Starting phenix.real_space_refine on Mon Jul 6 07:25:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ll2_23412/07_2026/7ll2_23412.map" } resolution = 3.73 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= 0.007 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10026 atoms to isotropic. 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 141 5.16 5 C 15933 2.51 5 N 4218 2.21 5 O 5220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25512 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1082 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 220, 1658 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1684 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "C" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1082 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 1658 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 220, 1658 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain breaks: 1 Chain: "J" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1684 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "E" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain breaks: 3 Chain: "F" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1082 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 1658 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 220, 1658 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain breaks: 1 Chain: "M" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1684 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 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: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "e" 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: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "g" 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 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: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 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: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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: 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: 5.80, per 1000 atoms: 0.23 Number of scatterers: 25512 At special positions: 0 Unit cell: (190.08, 173.88, 131.76, 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 141 16.00 O 5220 8.00 N 4218 7.00 C 15933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 202 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 7 " " MAN T 4 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " " BMA f 3 " - " MAN f 4 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 7 " " MAN p 4 " - " MAN p 5 " " BMA q 3 " - " MAN q 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 6 " " BMA U 3 " - " MAN U 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " " BMA f 3 " - " MAN f 5 " " BMA o 3 " - " MAN o 5 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 6 " " BMA q 3 " - " MAN q 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 601 " - " ASN A 295 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 355 " " NAG C 601 " - " ASN C 295 " " NAG C 602 " - " ASN C 301 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 355 " " NAG E 601 " - " ASN E 295 " " NAG E 602 " - " ASN E 301 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 355 " " NAG G 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 133 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 133 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 160 " " NAG b 1 " - " ASN C 197 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 262 " " NAG e 1 " - " ASN C 276 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN C 386 " " NAG h 1 " - " ASN C 392 " " NAG i 1 " - " ASN E 88 " " NAG j 1 " - " ASN E 133 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 234 " " NAG o 1 " - " ASN E 262 " " NAG p 1 " - " ASN E 276 " " NAG q 1 " - " ASN E 363 " " NAG r 1 " - " ASN E 386 " " NAG s 1 " - " ASN E 392 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 956.0 milliseconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 57 sheets defined 19.8% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.522A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.061A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 547 removed outlier: 4.417A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 554 removed outlier: 3.889A pdb=" N GLN B 552 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 554 " --> pdb=" O GLN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 removed outlier: 4.121A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.745A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.849A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 4.098A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.988A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 182 through 189 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.502A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.125A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 547 removed outlier: 4.230A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 568 through 596 removed outlier: 3.888A pdb=" N GLY D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.782A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.805A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 662 removed outlier: 3.857A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 191 through 197 Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.086A pdb=" N VAL J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 127 Processing helix chain 'J' and resid 182 through 189 Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.600A pdb=" N GLU E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.533A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.053A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.760A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 547 removed outlier: 4.145A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY F 547 " --> pdb=" O ASN F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 554 removed outlier: 3.801A pdb=" N GLN F 552 " --> pdb=" O VAL F 549 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 553 " --> pdb=" O GLN F 550 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN F 554 " --> pdb=" O GLN F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 596 removed outlier: 4.010A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.703A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.611A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.783A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.901A pdb=" N LEU K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY K 196 " --> pdb=" O SER K 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 191 through 196' Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.059A pdb=" N VAL M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 182 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.518A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.318A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.785A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.743A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 297 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.964A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.743A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 444 through 456 current: chain 'A' and resid 413 through 421 removed outlier: 3.701A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.760A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.502A pdb=" N GLN H 3 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.983A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.262A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.262A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.350A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.350A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.743A pdb=" N SER L 114 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AC3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.613A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.367A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.650A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.917A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 302 through 312 removed outlier: 6.786A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 3 through 8 removed outlier: 3.611A pdb=" N GLN I 3 " --> pdb=" O TYR I 25 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 11 through 12 removed outlier: 5.009A pdb=" N TYR I 33 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER I 40 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU I 45 " --> pdb=" O SER I 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 126 through 130 removed outlier: 6.138A pdb=" N TYR I 182 " --> pdb=" O ASP I 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 126 through 130 removed outlier: 6.138A pdb=" N TYR I 182 " --> pdb=" O ASP I 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 157 through 160 Processing sheet with id=AD7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 14 removed outlier: 6.389A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LYS J 107 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 14 removed outlier: 6.389A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LYS J 107 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 114 through 118 removed outlier: 5.272A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'E' and resid 494 through 499 Processing sheet with id=AE4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.683A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AE6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AE7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AE8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.351A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.658A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.944A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.944A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.777A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 3 through 8 removed outlier: 3.761A pdb=" N GLN K 3 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.963A pdb=" N TYR K 33 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP K 36 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER K 40 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU K 45 " --> pdb=" O SER K 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 126 through 130 removed outlier: 6.209A pdb=" N TYR K 182 " --> pdb=" O ASP K 150 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 126 through 130 removed outlier: 6.209A pdb=" N TYR K 182 " --> pdb=" O ASP K 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 156 through 160 Processing sheet with id=AF8, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.379A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.379A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.597A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 153 through 154 990 hydrogen bonds defined for protein. 2595 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: 5.87 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7243 1.34 - 1.46: 4378 1.46 - 1.58: 14221 1.58 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 26025 Sorted by residual: bond pdb=" C4 NAG s 2 " pdb=" O4 NAG s 2 " ideal model delta sigma weight residual 1.409 1.494 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C4 NAG Q 2 " pdb=" O4 NAG Q 2 " ideal model delta sigma weight residual 1.409 1.494 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4 NAG m 2 " pdb=" O4 NAG m 2 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C4 NAG b 2 " pdb=" O4 NAG b 2 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C4 NAG h 2 " pdb=" O4 NAG h 2 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 26020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 23537 1.69 - 3.39: 9617 3.39 - 5.08: 1946 5.08 - 6.77: 219 6.77 - 8.47: 21 Bond angle restraints: 35340 Sorted by residual: angle pdb=" CA ALA M 93 " pdb=" C ALA M 93 " pdb=" O ALA M 93 " ideal model delta sigma weight residual 117.94 121.35 -3.41 5.80e-01 2.97e+00 3.46e+01 angle pdb=" N ILE E 184 " pdb=" CA ILE E 184 " pdb=" C ILE E 184 " ideal model delta sigma weight residual 110.42 104.85 5.57 9.60e-01 1.09e+00 3.37e+01 angle pdb=" CA VAL C 182 " pdb=" C VAL C 182 " pdb=" O VAL C 182 " ideal model delta sigma weight residual 121.64 116.49 5.15 9.80e-01 1.04e+00 2.77e+01 angle pdb=" CA VAL E 182 " pdb=" C VAL E 182 " pdb=" O VAL E 182 " ideal model delta sigma weight residual 121.63 116.45 5.18 9.90e-01 1.02e+00 2.74e+01 angle pdb=" C LYS C 252 " pdb=" CA LYS C 252 " pdb=" CB LYS C 252 " ideal model delta sigma weight residual 109.85 115.19 -5.34 1.14e+00 7.69e-01 2.19e+01 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13495 17.86 - 35.72: 902 35.72 - 53.58: 176 53.58 - 71.44: 65 71.44 - 89.30: 32 Dihedral angle restraints: 14670 sinusoidal: 5829 harmonic: 8841 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 160.92 -67.92 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.22 -65.22 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 156.69 -63.69 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 14667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2444 0.089 - 0.178: 1568 0.178 - 0.266: 306 0.266 - 0.355: 43 0.355 - 0.444: 16 Chirality restraints: 4377 Sorted by residual: chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4374 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " -0.264 2.00e-02 2.50e+03 1.35e-01 4.57e+02 pdb=" CG TRP A 35 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " 0.112 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " 0.091 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " 0.175 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " -0.168 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " 0.074 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 35 " 0.255 2.00e-02 2.50e+03 1.30e-01 4.25e+02 pdb=" CG TRP E 35 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP E 35 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP E 35 " -0.113 2.00e-02 2.50e+03 pdb=" NE1 TRP E 35 " -0.086 2.00e-02 2.50e+03 pdb=" CE2 TRP E 35 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 35 " -0.172 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 35 " 0.155 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 35 " -0.064 2.00e-02 2.50e+03 pdb=" CH2 TRP E 35 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 35 " 0.223 2.00e-02 2.50e+03 1.17e-01 3.40e+02 pdb=" CG TRP C 35 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 35 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 35 " -0.103 2.00e-02 2.50e+03 pdb=" NE1 TRP C 35 " -0.078 2.00e-02 2.50e+03 pdb=" CE2 TRP C 35 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP C 35 " -0.170 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 35 " 0.120 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 35 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP C 35 " 0.145 2.00e-02 2.50e+03 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 13646 3.01 - 3.48: 24701 3.48 - 3.95: 41392 3.95 - 4.43: 45583 4.43 - 4.90: 75836 Nonbonded interactions: 201158 Sorted by model distance: nonbonded pdb=" O ILE C 184 " pdb=" C ASN C 185 " model vdw 2.531 3.270 nonbonded pdb=" O5 BMA p 3 " pdb=" O6 BMA p 3 " model vdw 2.549 2.432 nonbonded pdb=" OD1 ASP I 72 " pdb=" OG SER I 74 " model vdw 2.549 3.040 nonbonded pdb=" O5 BMA T 3 " pdb=" O6 BMA T 3 " model vdw 2.552 2.432 nonbonded pdb=" N VAL E 182 " pdb=" O VAL E 182 " model vdw 2.553 2.496 ... (remaining 201153 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'Y' selection = chain 'j' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'd' selection = chain 'f' selection = chain 'o' selection = chain 'q' } ncs_group { reference = chain 'T' selection = chain 'e' selection = chain 'p' } 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=0.50 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.600 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.015 0.085 26202 Z= 0.821 Angle : 1.910 19.615 35826 Z= 1.170 Chirality : 0.109 0.444 4377 Planarity : 0.016 0.159 4305 Dihedral : 13.705 89.298 8829 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.92 % Favored : 93.68 % Rotamer: Outliers : 0.63 % Allowed : 4.14 % Favored : 95.22 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 10.87 % 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: -0.81 (0.15), residues: 3006 helix: -1.34 (0.21), residues: 465 sheet: 0.27 (0.18), residues: 840 loop : -0.66 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 211 TYR 0.159 0.024 TYR A 39 PHE 0.092 0.013 PHE E 288 TRP 0.264 0.028 TRP A 35 HIS 0.020 0.004 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.01456 / 0.82 (26025) covalent geometry : angle 1.80211 / 1.16 (35340) SS BOND : bond 0.00591 / 0.37 ( 45) SS BOND : angle 1.75074 / 1.21 ( 90) hydrogen bonds : bond 0.16223 / 10.72 ( 921) hydrogen bonds : angle 8.24160 / 5.69 ( 2595) link_ALPHA1-3 : bond 0.02539 / 1.70 ( 12) link_ALPHA1-3 : angle 5.92636 / 3.82 ( 36) link_ALPHA1-6 : bond 0.01988 / 1.32 ( 12) link_ALPHA1-6 : angle 4.69306 / 3.04 ( 36) link_BETA1-4 : bond 0.03147 / 2.10 ( 63) link_BETA1-4 : angle 7.58895 / 5.31 ( 189) link_NAG-ASN : bond 0.01005 / 0.65 ( 45) link_NAG-ASN : angle 4.45285 / 3.03 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 444 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8506 (ptp-170) REVERT: D 530 MET cc_start: 0.8565 (mtp) cc_final: 0.8348 (mtp) outliers start: 17 outliers final: 5 residues processed: 86 average time/residue: 0.2015 time to fit residues: 27.4993 Evaluate side-chains 59 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain M residue 206 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 339 ASN B 575 GLN B 653 GLN C 339 ASN D 554 ASN D 653 GLN E 99 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.035177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.027574 restraints weight = 260027.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.028259 restraints weight = 141821.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.028688 restraints weight = 100640.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.028924 restraints weight = 82310.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.029096 restraints weight = 73602.302| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26202 Z= 0.177 Angle : 0.908 18.452 35826 Z= 0.418 Chirality : 0.049 0.377 4377 Planarity : 0.005 0.049 4305 Dihedral : 6.780 50.099 3269 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.75 % Allowed : 6.16 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.03 (0.16), residues: 3006 helix: 0.34 (0.25), residues: 444 sheet: 0.21 (0.17), residues: 1002 loop : -0.17 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 142 TYR 0.019 0.002 TYR D 638 PHE 0.018 0.002 PHE H 78 TRP 0.024 0.002 TRP A 69 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (26025) covalent geometry : angle 0.78578 / 0.39 (35340) SS BOND : bond 0.00296 / 0.18 ( 45) SS BOND : angle 0.89234 / 0.60 ( 90) hydrogen bonds : bond 0.05394 / 3.50 ( 921) hydrogen bonds : angle 6.19879 / 4.29 ( 2595) link_ALPHA1-3 : bond 0.00503 / 0.34 ( 12) link_ALPHA1-3 : angle 3.06930 / 1.88 ( 36) link_ALPHA1-6 : bond 0.00620 / 0.45 ( 12) link_ALPHA1-6 : angle 2.11162 / 1.30 ( 36) link_BETA1-4 : bond 0.01896 / 1.36 ( 63) link_BETA1-4 : angle 5.59279 / 3.93 ( 189) link_NAG-ASN : bond 0.00502 / 0.33 ( 45) link_NAG-ASN : angle 3.00581 / 2.01 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.9225 (ptm) cc_final: 0.8966 (ptp) REVERT: A 444 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8652 (ptp-170) outliers start: 20 outliers final: 10 residues processed: 72 average time/residue: 0.1662 time to fit residues: 20.8366 Evaluate side-chains 63 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 192 TYR Chi-restraints excluded: chain M residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN L 27 GLN L 79 GLN C 82 GLN C 99 ASN J 27 GLN J 79 GLN E 170 GLN F 640 GLN M 3 GLN M 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.034537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.027126 restraints weight = 255179.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.027784 restraints weight = 141496.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.028192 restraints weight = 101080.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.028442 restraints weight = 83039.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.028576 restraints weight = 73865.086| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26202 Z= 0.272 Angle : 0.906 18.635 35826 Z= 0.414 Chirality : 0.050 0.436 4377 Planarity : 0.005 0.050 4305 Dihedral : 6.284 47.288 3263 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.19 % Allowed : 8.88 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.30 (0.16), residues: 3006 helix: 0.41 (0.25), residues: 444 sheet: 0.06 (0.17), residues: 996 loop : -0.47 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 142 TYR 0.024 0.002 TYR J 49 PHE 0.028 0.002 PHE I 78 TRP 0.019 0.002 TRP A 35 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.27 (26025) covalent geometry : angle 0.80076 / 0.39 (35340) SS BOND : bond 0.00289 / 0.18 ( 45) SS BOND : angle 0.78752 / 0.51 ( 90) hydrogen bonds : bond 0.04877 / 3.19 ( 921) hydrogen bonds : angle 5.88940 / 4.08 ( 2595) link_ALPHA1-3 : bond 0.00576 / 0.37 ( 12) link_ALPHA1-3 : angle 2.60330 / 1.60 ( 36) link_ALPHA1-6 : bond 0.00643 / 0.48 ( 12) link_ALPHA1-6 : angle 2.18395 / 1.35 ( 36) link_BETA1-4 : bond 0.01855 / 1.38 ( 63) link_BETA1-4 : angle 5.25828 / 3.70 ( 189) link_NAG-ASN : bond 0.00513 / 0.29 ( 45) link_NAG-ASN : angle 2.75593 / 1.90 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 1.158 Fit side-chains REVERT: A 444 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8686 (ptp-170) outliers start: 32 outliers final: 16 residues processed: 78 average time/residue: 0.1623 time to fit residues: 22.2178 Evaluate side-chains 68 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 43 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 27 GLN M 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.034987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.027625 restraints weight = 250830.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.028294 restraints weight = 138083.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.028714 restraints weight = 98071.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.028943 restraints weight = 80182.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.029112 restraints weight = 71694.070| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26202 Z= 0.142 Angle : 0.779 18.116 35826 Z= 0.348 Chirality : 0.045 0.372 4377 Planarity : 0.004 0.047 4305 Dihedral : 5.753 45.557 3262 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.31 % Allowed : 10.19 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.22 (0.16), residues: 3006 helix: 0.62 (0.25), residues: 462 sheet: 0.05 (0.17), residues: 1011 loop : -0.44 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 304 TYR 0.013 0.001 TYR D 638 PHE 0.016 0.001 PHE H 78 TRP 0.015 0.001 TRP K 34 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (26025) covalent geometry : angle 0.66764 / 0.32 (35340) SS BOND : bond 0.00166 / 0.10 ( 45) SS BOND : angle 0.73747 / 0.49 ( 90) hydrogen bonds : bond 0.03997 / 2.60 ( 921) hydrogen bonds : angle 5.55628 / 3.84 ( 2595) link_ALPHA1-3 : bond 0.00457 / 0.29 ( 12) link_ALPHA1-3 : angle 2.25603 / 1.37 ( 36) link_ALPHA1-6 : bond 0.00721 / 0.53 ( 12) link_ALPHA1-6 : angle 1.89640 / 1.16 ( 36) link_BETA1-4 : bond 0.01761 / 1.29 ( 63) link_BETA1-4 : angle 5.01146 / 3.53 ( 189) link_NAG-ASN : bond 0.00294 / 0.17 ( 45) link_NAG-ASN : angle 2.54786 / 1.76 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 1.072 Fit side-chains REVERT: A 164 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: C 164 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: E 475 MET cc_start: 0.8597 (ptp) cc_final: 0.8260 (ptp) outliers start: 35 outliers final: 19 residues processed: 84 average time/residue: 0.1555 time to fit residues: 23.1450 Evaluate side-chains 70 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 192 TYR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 256 optimal weight: 10.0000 chunk 284 optimal weight: 0.0870 chunk 92 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 210 ASN M 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.034859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027511 restraints weight = 250559.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.028173 restraints weight = 138661.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.028587 restraints weight = 98849.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.028839 restraints weight = 81052.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.028984 restraints weight = 72047.707| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26202 Z= 0.163 Angle : 0.768 18.091 35826 Z= 0.342 Chirality : 0.045 0.372 4377 Planarity : 0.004 0.045 4305 Dihedral : 5.461 43.186 3258 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.49 % Allowed : 10.79 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.22 (0.16), residues: 3006 helix: 0.80 (0.25), residues: 465 sheet: 0.04 (0.16), residues: 1011 loop : -0.48 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 304 TYR 0.013 0.001 TYR M 49 PHE 0.019 0.002 PHE K 78 TRP 0.037 0.002 TRP F 571 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (26025) covalent geometry : angle 0.66002 / 0.32 (35340) SS BOND : bond 0.00217 / 0.15 ( 45) SS BOND : angle 0.73263 / 0.50 ( 90) hydrogen bonds : bond 0.03811 / 2.49 ( 921) hydrogen bonds : angle 5.39939 / 3.73 ( 2595) link_ALPHA1-3 : bond 0.00483 / 0.31 ( 12) link_ALPHA1-3 : angle 2.20125 / 1.34 ( 36) link_ALPHA1-6 : bond 0.00671 / 0.49 ( 12) link_ALPHA1-6 : angle 1.89546 / 1.16 ( 36) link_BETA1-4 : bond 0.01734 / 1.28 ( 63) link_BETA1-4 : angle 4.91925 / 3.47 ( 189) link_NAG-ASN : bond 0.00299 / 0.17 ( 45) link_NAG-ASN : angle 2.44178 / 1.70 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 50 time to evaluate : 0.974 Fit side-chains REVERT: A 164 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: C 164 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8836 (pm20) REVERT: D 535 MET cc_start: 0.8622 (mmm) cc_final: 0.8408 (mmp) REVERT: E 164 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: E 475 MET cc_start: 0.8638 (ptp) cc_final: 0.8281 (ptp) outliers start: 40 outliers final: 25 residues processed: 87 average time/residue: 0.1563 time to fit residues: 23.7933 Evaluate side-chains 76 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 192 TYR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 125 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 270 optimal weight: 40.0000 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 238 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.034736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.027217 restraints weight = 255681.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.027904 restraints weight = 136717.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.028332 restraints weight = 96049.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.028591 restraints weight = 78197.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.028730 restraints weight = 69358.442| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26202 Z= 0.145 Angle : 0.734 18.005 35826 Z= 0.325 Chirality : 0.044 0.370 4377 Planarity : 0.004 0.045 4305 Dihedral : 5.142 41.276 3257 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.57 % Allowed : 10.82 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.20 (0.16), residues: 3006 helix: 1.05 (0.25), residues: 465 sheet: 0.00 (0.16), residues: 1017 loop : -0.53 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.012 0.001 TYR M 49 PHE 0.014 0.001 PHE I 78 TRP 0.026 0.001 TRP F 571 HIS 0.005 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (26025) covalent geometry : angle 0.62882 / 0.30 (35340) SS BOND : bond 0.00181 / 0.11 ( 45) SS BOND : angle 0.65785 / 0.44 ( 90) hydrogen bonds : bond 0.03511 / 2.28 ( 921) hydrogen bonds : angle 5.17260 / 3.57 ( 2595) link_ALPHA1-3 : bond 0.00478 / 0.31 ( 12) link_ALPHA1-3 : angle 2.07177 / 1.26 ( 36) link_ALPHA1-6 : bond 0.00683 / 0.50 ( 12) link_ALPHA1-6 : angle 1.79269 / 1.10 ( 36) link_BETA1-4 : bond 0.01704 / 1.26 ( 63) link_BETA1-4 : angle 4.75692 / 3.36 ( 189) link_NAG-ASN : bond 0.00256 / 0.15 ( 45) link_NAG-ASN : angle 2.32335 / 1.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 51 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8782 (pm20) REVERT: D 535 MET cc_start: 0.8619 (mmm) cc_final: 0.8414 (mmp) REVERT: J 90 HIS cc_start: 0.9199 (OUTLIER) cc_final: 0.8834 (p-80) REVERT: E 164 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8693 (pm20) REVERT: M 4 MET cc_start: 0.7672 (mmp) cc_final: 0.7468 (mmp) REVERT: M 90 HIS cc_start: 0.9125 (OUTLIER) cc_final: 0.8771 (p-80) outliers start: 42 outliers final: 29 residues processed: 90 average time/residue: 0.1482 time to fit residues: 24.0067 Evaluate side-chains 84 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 90 HIS Chi-restraints excluded: chain J residue 192 TYR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 288 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.034283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.026814 restraints weight = 256307.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.027470 restraints weight = 141096.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.027879 restraints weight = 100574.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.028130 restraints weight = 82430.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.028257 restraints weight = 73350.818| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26202 Z= 0.213 Angle : 0.774 18.065 35826 Z= 0.346 Chirality : 0.046 0.370 4377 Planarity : 0.004 0.046 4305 Dihedral : 5.265 41.162 3257 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.75 % Allowed : 11.20 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.32 (0.16), residues: 3006 helix: 0.97 (0.25), residues: 465 sheet: -0.02 (0.17), residues: 993 loop : -0.64 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 151 TYR 0.019 0.002 TYR M 49 PHE 0.019 0.002 PHE I 78 TRP 0.020 0.002 TRP F 571 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (26025) covalent geometry : angle 0.67566 / 0.32 (35340) SS BOND : bond 0.00207 / 0.12 ( 45) SS BOND : angle 0.66365 / 0.44 ( 90) hydrogen bonds : bond 0.03818 / 2.48 ( 921) hydrogen bonds : angle 5.27204 / 3.65 ( 2595) link_ALPHA1-3 : bond 0.00508 / 0.32 ( 12) link_ALPHA1-3 : angle 2.08249 / 1.27 ( 36) link_ALPHA1-6 : bond 0.00604 / 0.45 ( 12) link_ALPHA1-6 : angle 1.87319 / 1.15 ( 36) link_BETA1-4 : bond 0.01682 / 1.25 ( 63) link_BETA1-4 : angle 4.73645 / 3.34 ( 189) link_NAG-ASN : bond 0.00401 / 0.23 ( 45) link_NAG-ASN : angle 2.37927 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 51 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: L 132 VAL cc_start: 0.6808 (OUTLIER) cc_final: 0.6442 (m) REVERT: C 164 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8776 (pm20) REVERT: C 475 MET cc_start: 0.8516 (ptt) cc_final: 0.8304 (ptt) REVERT: E 164 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: E 475 MET cc_start: 0.8767 (ptp) cc_final: 0.8554 (ptp) REVERT: M 4 MET cc_start: 0.7804 (mmp) cc_final: 0.7526 (mmp) REVERT: M 90 HIS cc_start: 0.9146 (OUTLIER) cc_final: 0.8789 (p-80) outliers start: 47 outliers final: 32 residues processed: 95 average time/residue: 0.1490 time to fit residues: 25.5961 Evaluate side-chains 87 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 51 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 192 TYR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 97 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.034363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026913 restraints weight = 257169.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.027566 restraints weight = 141335.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.027977 restraints weight = 100698.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.028226 restraints weight = 82568.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.028379 restraints weight = 73515.567| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26202 Z= 0.178 Angle : 0.747 18.038 35826 Z= 0.332 Chirality : 0.045 0.368 4377 Planarity : 0.004 0.045 4305 Dihedral : 5.166 41.516 3257 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.79 % Allowed : 11.46 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.31 (0.16), residues: 3006 helix: 1.05 (0.25), residues: 465 sheet: -0.05 (0.17), residues: 993 loop : -0.64 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 151 TYR 0.015 0.001 TYR M 49 PHE 0.017 0.001 PHE H 78 TRP 0.017 0.001 TRP F 571 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (26025) covalent geometry : angle 0.64817 / 0.31 (35340) SS BOND : bond 0.00170 / 0.10 ( 45) SS BOND : angle 0.65439 / 0.44 ( 90) hydrogen bonds : bond 0.03635 / 2.37 ( 921) hydrogen bonds : angle 5.18431 / 3.58 ( 2595) link_ALPHA1-3 : bond 0.00465 / 0.30 ( 12) link_ALPHA1-3 : angle 2.01451 / 1.22 ( 36) link_ALPHA1-6 : bond 0.00629 / 0.46 ( 12) link_ALPHA1-6 : angle 1.79903 / 1.10 ( 36) link_BETA1-4 : bond 0.01688 / 1.26 ( 63) link_BETA1-4 : angle 4.66972 / 3.29 ( 189) link_NAG-ASN : bond 0.00313 / 0.18 ( 45) link_NAG-ASN : angle 2.35154 / 1.64 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 53 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: L 132 VAL cc_start: 0.6792 (OUTLIER) cc_final: 0.6432 (m) REVERT: C 164 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8738 (pm20) REVERT: I 92 CYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6573 (p) REVERT: J 90 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8956 (p-80) REVERT: E 164 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: E 475 MET cc_start: 0.8757 (ptp) cc_final: 0.8548 (ptp) REVERT: M 4 MET cc_start: 0.7850 (mmp) cc_final: 0.7540 (mmp) REVERT: M 90 HIS cc_start: 0.9140 (OUTLIER) cc_final: 0.8802 (p-80) outliers start: 48 outliers final: 34 residues processed: 99 average time/residue: 0.1556 time to fit residues: 27.2718 Evaluate side-chains 91 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 51 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 90 HIS Chi-restraints excluded: chain J residue 192 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 276 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 197 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN ** J 90 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 = 0.3251 r_free = 0.3251 target = 0.034544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.027041 restraints weight = 259866.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.027706 restraints weight = 142930.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.028121 restraints weight = 101621.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.028373 restraints weight = 83246.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.028509 restraints weight = 74099.740| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26202 Z= 0.152 Angle : 0.733 18.046 35826 Z= 0.324 Chirality : 0.044 0.369 4377 Planarity : 0.004 0.047 4305 Dihedral : 4.983 21.498 3255 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.61 % Allowed : 11.53 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -0.27 (0.16), residues: 3006 helix: 1.16 (0.25), residues: 465 sheet: -0.07 (0.16), residues: 999 loop : -0.60 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.013 0.001 TYR M 49 PHE 0.015 0.001 PHE H 78 TRP 0.020 0.001 TRP F 571 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (26025) covalent geometry : angle 0.63568 / 0.30 (35340) SS BOND : bond 0.00154 / 0.09 ( 45) SS BOND : angle 0.66053 / 0.44 ( 90) hydrogen bonds : bond 0.03467 / 2.26 ( 921) hydrogen bonds : angle 5.08511 / 3.51 ( 2595) link_ALPHA1-3 : bond 0.00465 / 0.30 ( 12) link_ALPHA1-3 : angle 1.99945 / 1.22 ( 36) link_ALPHA1-6 : bond 0.00645 / 0.47 ( 12) link_ALPHA1-6 : angle 1.72136 / 1.05 ( 36) link_BETA1-4 : bond 0.01675 / 1.24 ( 63) link_BETA1-4 : angle 4.59882 / 3.24 ( 189) link_NAG-ASN : bond 0.00265 / 0.15 ( 45) link_NAG-ASN : angle 2.26801 / 1.58 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 52 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 132 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6415 (m) REVERT: J 90 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8907 (p-80) REVERT: M 4 MET cc_start: 0.7933 (mmp) cc_final: 0.7527 (mmp) REVERT: M 90 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.8785 (p-80) outliers start: 43 outliers final: 36 residues processed: 93 average time/residue: 0.1447 time to fit residues: 24.1725 Evaluate side-chains 91 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 52 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 90 HIS Chi-restraints excluded: chain J residue 192 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 183 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 HIS ** 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 = 0.3252 r_free = 0.3252 target = 0.034570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.027080 restraints weight = 259662.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.027744 restraints weight = 142929.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.028154 restraints weight = 101769.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.028408 restraints weight = 83418.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.028544 restraints weight = 74185.468| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26202 Z= 0.149 Angle : 0.724 17.974 35826 Z= 0.320 Chirality : 0.044 0.367 4377 Planarity : 0.004 0.045 4305 Dihedral : 4.899 21.005 3255 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.64 % Allowed : 11.53 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: 3006 helix: 1.22 (0.25), residues: 465 sheet: -0.03 (0.16), residues: 993 loop : -0.62 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 304 TYR 0.013 0.001 TYR M 49 PHE 0.015 0.001 PHE H 78 TRP 0.024 0.001 TRP F 571 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (26025) covalent geometry : angle 0.62777 / 0.30 (35340) SS BOND : bond 0.00147 / 0.09 ( 45) SS BOND : angle 0.66514 / 0.45 ( 90) hydrogen bonds : bond 0.03393 / 2.21 ( 921) hydrogen bonds : angle 5.01276 / 3.46 ( 2595) link_ALPHA1-3 : bond 0.00465 / 0.30 ( 12) link_ALPHA1-3 : angle 1.98368 / 1.21 ( 36) link_ALPHA1-6 : bond 0.00636 / 0.46 ( 12) link_ALPHA1-6 : angle 1.68181 / 1.03 ( 36) link_BETA1-4 : bond 0.01669 / 1.24 ( 63) link_BETA1-4 : angle 4.55007 / 3.21 ( 189) link_NAG-ASN : bond 0.00264 / 0.15 ( 45) link_NAG-ASN : angle 2.23538 / 1.56 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 52 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 132 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.6398 (m) REVERT: I 92 CYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6596 (p) REVERT: J 90 HIS cc_start: 0.9165 (OUTLIER) cc_final: 0.8890 (p-80) REVERT: M 4 MET cc_start: 0.7947 (mmp) cc_final: 0.7605 (mmp) REVERT: M 90 HIS cc_start: 0.9116 (OUTLIER) cc_final: 0.8787 (p-80) outliers start: 44 outliers final: 37 residues processed: 95 average time/residue: 0.1435 time to fit residues: 24.6238 Evaluate side-chains 93 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 52 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 90 HIS Chi-restraints excluded: chain J residue 192 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 137 optimal weight: 0.0670 chunk 206 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 HIS ** 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 = 0.3263 r_free = 0.3263 target = 0.034782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.027325 restraints weight = 257484.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.027996 restraints weight = 141114.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.028412 restraints weight = 100069.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.028649 restraints weight = 81833.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.028814 restraints weight = 73149.045| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26202 Z= 0.121 Angle : 0.701 17.919 35826 Z= 0.308 Chirality : 0.044 0.367 4377 Planarity : 0.004 0.045 4305 Dihedral : 4.710 19.824 3255 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.42 % Allowed : 11.68 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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 (0.16), residues: 3006 helix: 1.40 (0.26), residues: 465 sheet: 0.00 (0.17), residues: 987 loop : -0.48 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 66C TYR 0.010 0.001 TYR D 638 PHE 0.013 0.001 PHE K 78 TRP 0.023 0.001 TRP F 571 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (26025) covalent geometry : angle 0.60520 / 0.28 (35340) SS BOND : bond 0.00128 / 0.08 ( 45) SS BOND : angle 0.68124 / 0.47 ( 90) hydrogen bonds : bond 0.03150 / 2.05 ( 921) hydrogen bonds : angle 4.87402 / 3.36 ( 2595) link_ALPHA1-3 : bond 0.00469 / 0.31 ( 12) link_ALPHA1-3 : angle 1.96369 / 1.20 ( 36) link_ALPHA1-6 : bond 0.00672 / 0.48 ( 12) link_ALPHA1-6 : angle 1.59736 / 0.97 ( 36) link_BETA1-4 : bond 0.01668 / 1.24 ( 63) link_BETA1-4 : angle 4.47793 / 3.16 ( 189) link_NAG-ASN : bond 0.00211 / 0.13 ( 45) link_NAG-ASN : angle 2.13947 / 1.49 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.29 seconds wall clock time: 70 minutes 35.16 seconds (4235.16 seconds total)