) covalent geometry : angle 1.79494 / 1.14 (30201) SS BOND : bond 0.03156 / 1.72 ( 39) SS BOND : angle 2.67591 / 1.75 ( 78) hydrogen bonds : bond 0.15514 / 10.43 ( 836) hydrogen bonds : angle 7.58285 / 5.41 ( 2253) link_ALPHA1-2 : bond 0.03977 / 2.23 ( 5) link_ALPHA1-2 : angle 3.24932 / 1.81 ( 15) link_ALPHA1-3 : bond 0.03191 / 1.61 ( 6) link_ALPHA1-3 : angle 2.41868 / 1.32 ( 18) link_ALPHA1-6 : bond 0.02905 / 1.46 ( 4) link_ALPHA1-6 : angle 2.81623 / 1.54 ( 12) link_BETA1-4 : bond 0.03231 / 2.04 ( 50) link_BETA1-4 : angle 3.66395 / 2.40 ( 150) link_NAG-ASN : bond 0.03151 / 2.00 ( 57) link_NAG-ASN : angle 3.27993 / 2.16 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 601 time to evaluate : 0.732 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: 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: B 652 GLN cc_start: 0.8861 (tp40) cc_final: 0.8338 (tm-30) REVERT: A 368 ASP cc_start: 0.7830 (m-30) cc_final: 0.7448 (m-30) REVERT: H 100 TYR cc_start: 0.7061 (t80) cc_final: 0.6533 (t80) REVERT: I 79 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7542 (mp10) REVERT: E 530 MET cc_start: 0.9031 (mtm) cc_final: 0.8743 (mtp) REVERT: E 662 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7820 (mt-10) REVERT: O 33 LEU cc_start: 0.7624 (tp) cc_final: 0.7183 (tp) REVERT: O 36 TYR cc_start: 0.6914 (m-80) cc_final: 0.6489 (m-80) REVERT: O 38 GLN cc_start: 0.5532 (tt0) cc_final: 0.4954 (tm-30) REVERT: O 42 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7799 (mm110) REVERT: K 629 MET cc_start: 0.8349 (mtm) cc_final: 0.7508 (ttm) REVERT: K 635 ILE cc_start: 0.9300 (pt) cc_final: 0.9100 (pt) REVERT: J 61 TYR cc_start: 0.8237 (p90) cc_final: 0.7521 (p90) REVERT: J 95 MET cc_start: 0.8239 (ptm) cc_final: 0.8023 (ptm) REVERT: J 100 MET cc_start: 0.8986 (mtp) cc_final: 0.8653 (mtm) REVERT: J 215 ILE cc_start: 0.9489 (mm) cc_final: 0.9129 (pt) REVERT: J 435 TYR cc_start: 0.8267 (m-80) cc_final: 0.8023 (m-80) REVERT: J 486 TYR cc_start: 0.8973 (m-80) cc_final: 0.8476 (m-10) REVERT: M 85 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7507 (tm-30) REVERT: N 6 GLU cc_start: 0.6063 (pm20) cc_final: 0.5644 (pm20) REVERT: N 23 LYS cc_start: 0.7260 (tptt) cc_final: 0.7006 (tptt) REVERT: N 32 TYR cc_start: 0.7844 (p90) cc_final: 0.7320 (p90) REVERT: N 62 HIS cc_start: 0.8410 (p-80) cc_final: 0.8207 (p90) REVERT: N 63 LEU cc_start: 0.9062 (mt) cc_final: 0.8794 (mt) REVERT: N 81 GLU cc_start: 0.8976 (tt0) cc_final: 0.8757 (tm-30) REVERT: N 82 ASN cc_start: 0.8974 (m-40) cc_final: 0.8548 (m-40) REVERT: F 39 ASN cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: F 78 ASP cc_start: 0.7629 (m-30) cc_final: 0.7323 (m-30) REVERT: F 97 VAL cc_start: 0.4379 (t) cc_final: 0.3088 (t) outliers start: 13 outliers final: 9 residues processed: 612 average time/residue: 0.1709 time to fit residues: 154.8001 Evaluate side-chains 279 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 270 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain K residue 611 ASN Chi-restraints excluded: chain K residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN H 39 GLN H 102 HIS O 93 ASN K 652 GLN J 308 HIS F 33 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.101350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.081154 restraints weight = 64717.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084082 restraints weight = 33039.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.085953 restraints weight = 22290.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.087145 restraints weight = 17430.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.087822 restraints weight = 14886.215| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22421 Z= 0.182 Angle : 0.814 13.930 30645 Z= 0.412 Chirality : 0.048 0.248 3770 Planarity : 0.005 0.043 3672 Dihedral : 6.841 78.666 2774 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.20 % Allowed : 8.48 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 2511 helix: 1.78 (0.25), residues: 435 sheet: 0.35 (0.18), residues: 762 loop : -0.26 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.025 0.002 TYR N 32 PHE 0.029 0.003 PHE O 98 TRP 0.033 0.002 TRP J 96 HIS 0.007 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (22260) covalent geometry : angle 0.76540 / 0.40 (30201) SS BOND : bond 0.00476 / 0.33 ( 39) SS BOND : angle 1.57431 / 0.98 ( 78) hydrogen bonds : bond 0.05601 / 3.72 ( 836) hydrogen bonds : angle 6.17650 / 4.36 ( 2253) link_ALPHA1-2 : bond 0.00441 / 0.24 ( 5) link_ALPHA1-2 : angle 1.59865 / 0.83 ( 15) link_ALPHA1-3 : bond 0.00877 / 0.48 ( 6) link_ALPHA1-3 : angle 1.49968 / 0.72 ( 18) link_ALPHA1-6 : bond 0.00653 / 0.33 ( 4) link_ALPHA1-6 : angle 1.41259 / 0.72 ( 12) link_BETA1-4 : bond 0.00697 / 0.47 ( 50) link_BETA1-4 : angle 2.28874 / 1.47 ( 150) link_NAG-ASN : bond 0.00467 / 0.31 ( 57) link_NAG-ASN : angle 2.97984 / 2.02 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 362 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7374 (mmm-85) REVERT: B 636 ASP cc_start: 0.8386 (t0) cc_final: 0.8174 (t0) REVERT: A 400 ARG cc_start: 0.6610 (ttt180) cc_final: 0.6302 (ttt90) REVERT: A 426 MET cc_start: 0.8655 (mtp) cc_final: 0.8387 (mtm) REVERT: A 475 MET cc_start: 0.8311 (mmp) cc_final: 0.7579 (mmt) REVERT: A 479 TRP cc_start: 0.7759 (m-10) cc_final: 0.7308 (m-90) REVERT: C 56 ASP cc_start: 0.8414 (t70) cc_final: 0.8122 (m-30) REVERT: C 70 ILE cc_start: 0.8951 (mp) cc_final: 0.8732 (mt) REVERT: C 80 ASP cc_start: 0.8096 (m-30) cc_final: 0.7075 (m-30) REVERT: C 88 ASP cc_start: 0.8493 (p0) cc_final: 0.8180 (p0) REVERT: C 89 GLN cc_start: 0.8114 (mp10) cc_final: 0.7870 (tm-30) REVERT: H 100 TYR cc_start: 0.7270 (t80) cc_final: 0.6268 (t80) REVERT: H 100 ASN cc_start: 0.6004 (m-40) cc_final: 0.5548 (m-40) REVERT: H 100 PHE cc_start: 0.5469 (m-80) cc_final: 0.4864 (m-80) REVERT: D 100 MET cc_start: 0.8582 (mtp) cc_final: 0.8363 (mtm) REVERT: D 368 ASP cc_start: 0.7041 (m-30) cc_final: 0.6805 (m-30) REVERT: E 633 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8551 (mtmm) REVERT: E 638 TYR cc_start: 0.8050 (m-80) cc_final: 0.7785 (m-10) REVERT: G 12 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7931 (mmmt) REVERT: G 101 LYS cc_start: 0.8727 (tptt) cc_final: 0.8352 (tptp) REVERT: O 36 TYR cc_start: 0.6941 (m-80) cc_final: 0.6564 (m-80) REVERT: O 37 GLN cc_start: 0.5105 (OUTLIER) cc_final: 0.4656 (tm-30) REVERT: O 38 GLN cc_start: 0.6637 (tt0) cc_final: 0.5611 (tm-30) REVERT: K 629 MET cc_start: 0.8095 (mtm) cc_final: 0.6698 (mtp) REVERT: J 95 MET cc_start: 0.8188 (ptm) cc_final: 0.7966 (ptt) REVERT: J 100 MET cc_start: 0.8749 (mtp) cc_final: 0.8503 (mtm) REVERT: J 333 ILE cc_start: 0.8631 (mt) cc_final: 0.8368 (tt) REVERT: J 475 MET cc_start: 0.7963 (mmt) cc_final: 0.7511 (mmt) REVERT: N 19 LYS cc_start: 0.9027 (tttt) cc_final: 0.8285 (tptp) REVERT: N 63 LEU cc_start: 0.8744 (mt) cc_final: 0.8365 (mt) REVERT: N 90 TYR cc_start: 0.6869 (m-80) cc_final: 0.6667 (m-80) REVERT: F 73 ASN cc_start: 0.7931 (t0) cc_final: 0.7678 (p0) REVERT: F 87 GLU cc_start: 0.6761 (mp0) cc_final: 0.6550 (mp0) outliers start: 49 outliers final: 23 residues processed: 394 average time/residue: 0.1522 time to fit residues: 93.0761 Evaluate side-chains 298 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 3 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 201 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN F 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.100768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.080495 restraints weight = 64758.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.083509 restraints weight = 32107.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085419 restraints weight = 21295.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.086610 restraints weight = 16567.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.087307 restraints weight = 14078.722| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22421 Z= 0.146 Angle : 0.728 14.067 30645 Z= 0.361 Chirality : 0.046 0.451 3770 Planarity : 0.004 0.053 3672 Dihedral : 6.080 77.975 2759 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 1.97 % Allowed : 10.55 % Favored : 87.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2511 helix: 1.81 (0.25), residues: 452 sheet: 0.32 (0.19), residues: 709 loop : -0.46 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 61 TYR 0.024 0.002 TYR H 32 PHE 0.043 0.002 PHE H 29 TRP 0.041 0.002 TRP J 96 HIS 0.005 0.001 HIS N 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22260) covalent geometry : angle 0.68503 / 0.35 (30201) SS BOND : bond 0.00513 / 0.36 ( 39) SS BOND : angle 1.81518 / 1.10 ( 78) hydrogen bonds : bond 0.04582 / 3.04 ( 836) hydrogen bonds : angle 5.79650 / 4.09 ( 2253) link_ALPHA1-2 : bond 0.00325 / 0.17 ( 5) link_ALPHA1-2 : angle 1.57460 / 0.82 ( 15) link_ALPHA1-3 : bond 0.00675 / 0.35 ( 6) link_ALPHA1-3 : angle 1.34648 / 0.66 ( 18) link_ALPHA1-6 : bond 0.00490 / 0.25 ( 4) link_ALPHA1-6 : angle 1.33805 / 0.68 ( 12) link_BETA1-4 : bond 0.00593 / 0.40 ( 50) link_BETA1-4 : angle 1.77922 / 1.14 ( 150) link_NAG-ASN : bond 0.00532 / 0.40 ( 57) link_NAG-ASN : angle 2.69771 / 1.76 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 0.843 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8134 (mp0) cc_final: 0.7853 (mp0) REVERT: B 647 GLU cc_start: 0.7959 (tt0) cc_final: 0.7597 (tt0) REVERT: A 426 MET cc_start: 0.8729 (mtp) cc_final: 0.8497 (mtm) REVERT: A 475 MET cc_start: 0.8274 (mmp) cc_final: 0.7479 (mmt) REVERT: A 479 TRP cc_start: 0.7920 (m-10) cc_final: 0.7543 (m-90) REVERT: C 88 ASP cc_start: 0.8553 (p0) cc_final: 0.8285 (p0) REVERT: C 89 GLN cc_start: 0.8017 (mp10) cc_final: 0.7805 (tm-30) REVERT: H 13 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8247 (tppt) REVERT: H 97 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6616 (mm-30) REVERT: I 36 TYR cc_start: 0.7935 (m-80) cc_final: 0.7707 (m-10) REVERT: I 42 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6851 (mp10) REVERT: D 112 TRP cc_start: 0.8562 (t-100) cc_final: 0.8351 (t-100) REVERT: D 368 ASP cc_start: 0.7166 (m-30) cc_final: 0.6907 (m-30) REVERT: E 633 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8641 (mtmm) REVERT: G 12 LYS cc_start: 0.8219 (mmmm) cc_final: 0.7878 (mmmt) REVERT: G 101 LYS cc_start: 0.8749 (tptt) cc_final: 0.8383 (tptp) REVERT: O 36 TYR cc_start: 0.6927 (m-80) cc_final: 0.6351 (m-80) REVERT: O 37 GLN cc_start: 0.5064 (OUTLIER) cc_final: 0.4552 (tm-30) REVERT: O 95 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7979 (mmm-85) REVERT: K 584 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7718 (tm-30) REVERT: K 629 MET cc_start: 0.7901 (mtm) cc_final: 0.6479 (mtp) REVERT: J 100 MET cc_start: 0.8770 (mtp) cc_final: 0.8527 (mtm) REVERT: J 280 ASN cc_start: 0.7869 (m-40) cc_final: 0.6712 (t0) REVERT: J 333 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8472 (tt) REVERT: J 434 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7770 (ttt) REVERT: J 435 TYR cc_start: 0.8007 (m-80) cc_final: 0.7789 (m-10) REVERT: J 475 MET cc_start: 0.7925 (mmt) cc_final: 0.7460 (mmt) REVERT: J 486 TYR cc_start: 0.8858 (m-80) cc_final: 0.8420 (m-10) REVERT: M 24 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7954 (pt) REVERT: M 85 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6887 (tm-30) REVERT: M 89 GLN cc_start: 0.8427 (mp10) cc_final: 0.8088 (mp10) REVERT: F 73 ASN cc_start: 0.8013 (t0) cc_final: 0.7802 (t0) REVERT: F 87 GLU cc_start: 0.7249 (mp0) cc_final: 0.6961 (mp0) REVERT: F 89 GLN cc_start: 0.7979 (mp10) cc_final: 0.7479 (mp10) outliers start: 44 outliers final: 24 residues processed: 334 average time/residue: 0.1425 time to fit residues: 75.1412 Evaluate side-chains 286 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 82 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 185 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 93 ASN B 575 GLN A 462 GLN H 39 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.097319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.076983 restraints weight = 65302.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.079735 restraints weight = 33785.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081494 restraints weight = 23108.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.082587 restraints weight = 18333.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.083313 restraints weight = 15796.657| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22421 Z= 0.211 Angle : 0.736 14.517 30645 Z= 0.364 Chirality : 0.047 0.401 3770 Planarity : 0.005 0.048 3672 Dihedral : 5.920 75.021 2757 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 2.74 % Allowed : 11.36 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2511 helix: 1.75 (0.25), residues: 454 sheet: 0.17 (0.19), residues: 719 loop : -0.66 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 103 TYR 0.025 0.002 TYR L 91 PHE 0.027 0.002 PHE H 29 TRP 0.063 0.002 TRP J 96 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (22260) covalent geometry : angle 0.69597 / 0.36 (30201) SS BOND : bond 0.00326 / 0.21 ( 39) SS BOND : angle 1.75787 / 1.06 ( 78) hydrogen bonds : bond 0.04545 / 3.05 ( 836) hydrogen bonds : angle 5.60850 / 3.94 ( 2253) link_ALPHA1-2 : bond 0.00230 / 0.13 ( 5) link_ALPHA1-2 : angle 1.64962 / 0.86 ( 15) link_ALPHA1-3 : bond 0.00620 / 0.31 ( 6) link_ALPHA1-3 : angle 1.48806 / 0.73 ( 18) link_ALPHA1-6 : bond 0.00385 / 0.19 ( 4) link_ALPHA1-6 : angle 1.46303 / 0.74 ( 12) link_BETA1-4 : bond 0.00621 / 0.44 ( 50) link_BETA1-4 : angle 1.69478 / 1.08 ( 150) link_NAG-ASN : bond 0.00771 / 0.61 ( 57) link_NAG-ASN : angle 2.62327 / 1.70 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 0.824 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLU cc_start: 0.8535 (tp30) cc_final: 0.8326 (tp30) REVERT: L 70 GLU cc_start: 0.8172 (mp0) cc_final: 0.7894 (mp0) REVERT: A 368 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7031 (t70) REVERT: A 426 MET cc_start: 0.8809 (mtp) cc_final: 0.8598 (mtm) REVERT: A 475 MET cc_start: 0.8203 (mmp) cc_final: 0.7416 (mmt) REVERT: A 479 TRP cc_start: 0.8019 (m-10) cc_final: 0.7571 (m-90) REVERT: C 88 ASP cc_start: 0.8610 (p0) cc_final: 0.8313 (p0) REVERT: H 48 MET cc_start: 0.8046 (tpp) cc_final: 0.7792 (mpp) REVERT: H 80 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8559 (tt) REVERT: H 100 ASP cc_start: 0.8271 (t0) cc_final: 0.8069 (t0) REVERT: E 633 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8586 (mtmm) REVERT: O 36 TYR cc_start: 0.6912 (m-80) cc_final: 0.6567 (m-80) REVERT: O 37 GLN cc_start: 0.5026 (OUTLIER) cc_final: 0.4610 (tm-30) REVERT: K 633 LYS cc_start: 0.8985 (tppt) cc_final: 0.8607 (mppt) REVERT: K 659 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7735 (tm-30) REVERT: J 100 MET cc_start: 0.8878 (mtp) cc_final: 0.8611 (mtm) REVERT: J 280 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.6790 (t0) REVERT: J 333 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8436 (tt) REVERT: J 434 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7647 (tmm) REVERT: J 475 MET cc_start: 0.8071 (mmt) cc_final: 0.7605 (mmt) REVERT: J 486 TYR cc_start: 0.8951 (m-80) cc_final: 0.8353 (m-10) REVERT: M 24 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8214 (pt) REVERT: M 66 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8502 (t0) REVERT: M 85 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7313 (tm-30) REVERT: N 2 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7952 (t) REVERT: N 13 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8466 (mmmt) REVERT: N 32 TYR cc_start: 0.7887 (p90) cc_final: 0.7355 (p90) REVERT: F 73 ASN cc_start: 0.8054 (t0) cc_final: 0.7810 (t0) REVERT: F 87 GLU cc_start: 0.7201 (mp0) cc_final: 0.6925 (mp0) REVERT: F 89 GLN cc_start: 0.8054 (mp10) cc_final: 0.7828 (mp10) outliers start: 61 outliers final: 34 residues processed: 319 average time/residue: 0.1425 time to fit residues: 71.0048 Evaluate side-chains 293 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 232 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 100HASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS ** J 72 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 = 0.3797 r_free = 0.3797 target = 0.097395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077214 restraints weight = 64955.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.079976 restraints weight = 33482.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.081741 restraints weight = 22846.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.082839 restraints weight = 18097.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.083547 restraints weight = 15590.624| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22421 Z= 0.163 Angle : 0.673 10.923 30645 Z= 0.335 Chirality : 0.045 0.270 3770 Planarity : 0.004 0.049 3672 Dihedral : 5.743 71.988 2757 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 2.47 % Allowed : 12.52 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2511 helix: 2.26 (0.25), residues: 436 sheet: 0.10 (0.19), residues: 729 loop : -0.65 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.034 0.002 TYR H 90 PHE 0.030 0.002 PHE H 29 TRP 0.025 0.002 TRP J 45 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (22260) covalent geometry : angle 0.64128 / 0.33 (30201) SS BOND : bond 0.00362 / 0.26 ( 39) SS BOND : angle 1.68080 / 1.01 ( 78) hydrogen bonds : bond 0.04160 / 2.80 ( 836) hydrogen bonds : angle 5.48286 / 3.85 ( 2253) link_ALPHA1-2 : bond 0.00134 / 0.07 ( 5) link_ALPHA1-2 : angle 1.60666 / 0.83 ( 15) link_ALPHA1-3 : bond 0.00537 / 0.28 ( 6) link_ALPHA1-3 : angle 1.44512 / 0.70 ( 18) link_ALPHA1-6 : bond 0.00401 / 0.20 ( 4) link_ALPHA1-6 : angle 1.43277 / 0.74 ( 12) link_BETA1-4 : bond 0.00505 / 0.35 ( 50) link_BETA1-4 : angle 1.48636 / 0.96 ( 150) link_NAG-ASN : bond 0.00551 / 0.43 ( 57) link_NAG-ASN : angle 2.18560 / 1.45 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 0.836 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7014 (mmm-85) REVERT: L 70 GLU cc_start: 0.8132 (mp0) cc_final: 0.7827 (mp0) REVERT: B 647 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 368 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7039 (t70) REVERT: A 475 MET cc_start: 0.8113 (mmp) cc_final: 0.7596 (mmp) REVERT: A 479 TRP cc_start: 0.7951 (m-10) cc_final: 0.7531 (m-90) REVERT: H 13 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8547 (tppt) REVERT: H 64 GLN cc_start: 0.8718 (pm20) cc_final: 0.8225 (pm20) REVERT: I 42 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7272 (mp10) REVERT: E 633 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8665 (mtmm) REVERT: G 12 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7405 (mttp) REVERT: O 36 TYR cc_start: 0.6826 (m-80) cc_final: 0.6533 (m-80) REVERT: O 37 GLN cc_start: 0.5070 (OUTLIER) cc_final: 0.4670 (tm-30) REVERT: K 629 MET cc_start: 0.8070 (mtp) cc_final: 0.7708 (mtm) REVERT: K 633 LYS cc_start: 0.8949 (tppt) cc_final: 0.8527 (mppt) REVERT: K 659 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7855 (tm-30) REVERT: J 100 MET cc_start: 0.8848 (mtp) cc_final: 0.8558 (mtm) REVERT: J 280 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.6823 (t0) REVERT: J 333 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8382 (tt) REVERT: J 475 MET cc_start: 0.8076 (mmt) cc_final: 0.7592 (mmt) REVERT: J 486 TYR cc_start: 0.8952 (m-80) cc_final: 0.8463 (m-10) REVERT: M 24 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8294 (pt) REVERT: M 66 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8424 (t0) REVERT: M 85 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7284 (tm-30) REVERT: M 89 GLN cc_start: 0.8418 (mp10) cc_final: 0.8169 (mp10) REVERT: F 73 ASN cc_start: 0.8011 (t0) cc_final: 0.7683 (t0) REVERT: F 87 GLU cc_start: 0.7120 (mp0) cc_final: 0.6885 (mp0) outliers start: 55 outliers final: 30 residues processed: 300 average time/residue: 0.1391 time to fit residues: 66.4010 Evaluate side-chains 279 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 61 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 105 HIS ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 GLN O 42 GLN J 66 HIS ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS J 462 GLN F 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.093524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.073043 restraints weight = 65540.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075672 restraints weight = 34381.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077349 restraints weight = 23725.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078391 restraints weight = 18965.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078984 restraints weight = 16465.294| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 22421 Z= 0.289 Angle : 0.787 10.640 30645 Z= 0.390 Chirality : 0.049 0.370 3770 Planarity : 0.005 0.050 3672 Dihedral : 5.984 66.882 2757 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 2.96 % Allowed : 12.61 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2511 helix: 1.98 (0.25), residues: 432 sheet: -0.11 (0.19), residues: 748 loop : -0.90 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 480 TYR 0.034 0.003 TYR H 90 PHE 0.030 0.002 PHE D 376 TRP 0.044 0.002 TRP A 45 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.29 (22260) covalent geometry : angle 0.75322 / 0.38 (30201) SS BOND : bond 0.00425 / 0.29 ( 39) SS BOND : angle 1.71304 / 1.03 ( 78) hydrogen bonds : bond 0.04762 / 3.23 ( 836) hydrogen bonds : angle 5.65915 / 3.98 ( 2253) link_ALPHA1-2 : bond 0.00392 / 0.22 ( 5) link_ALPHA1-2 : angle 1.82701 / 0.95 ( 15) link_ALPHA1-3 : bond 0.00466 / 0.22 ( 6) link_ALPHA1-3 : angle 1.66392 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00337 / 0.17 ( 4) link_ALPHA1-6 : angle 1.55368 / 0.79 ( 12) link_BETA1-4 : bond 0.00496 / 0.34 ( 50) link_BETA1-4 : angle 1.63204 / 1.05 ( 150) link_NAG-ASN : bond 0.00664 / 0.49 ( 57) link_NAG-ASN : angle 2.54237 / 1.68 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 0.919 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: symmetry clash revert: symmetry clash REVERT: L 39 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.5327 (mtmm) REVERT: B 647 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 368 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7091 (t70) REVERT: H 13 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8624 (tppt) REVERT: H 48 MET cc_start: 0.8241 (tpp) cc_final: 0.7953 (mmt) REVERT: H 100 TYR cc_start: 0.8171 (t80) cc_final: 0.7927 (t80) REVERT: H 100 ASP cc_start: 0.8257 (t0) cc_final: 0.8026 (t0) REVERT: I 39 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6264 (mtmm) REVERT: I 42 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7328 (mp10) REVERT: E 633 LYS cc_start: 0.9017 (mtmm) cc_final: 0.8668 (mtmm) REVERT: G 12 LYS cc_start: 0.8387 (mmmm) cc_final: 0.7758 (ttmm) REVERT: O 36 TYR cc_start: 0.6857 (m-80) cc_final: 0.6406 (m-80) REVERT: O 37 GLN cc_start: 0.5256 (OUTLIER) cc_final: 0.4850 (tm-30) REVERT: K 633 LYS cc_start: 0.8959 (tppt) cc_final: 0.8628 (mppt) REVERT: K 659 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7810 (tm-30) REVERT: J 280 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.6766 (t0) REVERT: J 333 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8377 (tt) REVERT: J 486 TYR cc_start: 0.9071 (m-80) cc_final: 0.8486 (m-10) REVERT: M 24 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8475 (pt) REVERT: M 66 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8412 (t0) REVERT: M 85 GLU cc_start: 0.7677 (tm-30) cc_final: 0.6945 (tm-30) REVERT: M 89 GLN cc_start: 0.8526 (mp10) cc_final: 0.8276 (mp10) REVERT: F 73 ASN cc_start: 0.8208 (t0) cc_final: 0.7882 (t0) REVERT: F 74 LEU cc_start: 0.8757 (tp) cc_final: 0.8455 (tp) outliers start: 66 outliers final: 44 residues processed: 293 average time/residue: 0.1446 time to fit residues: 66.9199 Evaluate side-chains 289 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 9.9990 chunk 232 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 1 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 245 optimal weight: 0.4980 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.096758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.076629 restraints weight = 64964.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.079382 restraints weight = 33375.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.081124 restraints weight = 22707.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082222 restraints weight = 17957.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.082834 restraints weight = 15474.323| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22421 Z= 0.124 Angle : 0.668 12.840 30645 Z= 0.331 Chirality : 0.046 0.602 3770 Planarity : 0.004 0.045 3672 Dihedral : 5.687 63.531 2757 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 2.15 % Allowed : 13.82 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2511 helix: 2.22 (0.25), residues: 439 sheet: 0.08 (0.20), residues: 708 loop : -0.84 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 95B TYR 0.029 0.002 TYR O 96 PHE 0.027 0.002 PHE H 29 TRP 0.033 0.002 TRP A 45 HIS 0.004 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22260) covalent geometry : angle 0.63391 / 0.32 (30201) SS BOND : bond 0.00245 / 0.16 ( 39) SS BOND : angle 1.44376 / 0.90 ( 78) hydrogen bonds : bond 0.03999 / 2.69 ( 836) hydrogen bonds : angle 5.43229 / 3.83 ( 2253) link_ALPHA1-2 : bond 0.00141 / 0.08 ( 5) link_ALPHA1-2 : angle 1.62432 / 0.84 ( 15) link_ALPHA1-3 : bond 0.00586 / 0.32 ( 6) link_ALPHA1-3 : angle 1.48055 / 0.72 ( 18) link_ALPHA1-6 : bond 0.00425 / 0.21 ( 4) link_ALPHA1-6 : angle 1.43287 / 0.74 ( 12) link_BETA1-4 : bond 0.00508 / 0.35 ( 50) link_BETA1-4 : angle 1.40100 / 0.90 ( 150) link_NAG-ASN : bond 0.00491 / 0.36 ( 57) link_NAG-ASN : angle 2.37796 / 1.59 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 0.721 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: symmetry clash REVERT: L 3 GLU cc_start: 0.8543 (tp30) cc_final: 0.8334 (tp30) REVERT: L 18 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.6979 (mmm-85) REVERT: B 519 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 647 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 368 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7078 (t70) REVERT: A 479 TRP cc_start: 0.7883 (m-10) cc_final: 0.7494 (m-90) REVERT: H 13 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8705 (tppt) REVERT: H 64 GLN cc_start: 0.8765 (pm20) cc_final: 0.8366 (pm20) REVERT: H 100 ASP cc_start: 0.8119 (t0) cc_final: 0.7800 (t0) REVERT: I 39 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6947 (mtmm) REVERT: E 633 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8618 (mtmm) REVERT: O 36 TYR cc_start: 0.6711 (m-80) cc_final: 0.6334 (m-80) REVERT: O 37 GLN cc_start: 0.5287 (OUTLIER) cc_final: 0.4907 (tm-30) REVERT: K 629 MET cc_start: 0.7940 (mtm) cc_final: 0.7642 (mtm) REVERT: K 633 LYS cc_start: 0.8922 (tppt) cc_final: 0.8599 (mppt) REVERT: K 659 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7869 (tm-30) REVERT: J 280 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.6866 (t0) REVERT: J 333 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8361 (tt) REVERT: J 475 MET cc_start: 0.8074 (mmt) cc_final: 0.7795 (mmt) REVERT: J 486 TYR cc_start: 0.8944 (m-80) cc_final: 0.8466 (m-10) REVERT: M 24 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8405 (pt) REVERT: M 66 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8428 (t0) REVERT: M 85 GLU cc_start: 0.7658 (tm-30) cc_final: 0.6950 (tm-30) REVERT: M 89 GLN cc_start: 0.8461 (mp10) cc_final: 0.8239 (mp10) REVERT: F 73 ASN cc_start: 0.8123 (t0) cc_final: 0.7824 (t0) REVERT: F 74 LEU cc_start: 0.8822 (tp) cc_final: 0.8448 (tp) outliers start: 48 outliers final: 30 residues processed: 297 average time/residue: 0.1465 time to fit residues: 68.1656 Evaluate side-chains 287 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 166 optimal weight: 0.0670 chunk 222 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 171 optimal weight: 0.0870 chunk 135 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.089120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070492 restraints weight = 62135.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.072587 restraints weight = 36942.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073957 restraints weight = 26786.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074822 restraints weight = 21887.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075327 restraints weight = 19289.948| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22421 Z= 0.121 Angle : 0.648 14.008 30645 Z= 0.322 Chirality : 0.045 0.655 3770 Planarity : 0.004 0.044 3672 Dihedral : 5.452 59.519 2757 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.15 % Allowed : 13.78 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2511 helix: 2.35 (0.25), residues: 439 sheet: 0.25 (0.20), residues: 703 loop : -0.84 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 103 TYR 0.026 0.001 TYR O 96 PHE 0.026 0.001 PHE H 29 TRP 0.034 0.001 TRP A 45 HIS 0.004 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (22260) covalent geometry : angle 0.61665 / 0.32 (30201) SS BOND : bond 0.00285 / 0.19 ( 39) SS BOND : angle 1.17117 / 0.73 ( 78) hydrogen bonds : bond 0.03698 / 2.48 ( 836) hydrogen bonds : angle 5.29367 / 3.72 ( 2253) link_ALPHA1-2 : bond 0.00163 / 0.08 ( 5) link_ALPHA1-2 : angle 1.58495 / 0.83 ( 15) link_ALPHA1-3 : bond 0.00537 / 0.29 ( 6) link_ALPHA1-3 : angle 1.46004 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00432 / 0.22 ( 4) link_ALPHA1-6 : angle 1.41676 / 0.74 ( 12) link_BETA1-4 : bond 0.00517 / 0.35 ( 50) link_BETA1-4 : angle 1.34036 / 0.86 ( 150) link_NAG-ASN : bond 0.00361 / 0.27 ( 57) link_NAG-ASN : angle 2.31896 / 1.57 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.752 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: L 18 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.7208 (mmm-85) REVERT: B 519 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8349 (mp) REVERT: B 629 MET cc_start: 0.7166 (mtp) cc_final: 0.6943 (mtp) REVERT: B 647 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 368 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7105 (t70) REVERT: A 479 TRP cc_start: 0.7764 (m-10) cc_final: 0.7546 (m-90) REVERT: H 13 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8497 (tppt) REVERT: H 64 GLN cc_start: 0.8712 (pm20) cc_final: 0.8453 (pm20) REVERT: H 90 TYR cc_start: 0.6933 (m-80) cc_final: 0.6641 (m-80) REVERT: H 100 ASP cc_start: 0.8008 (t0) cc_final: 0.7713 (t0) REVERT: I 39 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6732 (mtmm) REVERT: E 633 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8544 (mtmm) REVERT: G 83 ARG cc_start: 0.7381 (mtp-110) cc_final: 0.7145 (mtm110) REVERT: O 36 TYR cc_start: 0.6737 (m-80) cc_final: 0.6442 (m-80) REVERT: O 37 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.5258 (tm-30) REVERT: K 629 MET cc_start: 0.7829 (mtm) cc_final: 0.7533 (mtm) REVERT: J 280 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.6707 (t0) REVERT: J 333 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8396 (tt) REVERT: J 475 MET cc_start: 0.8031 (mmt) cc_final: 0.7694 (mmt) REVERT: J 486 TYR cc_start: 0.8878 (m-80) cc_final: 0.8431 (m-10) REVERT: M 24 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8326 (pt) REVERT: M 66 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8335 (t0) REVERT: M 85 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7167 (tm-30) outliers start: 48 outliers final: 33 residues processed: 306 average time/residue: 0.1462 time to fit residues: 70.0263 Evaluate side-chains 293 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 62 PHE Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 98 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 219 optimal weight: 0.0980 chunk 192 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.089062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070458 restraints weight = 62559.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.072538 restraints weight = 37111.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073912 restraints weight = 26945.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074789 restraints weight = 21997.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075367 restraints weight = 19302.912| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22421 Z= 0.131 Angle : 0.664 12.208 30645 Z= 0.330 Chirality : 0.045 0.489 3770 Planarity : 0.004 0.043 3672 Dihedral : 5.324 56.244 2757 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.15 % Allowed : 14.50 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2511 helix: 2.41 (0.25), residues: 441 sheet: 0.32 (0.20), residues: 680 loop : -0.88 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 95B TYR 0.024 0.002 TYR O 96 PHE 0.026 0.001 PHE H 29 TRP 0.034 0.001 TRP A 45 HIS 0.005 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22260) covalent geometry : angle 0.63562 / 0.32 (30201) SS BOND : bond 0.00278 / 0.18 ( 39) SS BOND : angle 1.14012 / 0.70 ( 78) hydrogen bonds : bond 0.03623 / 2.42 ( 836) hydrogen bonds : angle 5.21066 / 3.67 ( 2253) link_ALPHA1-2 : bond 0.00228 / 0.16 ( 5) link_ALPHA1-2 : angle 1.78290 / 0.90 ( 15) link_ALPHA1-3 : bond 0.00540 / 0.30 ( 6) link_ALPHA1-3 : angle 1.46422 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00431 / 0.22 ( 4) link_ALPHA1-6 : angle 1.42605 / 0.74 ( 12) link_BETA1-4 : bond 0.00491 / 0.33 ( 50) link_BETA1-4 : angle 1.33299 / 0.86 ( 150) link_NAG-ASN : bond 0.00360 / 0.27 ( 57) link_NAG-ASN : angle 2.18453 / 1.45 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.777 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: B 519 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 647 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7701 (tm-30) REVERT: A 368 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7137 (t70) REVERT: A 479 TRP cc_start: 0.7830 (m-10) cc_final: 0.7460 (m-90) REVERT: H 13 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8462 (tppt) REVERT: H 55 ASP cc_start: 0.7658 (t0) cc_final: 0.7319 (m-30) REVERT: H 64 GLN cc_start: 0.8727 (pm20) cc_final: 0.8504 (pm20) REVERT: H 90 TYR cc_start: 0.6835 (m-80) cc_final: 0.6573 (m-80) REVERT: H 100 TYR cc_start: 0.7998 (t80) cc_final: 0.7680 (t80) REVERT: H 100 ASP cc_start: 0.8019 (t0) cc_final: 0.7759 (t0) REVERT: I 39 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6829 (mmtm) REVERT: E 633 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8553 (mtmm) REVERT: O 36 TYR cc_start: 0.6720 (m-80) cc_final: 0.6418 (m-80) REVERT: O 37 GLN cc_start: 0.5762 (OUTLIER) cc_final: 0.5374 (tm-30) REVERT: K 629 MET cc_start: 0.7747 (mtm) cc_final: 0.7493 (mtm) REVERT: J 280 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.6740 (t0) REVERT: J 333 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8505 (tt) REVERT: J 486 TYR cc_start: 0.8865 (m-80) cc_final: 0.8358 (m-10) REVERT: M 63 ASP cc_start: 0.8349 (p0) cc_final: 0.8101 (p0) REVERT: M 66 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8339 (t0) REVERT: M 85 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7137 (tm-30) outliers start: 48 outliers final: 36 residues processed: 287 average time/residue: 0.1374 time to fit residues: 62.7492 Evaluate side-chains 289 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.087355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068665 restraints weight = 62527.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070670 restraints weight = 37327.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.071990 restraints weight = 27309.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072847 restraints weight = 22410.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073325 restraints weight = 19709.255| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22421 Z= 0.193 Angle : 0.707 11.425 30645 Z= 0.353 Chirality : 0.046 0.467 3770 Planarity : 0.004 0.079 3672 Dihedral : 5.394 54.104 2757 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.93 % Allowed : 14.95 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2511 helix: 2.30 (0.25), residues: 435 sheet: 0.32 (0.20), residues: 705 loop : -1.02 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG I 103 TYR 0.025 0.002 TYR O 96 PHE 0.025 0.002 PHE H 29 TRP 0.038 0.002 TRP A 45 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (22260) covalent geometry : angle 0.67929 / 0.35 (30201) SS BOND : bond 0.00319 / 0.21 ( 39) SS BOND : angle 1.21072 / 0.74 ( 78) hydrogen bonds : bond 0.03963 / 2.66 ( 836) hydrogen bonds : angle 5.27606 / 3.72 ( 2253) link_ALPHA1-2 : bond 0.00107 / 0.06 ( 5) link_ALPHA1-2 : angle 1.73400 / 0.89 ( 15) link_ALPHA1-3 : bond 0.00471 / 0.25 ( 6) link_ALPHA1-3 : angle 1.50078 / 0.72 ( 18) link_ALPHA1-6 : bond 0.00396 / 0.20 ( 4) link_ALPHA1-6 : angle 1.49584 / 0.77 ( 12) link_BETA1-4 : bond 0.00465 / 0.31 ( 50) link_BETA1-4 : angle 1.41500 / 0.91 ( 150) link_NAG-ASN : bond 0.00411 / 0.30 ( 57) link_NAG-ASN : angle 2.24842 / 1.50 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.745 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: B 519 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8327 (mp) REVERT: B 647 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7725 (tm-30) REVERT: A 368 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7160 (t70) REVERT: A 479 TRP cc_start: 0.7883 (m-10) cc_final: 0.7511 (m-90) REVERT: H 13 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8463 (tppt) REVERT: H 55 ASP cc_start: 0.7734 (t0) cc_final: 0.7431 (m-30) REVERT: H 100 ASP cc_start: 0.8047 (t0) cc_final: 0.7804 (t0) REVERT: E 633 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8581 (mtmm) REVERT: O 36 TYR cc_start: 0.6834 (m-80) cc_final: 0.6461 (m-80) REVERT: O 37 GLN cc_start: 0.5970 (OUTLIER) cc_final: 0.5576 (tm-30) REVERT: J 280 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.6805 (t0) REVERT: J 333 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8433 (tt) REVERT: J 475 MET cc_start: 0.8045 (mmt) cc_final: 0.7768 (mmt) REVERT: J 486 TYR cc_start: 0.8901 (m-80) cc_final: 0.8436 (m-10) REVERT: M 63 ASP cc_start: 0.8362 (p0) cc_final: 0.8123 (p0) REVERT: M 66 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8243 (t0) REVERT: M 85 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6853 (tm-30) REVERT: F 74 LEU cc_start: 0.8495 (tp) cc_final: 0.8262 (tp) outliers start: 43 outliers final: 35 residues processed: 274 average time/residue: 0.1410 time to fit residues: 61.7295 Evaluate side-chains 277 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 87 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 chunk 105 optimal weight: 0.2980 chunk 230 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 HIS F 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.089337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070849 restraints weight = 62244.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.072928 restraints weight = 36737.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074282 restraints weight = 26605.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075083 restraints weight = 21739.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075701 restraints weight = 19197.184| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22421 Z= 0.124 Angle : 0.681 10.502 30645 Z= 0.339 Chirality : 0.045 0.424 3770 Planarity : 0.004 0.076 3672 Dihedral : 5.260 58.084 2757 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 15.75 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2511 helix: 2.43 (0.25), residues: 441 sheet: 0.36 (0.19), residues: 723 loop : -0.99 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 103 TYR 0.023 0.001 TYR O 96 PHE 0.026 0.001 PHE H 29 TRP 0.031 0.001 TRP A 45 HIS 0.005 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (22260) covalent geometry : angle 0.65791 / 0.33 (30201) SS BOND : bond 0.00263 / 0.17 ( 39) SS BOND : angle 1.05408 / 0.66 ( 78) hydrogen bonds : bond 0.03530 / 2.34 ( 836) hydrogen bonds : angle 5.15733 / 3.64 ( 2253) link_ALPHA1-2 : bond 0.00116 / 0.06 ( 5) link_ALPHA1-2 : angle 1.67478 / 0.86 ( 15) link_ALPHA1-3 : bond 0.00548 / 0.30 ( 6) link_ALPHA1-3 : angle 1.45772 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00448 / 0.22 ( 4) link_ALPHA1-6 : angle 1.41040 / 0.73 ( 12) link_BETA1-4 : bond 0.00497 / 0.33 ( 50) link_BETA1-4 : angle 1.28428 / 0.82 ( 150) link_NAG-ASN : bond 0.00336 / 0.24 ( 57) link_NAG-ASN : angle 2.05416 / 1.36 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.77 seconds wall clock time: 60 minutes 26.36 seconds (3626.36 seconds total)