Starting phenix.real_space_refine on Sun Sep 13 02:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn0_21246/09_2026/6vn0_21246.cif" } resolution = 4.25 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= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12525 2.51 5 N 3306 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19962 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "K" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" 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: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "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: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.12, per 1000 atoms: 0.26 Number of scatterers: 19962 At special positions: 0 Unit cell: (141.11, 145.23, 119.48, 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 126 16.00 O 4005 8.00 N 3306 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.18 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.18 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.10 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.02 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.09 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.18 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.05 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.10 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " BMA i 3 " - " MAN i 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA X 3 " - " MAN X 5 " " BMA i 3 " - " MAN i 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 619 " - " ASN A 295 " " NAG A 622 " - " ASN A 355 " " NAG A 629 " - " ASN A 133 " " NAG A 632 " - " ASN A 301 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 619 " - " ASN C 295 " " NAG C 622 " - " ASN C 355 " " NAG C 629 " - " ASN C 133 " " NAG C 632 " - " ASN C 301 " " NAG D 619 " - " ASN D 295 " " NAG D 622 " - " ASN D 355 " " NAG D 629 " - " ASN D 133 " " NAG D 632 " - " ASN D 301 " " NAG E 701 " - " ASN E 618 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN C 392 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 448 " " NAG i 1 " - " ASN D 88 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 160 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 262 " " NAG n 1 " - " ASN D 276 " " NAG o 1 " - " ASN D 332 " " NAG p 1 " - " ASN D 386 " " NAG q 1 " - " ASN D 392 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 448 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 993.5 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 23.1% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.312A 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 476 through 484 removed outlier: 5.134A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 661 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.312A 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 476 through 484 removed outlier: 5.133A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 528 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 646 Processing helix chain 'E' and resid 648 through 661 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 476 through 484 removed outlier: 5.133A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 528 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 547 through 551 Processing helix chain 'F' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 646 Processing helix chain 'F' and resid 648 through 661 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.513A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.486A 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 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.514A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 55 removed outlier: 5.513A pdb=" N ILE D 215 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY D 250 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR D 217 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.585A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 795 hydrogen bonds defined for protein. 1980 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: 5.44 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5262 1.33 - 1.47: 6322 1.47 - 1.60: 8620 1.60 - 1.74: 13 1.74 - 1.88: 159 Bond restraints: 20376 Sorted by residual: bond pdb=" CB HIS I 32 " pdb=" CG HIS I 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" CB HIS G 32 " pdb=" CG HIS G 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CB HIS H 32 " pdb=" CG HIS H 32 " ideal model delta sigma weight residual 1.497 1.436 0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 bond pdb=" CA PHE D 53 " pdb=" C PHE D 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 ... (remaining 20371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 23849 2.42 - 4.84: 3222 4.84 - 7.26: 530 7.26 - 9.68: 53 9.68 - 12.10: 3 Bond angle restraints: 27657 Sorted by residual: angle pdb=" N LEU B 520 " pdb=" CA LEU B 520 " pdb=" C LEU B 520 " ideal model delta sigma weight residual 113.50 101.40 12.10 1.23e+00 6.61e-01 9.69e+01 angle pdb=" N LEU E 520 " pdb=" CA LEU E 520 " pdb=" C LEU E 520 " ideal model delta sigma weight residual 113.50 101.42 12.08 1.23e+00 6.61e-01 9.65e+01 angle pdb=" N LEU F 520 " pdb=" CA LEU F 520 " pdb=" C LEU F 520 " ideal model delta sigma weight residual 113.50 101.45 12.05 1.23e+00 6.61e-01 9.60e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.26 -7.70 1.02e+00 9.61e-01 5.69e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.24 -7.68 1.02e+00 9.61e-01 5.66e+01 ... (remaining 27652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 10842 16.66 - 33.31: 330 33.31 - 49.97: 96 49.97 - 66.62: 54 66.62 - 83.28: 33 Dihedral angle restraints: 11355 sinusoidal: 4578 harmonic: 6777 Sorted by residual: dihedral pdb=" CA CYS D 126 " pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.72 73.28 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS A 126 " pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.73 73.27 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS C 126 " pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.75 73.25 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 11352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2473 0.106 - 0.212: 821 0.212 - 0.319: 86 0.319 - 0.425: 1 0.425 - 0.531: 6 Chirality restraints: 3387 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.43e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.39e+01 chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.29e+01 ... (remaining 3384 not shown) Planarity restraints: 3429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " 0.076 2.00e-02 2.50e+03 7.95e-02 7.90e+01 pdb=" CG ASN E 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG E 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.89e+01 pdb=" CG ASN B 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.88e+01 pdb=" CG ASN F 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " 0.095 2.00e-02 2.50e+03 ... (remaining 3426 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5065 2.80 - 3.32: 17794 3.32 - 3.85: 33633 3.85 - 4.37: 39409 4.37 - 4.90: 63111 Nonbonded interactions: 159012 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG i 1 " pdb=" O7 NAG i 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG X 1 " pdb=" O7 NAG X 1 " model vdw 2.270 3.040 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.308 3.120 nonbonded pdb=" N ASN C 355 " pdb=" OD1 ASN C 355 " model vdw 2.308 3.120 ... (remaining 159007 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'X' selection = chain 'b' selection = chain 'i' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.620 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.019 0.145 20520 Z= 0.985 Angle : 1.779 12.105 28050 Z= 1.123 Chirality : 0.098 0.531 3387 Planarity : 0.009 0.049 3375 Dihedral : 10.798 83.277 6876 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.65 % Allowed : 2.86 % Favored : 96.49 % Rotamer: Outliers : 0.15 % Allowed : 1.02 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.70 (0.17), residues: 2310 helix: -0.39 (0.24), residues: 390 sheet: 1.07 (0.20), residues: 630 loop : 0.58 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 273 TYR 0.060 0.009 TYR E 638 PHE 0.040 0.007 PHE E 522 TRP 0.051 0.010 TRP E 571 HIS 0.017 0.004 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01834 / 0.98 (20376) covalent geometry : angle 1.76049 / 1.12 (27657) SS BOND : bond 0.05049 / 3.67 ( 39) SS BOND : angle 2.96607 / 1.95 ( 78) hydrogen bonds : bond 0.19258 / 13.22 ( 747) hydrogen bonds : angle 8.16803 / 5.70 ( 1980) link_ALPHA1-2 : bond 0.04085 / 2.05 ( 3) link_ALPHA1-2 : angle 2.35557 / 1.54 ( 9) link_ALPHA1-3 : bond 0.04231 / 2.34 ( 6) link_ALPHA1-3 : angle 3.46683 / 1.98 ( 18) link_ALPHA1-6 : bond 0.03315 / 1.66 ( 3) link_ALPHA1-6 : angle 2.36337 / 1.60 ( 9) link_BETA1-4 : bond 0.03475 / 2.21 ( 39) link_BETA1-4 : angle 3.33177 / 2.32 ( 117) link_NAG-ASN : bond 0.02955 / 1.91 ( 54) link_NAG-ASN : angle 2.16018 / 1.52 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 815 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8629 (mt) cc_final: 0.8171 (mm) REVERT: A 116 LEU cc_start: 0.8467 (mt) cc_final: 0.7941 (mt) REVERT: A 323 ILE cc_start: 0.8410 (mt) cc_final: 0.8158 (mt) REVERT: A 373 THR cc_start: 0.8850 (p) cc_final: 0.8397 (p) REVERT: A 450 THR cc_start: 0.8387 (p) cc_final: 0.7691 (t) REVERT: B 586 TYR cc_start: 0.9136 (t80) cc_final: 0.8540 (t80) REVERT: B 604 CYS cc_start: 0.5202 (t) cc_final: 0.4881 (t) REVERT: H 25 SER cc_start: 0.7152 (t) cc_final: 0.5123 (p) REVERT: L 10 PHE cc_start: 0.7351 (p90) cc_final: 0.7092 (p90) REVERT: L 21 ILE cc_start: 0.8754 (pt) cc_final: 0.8534 (mm) REVERT: L 92 ASN cc_start: 0.8912 (t0) cc_final: 0.8368 (t0) REVERT: C 52 LEU cc_start: 0.8588 (mt) cc_final: 0.8220 (mm) REVERT: C 116 LEU cc_start: 0.8643 (mt) cc_final: 0.8263 (mt) REVERT: C 251 ILE cc_start: 0.9410 (mt) cc_final: 0.9198 (tp) REVERT: C 373 THR cc_start: 0.8858 (p) cc_final: 0.8398 (p) REVERT: C 450 THR cc_start: 0.8362 (p) cc_final: 0.7676 (t) REVERT: E 584 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8502 (mt-10) REVERT: E 610 TRP cc_start: 0.8569 (t-100) cc_final: 0.8155 (t-100) REVERT: G 25 SER cc_start: 0.7059 (t) cc_final: 0.5144 (p) REVERT: J 10 PHE cc_start: 0.7430 (p90) cc_final: 0.7156 (p90) REVERT: J 21 ILE cc_start: 0.8875 (pt) cc_final: 0.8666 (mm) REVERT: J 92 ASN cc_start: 0.8877 (t0) cc_final: 0.8672 (t0) REVERT: D 52 LEU cc_start: 0.8583 (mt) cc_final: 0.8131 (mm) REVERT: D 107 ASP cc_start: 0.8614 (m-30) cc_final: 0.8386 (p0) REVERT: D 114 GLN cc_start: 0.8831 (tp40) cc_final: 0.8606 (tm-30) REVERT: D 217 TYR cc_start: 0.8344 (m-80) cc_final: 0.7409 (m-80) REVERT: D 373 THR cc_start: 0.8822 (p) cc_final: 0.8572 (p) REVERT: D 450 THR cc_start: 0.8213 (p) cc_final: 0.7537 (t) REVERT: F 543 ASN cc_start: 0.8871 (m-40) cc_final: 0.8593 (t0) REVERT: F 584 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8249 (mt-10) REVERT: I 25 SER cc_start: 0.6930 (t) cc_final: 0.4812 (p) REVERT: K 10 PHE cc_start: 0.7492 (p90) cc_final: 0.7260 (p90) REVERT: K 21 ILE cc_start: 0.8866 (pt) cc_final: 0.8636 (mm) REVERT: K 92 ASN cc_start: 0.8832 (t0) cc_final: 0.8576 (t0) outliers start: 3 outliers final: 3 residues processed: 818 average time/residue: 0.1397 time to fit residues: 174.7590 Evaluate side-chains 435 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 550 GLN H 32 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 76 ASN E 550 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 35 HIS G 39 GLN J 76 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS I 39 GLN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.061260 restraints weight = 72276.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063750 restraints weight = 39269.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065527 restraints weight = 25529.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066808 restraints weight = 18473.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067721 restraints weight = 14431.375| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20520 Z= 0.185 Angle : 0.871 11.419 28050 Z= 0.431 Chirality : 0.050 0.372 3387 Planarity : 0.005 0.036 3375 Dihedral : 5.478 41.791 2520 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.72 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.54 (0.17), residues: 2310 helix: 0.58 (0.27), residues: 390 sheet: 1.05 (0.20), residues: 654 loop : -0.01 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 151 TYR 0.025 0.002 TYR I 100I PHE 0.031 0.003 PHE K 71 TRP 0.026 0.002 TRP B 610 HIS 0.010 0.002 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (20376) covalent geometry : angle 0.82062 / 0.42 (27657) SS BOND : bond 0.00330 / 0.21 ( 39) SS BOND : angle 1.18444 / 0.82 ( 78) hydrogen bonds : bond 0.06246 / 4.28 ( 747) hydrogen bonds : angle 6.29236 / 4.40 ( 1980) link_ALPHA1-2 : bond 0.00807 / 0.40 ( 3) link_ALPHA1-2 : angle 1.55216 / 1.11 ( 9) link_ALPHA1-3 : bond 0.00673 / 0.36 ( 6) link_ALPHA1-3 : angle 1.44363 / 0.87 ( 18) link_ALPHA1-6 : bond 0.00657 / 0.33 ( 3) link_ALPHA1-6 : angle 1.63799 / 1.12 ( 9) link_BETA1-4 : bond 0.00533 / 0.32 ( 39) link_BETA1-4 : angle 2.39717 / 1.70 ( 117) link_NAG-ASN : bond 0.00693 / 0.51 ( 54) link_NAG-ASN : angle 3.33049 / 2.23 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.8586 (m-40) cc_final: 0.8182 (m110) REVERT: A 210 PHE cc_start: 0.6170 (m-80) cc_final: 0.5883 (m-80) REVERT: A 217 TYR cc_start: 0.7659 (m-80) cc_final: 0.7193 (m-80) REVERT: A 256 SER cc_start: 0.8517 (p) cc_final: 0.8049 (p) REVERT: A 373 THR cc_start: 0.8777 (p) cc_final: 0.8498 (t) REVERT: B 543 ASN cc_start: 0.9287 (t0) cc_final: 0.8907 (t0) REVERT: B 586 TYR cc_start: 0.8894 (t80) cc_final: 0.8513 (t80) REVERT: B 606 THR cc_start: 0.8698 (p) cc_final: 0.8437 (p) REVERT: B 626 MET cc_start: 0.9124 (mmp) cc_final: 0.8840 (mmm) REVERT: B 653 GLN cc_start: 0.9155 (tt0) cc_final: 0.8911 (mp10) REVERT: H 18 LEU cc_start: 0.7805 (tt) cc_final: 0.7048 (tt) REVERT: H 61 ASP cc_start: 0.9195 (p0) cc_final: 0.8965 (p0) REVERT: H 100 TYR cc_start: 0.8035 (t80) cc_final: 0.7821 (t80) REVERT: L 8 PRO cc_start: 0.3802 (Cg_endo) cc_final: 0.3512 (Cg_exo) REVERT: L 21 ILE cc_start: 0.9477 (pt) cc_final: 0.9214 (mm) REVERT: L 37 GLN cc_start: 0.8927 (pp30) cc_final: 0.8519 (pp30) REVERT: L 53 GLN cc_start: 0.8699 (tp40) cc_final: 0.8430 (tp-100) REVERT: L 82 ASP cc_start: 0.8057 (m-30) cc_final: 0.7833 (m-30) REVERT: C 211 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 217 TYR cc_start: 0.7604 (m-10) cc_final: 0.7320 (m-10) REVERT: C 256 SER cc_start: 0.7326 (t) cc_final: 0.6995 (t) REVERT: C 373 THR cc_start: 0.8834 (p) cc_final: 0.8520 (t) REVERT: C 387 THR cc_start: 0.9521 (p) cc_final: 0.9218 (t) REVERT: C 435 TYR cc_start: 0.8001 (t80) cc_final: 0.7702 (t80) REVERT: E 529 THR cc_start: 0.8969 (p) cc_final: 0.8734 (t) REVERT: E 543 ASN cc_start: 0.9242 (t0) cc_final: 0.8850 (t0) REVERT: E 545 LEU cc_start: 0.8841 (tp) cc_final: 0.8443 (tt) REVERT: E 588 ARG cc_start: 0.9180 (ttp80) cc_final: 0.8926 (ttp80) REVERT: E 591 GLN cc_start: 0.9455 (tp40) cc_final: 0.8908 (tp40) REVERT: E 593 LEU cc_start: 0.9609 (mt) cc_final: 0.9391 (tp) REVERT: E 606 THR cc_start: 0.8818 (p) cc_final: 0.8613 (p) REVERT: E 626 MET cc_start: 0.9112 (mmp) cc_final: 0.8708 (mmm) REVERT: G 18 LEU cc_start: 0.7670 (tt) cc_final: 0.6829 (tt) REVERT: G 20 LEU cc_start: 0.9185 (mt) cc_final: 0.8815 (mp) REVERT: G 61 ASP cc_start: 0.9065 (p0) cc_final: 0.8712 (p0) REVERT: J 8 PRO cc_start: 0.3884 (Cg_endo) cc_final: 0.3675 (Cg_exo) REVERT: J 10 PHE cc_start: 0.7462 (p90) cc_final: 0.7259 (p90) REVERT: J 21 ILE cc_start: 0.9513 (pt) cc_final: 0.9196 (mm) REVERT: J 37 GLN cc_start: 0.9029 (pp30) cc_final: 0.8813 (pp30) REVERT: J 53 GLN cc_start: 0.8787 (tp40) cc_final: 0.8547 (tp-100) REVERT: J 73 LEU cc_start: 0.9347 (tp) cc_final: 0.9058 (tp) REVERT: J 82 ASP cc_start: 0.7947 (m-30) cc_final: 0.7665 (m-30) REVERT: D 107 ASP cc_start: 0.9147 (m-30) cc_final: 0.8760 (p0) REVERT: D 114 GLN cc_start: 0.9361 (tp40) cc_final: 0.8877 (tm-30) REVERT: D 116 LEU cc_start: 0.8531 (mt) cc_final: 0.8245 (mt) REVERT: D 217 TYR cc_start: 0.8033 (m-80) cc_final: 0.7494 (m-80) REVERT: D 256 SER cc_start: 0.7522 (t) cc_final: 0.7225 (t) REVERT: D 323 ILE cc_start: 0.8235 (mt) cc_final: 0.7973 (tt) REVERT: D 373 THR cc_start: 0.8787 (p) cc_final: 0.8418 (t) REVERT: D 435 TYR cc_start: 0.8198 (t80) cc_final: 0.7847 (t80) REVERT: F 529 THR cc_start: 0.8955 (p) cc_final: 0.8482 (t) REVERT: F 606 THR cc_start: 0.8764 (p) cc_final: 0.8482 (p) REVERT: F 626 MET cc_start: 0.9146 (mmp) cc_final: 0.8587 (mmm) REVERT: I 18 LEU cc_start: 0.7963 (tt) cc_final: 0.7040 (tt) REVERT: I 34 MET cc_start: 0.8885 (mmm) cc_final: 0.8592 (mmp) REVERT: I 61 ASP cc_start: 0.8992 (p0) cc_final: 0.8705 (p0) REVERT: K 8 PRO cc_start: 0.3889 (Cg_endo) cc_final: 0.3602 (Cg_exo) REVERT: K 21 ILE cc_start: 0.9521 (pt) cc_final: 0.9295 (mm) REVERT: K 33 LEU cc_start: 0.8565 (tp) cc_final: 0.7965 (tp) REVERT: K 53 GLN cc_start: 0.8851 (tp40) cc_final: 0.8615 (tp-100) REVERT: K 78 LEU cc_start: 0.9254 (tp) cc_final: 0.8906 (tp) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.1193 time to fit residues: 111.8468 Evaluate side-chains 438 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 10 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 176 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 HIS ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 432 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055978 restraints weight = 76003.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058235 restraints weight = 41841.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059821 restraints weight = 27604.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060986 restraints weight = 20398.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061824 restraints weight = 16184.530| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20520 Z= 0.215 Angle : 0.814 13.816 28050 Z= 0.401 Chirality : 0.047 0.275 3387 Planarity : 0.005 0.070 3375 Dihedral : 5.400 30.231 2520 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.50 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.26 (0.17), residues: 2310 helix: 0.87 (0.28), residues: 372 sheet: 0.70 (0.18), residues: 705 loop : -0.30 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 585 TYR 0.028 0.002 TYR C 217 PHE 0.027 0.002 PHE D 53 TRP 0.015 0.002 TRP A 112 HIS 0.009 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (20376) covalent geometry : angle 0.77070 / 0.39 (27657) SS BOND : bond 0.00384 / 0.25 ( 39) SS BOND : angle 1.04227 / 0.74 ( 78) hydrogen bonds : bond 0.05249 / 3.57 ( 747) hydrogen bonds : angle 5.89972 / 4.08 ( 1980) link_ALPHA1-2 : bond 0.00450 / 0.22 ( 3) link_ALPHA1-2 : angle 1.54540 / 1.13 ( 9) link_ALPHA1-3 : bond 0.00832 / 0.48 ( 6) link_ALPHA1-3 : angle 1.70594 / 1.10 ( 18) link_ALPHA1-6 : bond 0.00764 / 0.38 ( 3) link_ALPHA1-6 : angle 1.76894 / 1.26 ( 9) link_BETA1-4 : bond 0.00325 / 0.21 ( 39) link_BETA1-4 : angle 1.81051 / 1.28 ( 117) link_NAG-ASN : bond 0.00535 / 0.36 ( 54) link_NAG-ASN : angle 3.12137 / 2.04 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8717 (p0) cc_final: 0.8494 (p0) REVERT: A 98 ASN cc_start: 0.8965 (t0) cc_final: 0.8741 (t0) REVERT: A 116 LEU cc_start: 0.8591 (mt) cc_final: 0.8360 (mt) REVERT: A 136 ASN cc_start: 0.8730 (m-40) cc_final: 0.8384 (m110) REVERT: A 211 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 256 SER cc_start: 0.8314 (p) cc_final: 0.7720 (p) REVERT: A 271 MET cc_start: 0.8719 (mmm) cc_final: 0.8517 (mmm) REVERT: B 529 THR cc_start: 0.9087 (p) cc_final: 0.8729 (t) REVERT: B 543 ASN cc_start: 0.9375 (t0) cc_final: 0.9044 (t0) REVERT: B 591 GLN cc_start: 0.9454 (tp40) cc_final: 0.9089 (tp40) REVERT: B 626 MET cc_start: 0.9272 (mmp) cc_final: 0.8801 (mmm) REVERT: B 653 GLN cc_start: 0.9363 (tt0) cc_final: 0.9067 (mp10) REVERT: H 27 PHE cc_start: 0.7473 (p90) cc_final: 0.7064 (p90) REVERT: H 100 TYR cc_start: 0.8444 (t80) cc_final: 0.8074 (t80) REVERT: L 37 GLN cc_start: 0.8879 (pp30) cc_final: 0.8583 (pp30) REVERT: L 47 LEU cc_start: 0.9677 (mm) cc_final: 0.9394 (mm) REVERT: L 55 ILE cc_start: 0.8739 (mt) cc_final: 0.8447 (pt) REVERT: L 58 VAL cc_start: 0.8339 (t) cc_final: 0.8112 (t) REVERT: C 67 ASN cc_start: 0.8596 (p0) cc_final: 0.8377 (p0) REVERT: C 122 LEU cc_start: 0.9483 (mp) cc_final: 0.9262 (mp) REVERT: C 136 ASN cc_start: 0.8578 (m-40) cc_final: 0.8213 (m110) REVERT: C 424 ILE cc_start: 0.9371 (mp) cc_final: 0.8817 (mp) REVERT: C 434 MET cc_start: 0.8229 (mpp) cc_final: 0.7768 (mpp) REVERT: C 435 TYR cc_start: 0.8346 (t80) cc_final: 0.7724 (t80) REVERT: E 543 ASN cc_start: 0.9327 (t0) cc_final: 0.9047 (t0) REVERT: E 545 LEU cc_start: 0.8948 (tp) cc_final: 0.8415 (tt) REVERT: E 591 GLN cc_start: 0.9507 (tp40) cc_final: 0.9010 (tp40) REVERT: G 18 LEU cc_start: 0.7937 (tt) cc_final: 0.7284 (tt) REVERT: G 20 LEU cc_start: 0.9362 (mt) cc_final: 0.9041 (mp) REVERT: G 61 ASP cc_start: 0.9104 (p0) cc_final: 0.8801 (p0) REVERT: J 21 ILE cc_start: 0.9555 (pt) cc_final: 0.9276 (mm) REVERT: J 47 LEU cc_start: 0.9643 (mm) cc_final: 0.9343 (mm) REVERT: J 55 ILE cc_start: 0.8675 (mt) cc_final: 0.8469 (pt) REVERT: J 58 VAL cc_start: 0.8503 (t) cc_final: 0.8261 (t) REVERT: J 71 PHE cc_start: 0.9020 (m-10) cc_final: 0.8742 (m-10) REVERT: D 104 MET cc_start: 0.9639 (ttm) cc_final: 0.9437 (ttm) REVERT: D 107 ASP cc_start: 0.9155 (m-30) cc_final: 0.8791 (m-30) REVERT: D 116 LEU cc_start: 0.8887 (mt) cc_final: 0.8665 (mt) REVERT: D 136 ASN cc_start: 0.8449 (m-40) cc_final: 0.8010 (m110) REVERT: D 211 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 260 LEU cc_start: 0.9075 (mt) cc_final: 0.8773 (mp) REVERT: D 323 ILE cc_start: 0.8323 (mt) cc_final: 0.8057 (tt) REVERT: D 424 ILE cc_start: 0.9443 (mp) cc_final: 0.9237 (mp) REVERT: D 434 MET cc_start: 0.8249 (mpp) cc_final: 0.7857 (mpp) REVERT: D 435 TYR cc_start: 0.8328 (t80) cc_final: 0.7845 (t80) REVERT: F 543 ASN cc_start: 0.9358 (t0) cc_final: 0.9032 (t0) REVERT: F 584 GLU cc_start: 0.9198 (tt0) cc_final: 0.8565 (tm-30) REVERT: F 603 ILE cc_start: 0.8977 (mm) cc_final: 0.8750 (mm) REVERT: F 604 CYS cc_start: 0.5102 (t) cc_final: 0.4659 (t) REVERT: F 621 GLU cc_start: 0.8462 (tp30) cc_final: 0.7831 (tp30) REVERT: I 18 LEU cc_start: 0.7836 (tt) cc_final: 0.7402 (tt) REVERT: I 20 LEU cc_start: 0.9351 (mt) cc_final: 0.9132 (mp) REVERT: I 34 MET cc_start: 0.8954 (mmm) cc_final: 0.8673 (mmm) REVERT: I 100 TYR cc_start: 0.8255 (t80) cc_final: 0.7825 (t80) REVERT: K 37 GLN cc_start: 0.8955 (pp30) cc_final: 0.8693 (pp30) REVERT: K 47 LEU cc_start: 0.9675 (mm) cc_final: 0.9359 (mm) REVERT: K 78 LEU cc_start: 0.9267 (tp) cc_final: 0.8961 (tp) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.1140 time to fit residues: 93.3581 Evaluate side-chains 371 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 175 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 214 optimal weight: 20.0000 chunk 205 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.068380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055331 restraints weight = 77921.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057488 restraints weight = 42675.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059025 restraints weight = 28087.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060095 restraints weight = 20663.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060902 restraints weight = 16469.298| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20520 Z= 0.183 Angle : 0.763 13.215 28050 Z= 0.371 Chirality : 0.046 0.256 3387 Planarity : 0.004 0.059 3375 Dihedral : 5.178 26.738 2520 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.32 % Favored : 94.42 % Rotamer: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2310 helix: 0.43 (0.27), residues: 414 sheet: 0.62 (0.18), residues: 714 loop : -0.38 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 617 TYR 0.016 0.001 TYR G 100A PHE 0.030 0.002 PHE A 53 TRP 0.028 0.002 TRP G 100H HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (20376) covalent geometry : angle 0.72168 / 0.36 (27657) SS BOND : bond 0.00363 / 0.23 ( 39) SS BOND : angle 1.15982 / 0.80 ( 78) hydrogen bonds : bond 0.04605 / 3.16 ( 747) hydrogen bonds : angle 5.68524 / 3.92 ( 1980) link_ALPHA1-2 : bond 0.00547 / 0.27 ( 3) link_ALPHA1-2 : angle 1.57204 / 1.14 ( 9) link_ALPHA1-3 : bond 0.00518 / 0.30 ( 6) link_ALPHA1-3 : angle 1.57570 / 1.06 ( 18) link_ALPHA1-6 : bond 0.00591 / 0.30 ( 3) link_ALPHA1-6 : angle 1.90921 / 1.33 ( 9) link_BETA1-4 : bond 0.00320 / 0.20 ( 39) link_BETA1-4 : angle 1.55813 / 1.10 ( 117) link_NAG-ASN : bond 0.00548 / 0.38 ( 54) link_NAG-ASN : angle 2.96852 / 1.93 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8611 (mp0) cc_final: 0.8370 (mm-30) REVERT: A 94 ASN cc_start: 0.9282 (t0) cc_final: 0.9066 (t0) REVERT: A 98 ASN cc_start: 0.9262 (t0) cc_final: 0.8972 (t0) REVERT: A 116 LEU cc_start: 0.8719 (mt) cc_final: 0.8412 (mt) REVERT: A 136 ASN cc_start: 0.8663 (m-40) cc_final: 0.8348 (m110) REVERT: B 530 MET cc_start: 0.9341 (mmm) cc_final: 0.9095 (mmm) REVERT: B 543 ASN cc_start: 0.9206 (t0) cc_final: 0.8905 (t0) REVERT: B 626 MET cc_start: 0.9069 (mmp) cc_final: 0.8633 (mmm) REVERT: B 653 GLN cc_start: 0.9320 (tt0) cc_final: 0.9102 (mp10) REVERT: H 100 TYR cc_start: 0.8528 (t80) cc_final: 0.8276 (t80) REVERT: L 21 ILE cc_start: 0.9447 (pt) cc_final: 0.9121 (mm) REVERT: L 47 LEU cc_start: 0.9668 (mm) cc_final: 0.9385 (mm) REVERT: L 53 GLN cc_start: 0.9003 (tp40) cc_final: 0.8571 (tp-100) REVERT: L 55 ILE cc_start: 0.8921 (mt) cc_final: 0.8647 (pt) REVERT: L 73 LEU cc_start: 0.9246 (tp) cc_final: 0.9026 (tp) REVERT: C 116 LEU cc_start: 0.8644 (mt) cc_final: 0.8379 (mt) REVERT: C 136 ASN cc_start: 0.8665 (m-40) cc_final: 0.8365 (m110) REVERT: C 256 SER cc_start: 0.8144 (m) cc_final: 0.7880 (m) REVERT: C 435 TYR cc_start: 0.8375 (t80) cc_final: 0.7770 (t80) REVERT: E 543 ASN cc_start: 0.9177 (t0) cc_final: 0.8890 (t0) REVERT: E 591 GLN cc_start: 0.9525 (tp40) cc_final: 0.9202 (tp40) REVERT: E 632 ASP cc_start: 0.9314 (t70) cc_final: 0.9012 (t70) REVERT: G 18 LEU cc_start: 0.8113 (tt) cc_final: 0.7402 (tt) REVERT: G 20 LEU cc_start: 0.9428 (mt) cc_final: 0.9204 (mp) REVERT: G 26 GLU cc_start: 0.7986 (mp0) cc_final: 0.7762 (mp0) REVERT: G 34 MET cc_start: 0.8582 (mmm) cc_final: 0.8144 (mmp) REVERT: G 35 HIS cc_start: 0.9103 (m90) cc_final: 0.8729 (m-70) REVERT: G 61 ASP cc_start: 0.9098 (p0) cc_final: 0.8650 (t0) REVERT: J 21 ILE cc_start: 0.9493 (pt) cc_final: 0.9185 (mm) REVERT: J 37 GLN cc_start: 0.9065 (pp30) cc_final: 0.8841 (pp30) REVERT: J 47 LEU cc_start: 0.9610 (mm) cc_final: 0.9360 (mm) REVERT: J 55 ILE cc_start: 0.8816 (mt) cc_final: 0.8611 (pt) REVERT: J 71 PHE cc_start: 0.9089 (m-80) cc_final: 0.8840 (m-10) REVERT: D 95 MET cc_start: 0.9113 (pmm) cc_final: 0.8873 (pmm) REVERT: D 98 ASN cc_start: 0.9245 (t0) cc_final: 0.8933 (t0) REVERT: D 107 ASP cc_start: 0.9145 (m-30) cc_final: 0.8823 (m-30) REVERT: D 111 LEU cc_start: 0.9419 (tt) cc_final: 0.9135 (pp) REVERT: D 116 LEU cc_start: 0.8816 (mt) cc_final: 0.7514 (mt) REVERT: D 136 ASN cc_start: 0.8492 (m-40) cc_final: 0.8101 (m110) REVERT: D 173 TYR cc_start: 0.8410 (p90) cc_final: 0.7821 (p90) REVERT: D 256 SER cc_start: 0.8491 (m) cc_final: 0.8272 (m) REVERT: D 435 TYR cc_start: 0.8346 (t80) cc_final: 0.7979 (t80) REVERT: F 530 MET cc_start: 0.9274 (mtp) cc_final: 0.8713 (mtp) REVERT: F 543 ASN cc_start: 0.9175 (t0) cc_final: 0.8904 (t0) REVERT: F 593 LEU cc_start: 0.9787 (mt) cc_final: 0.9551 (tp) REVERT: F 621 GLU cc_start: 0.8342 (tp30) cc_final: 0.7786 (tp30) REVERT: I 34 MET cc_start: 0.8969 (mmm) cc_final: 0.8660 (mmm) REVERT: I 61 ASP cc_start: 0.8989 (p0) cc_final: 0.8455 (t0) REVERT: I 100 TYR cc_start: 0.8415 (t80) cc_final: 0.8134 (t80) REVERT: K 37 GLN cc_start: 0.8988 (pp30) cc_final: 0.8669 (pp30) REVERT: K 53 GLN cc_start: 0.9145 (tp40) cc_final: 0.8868 (tp-100) REVERT: K 92 ASN cc_start: 0.9099 (t0) cc_final: 0.8829 (t0) outliers start: 1 outliers final: 1 residues processed: 475 average time/residue: 0.1109 time to fit residues: 87.4469 Evaluate side-chains 376 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 226 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.055738 restraints weight = 79154.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057850 restraints weight = 43469.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059339 restraints weight = 28777.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060400 restraints weight = 21327.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061160 restraints weight = 17091.424| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20520 Z= 0.156 Angle : 0.732 13.026 28050 Z= 0.355 Chirality : 0.046 0.247 3387 Planarity : 0.004 0.069 3375 Dihedral : 5.104 24.730 2520 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.18), residues: 2310 helix: 0.62 (0.27), residues: 414 sheet: 0.62 (0.19), residues: 675 loop : -0.43 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 66 TYR 0.023 0.001 TYR A 435 PHE 0.029 0.002 PHE B 522 TRP 0.023 0.002 TRP A 96 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (20376) covalent geometry : angle 0.69539 / 0.35 (27657) SS BOND : bond 0.00453 / 0.25 ( 39) SS BOND : angle 1.04526 / 0.70 ( 78) hydrogen bonds : bond 0.04415 / 3.01 ( 747) hydrogen bonds : angle 5.65241 / 3.89 ( 1980) link_ALPHA1-2 : bond 0.00511 / 0.26 ( 3) link_ALPHA1-2 : angle 1.56202 / 1.13 ( 9) link_ALPHA1-3 : bond 0.00640 / 0.36 ( 6) link_ALPHA1-3 : angle 1.63115 / 1.06 ( 18) link_ALPHA1-6 : bond 0.00658 / 0.33 ( 3) link_ALPHA1-6 : angle 1.83053 / 1.29 ( 9) link_BETA1-4 : bond 0.00335 / 0.21 ( 39) link_BETA1-4 : angle 1.45564 / 1.02 ( 117) link_NAG-ASN : bond 0.00432 / 0.30 ( 54) link_NAG-ASN : angle 2.74312 / 1.76 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8590 (mp0) cc_final: 0.8356 (mm-30) REVERT: A 67 ASN cc_start: 0.8613 (m-40) cc_final: 0.8371 (p0) REVERT: A 116 LEU cc_start: 0.8782 (mt) cc_final: 0.8428 (mt) REVERT: A 136 ASN cc_start: 0.8594 (m-40) cc_final: 0.8272 (m110) REVERT: A 435 TYR cc_start: 0.8660 (t80) cc_final: 0.8418 (t80) REVERT: B 543 ASN cc_start: 0.9090 (t0) cc_final: 0.8859 (t0) REVERT: B 593 LEU cc_start: 0.9743 (tp) cc_final: 0.9517 (tp) REVERT: B 626 MET cc_start: 0.9099 (mmp) cc_final: 0.8772 (mmm) REVERT: B 653 GLN cc_start: 0.9297 (tt0) cc_final: 0.8877 (mt0) REVERT: H 27 PHE cc_start: 0.7872 (p90) cc_final: 0.7638 (p90) REVERT: L 21 ILE cc_start: 0.9454 (pt) cc_final: 0.9087 (mm) REVERT: L 37 GLN cc_start: 0.9028 (pp30) cc_final: 0.8695 (pp30) REVERT: L 47 LEU cc_start: 0.9679 (mm) cc_final: 0.9415 (mm) REVERT: L 53 GLN cc_start: 0.9041 (tp40) cc_final: 0.8635 (tp-100) REVERT: L 55 ILE cc_start: 0.8955 (mt) cc_final: 0.8723 (pt) REVERT: L 73 LEU cc_start: 0.9240 (tp) cc_final: 0.9028 (tp) REVERT: C 49 GLU cc_start: 0.8563 (mp0) cc_final: 0.8290 (mm-30) REVERT: C 66 HIS cc_start: 0.8371 (m-70) cc_final: 0.8003 (m-70) REVERT: C 67 ASN cc_start: 0.8824 (m-40) cc_final: 0.8480 (p0) REVERT: C 95 MET cc_start: 0.9329 (pmm) cc_final: 0.9077 (pmm) REVERT: C 116 LEU cc_start: 0.8624 (mt) cc_final: 0.7720 (mt) REVERT: C 256 SER cc_start: 0.8272 (m) cc_final: 0.7987 (m) REVERT: C 435 TYR cc_start: 0.8418 (t80) cc_final: 0.7765 (t80) REVERT: E 543 ASN cc_start: 0.9086 (t0) cc_final: 0.8866 (t0) REVERT: E 584 GLU cc_start: 0.9229 (tt0) cc_final: 0.9025 (tt0) REVERT: E 589 ASP cc_start: 0.9218 (m-30) cc_final: 0.8957 (m-30) REVERT: E 591 GLN cc_start: 0.9500 (tp40) cc_final: 0.9124 (tp40) REVERT: E 626 MET cc_start: 0.9143 (mmp) cc_final: 0.8770 (mmm) REVERT: E 632 ASP cc_start: 0.9322 (t70) cc_final: 0.9028 (t70) REVERT: G 26 GLU cc_start: 0.7894 (mp0) cc_final: 0.7652 (mp0) REVERT: G 33 ASP cc_start: 0.8042 (p0) cc_final: 0.7239 (p0) REVERT: G 61 ASP cc_start: 0.9102 (p0) cc_final: 0.8592 (t0) REVERT: J 37 GLN cc_start: 0.9089 (pp30) cc_final: 0.8845 (pp30) REVERT: J 53 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8604 (tp-100) REVERT: J 71 PHE cc_start: 0.9151 (m-80) cc_final: 0.8701 (m-10) REVERT: D 104 MET cc_start: 0.9745 (ttt) cc_final: 0.9499 (ttt) REVERT: D 111 LEU cc_start: 0.9371 (tt) cc_final: 0.9052 (pp) REVERT: D 114 GLN cc_start: 0.9264 (tp40) cc_final: 0.8959 (tm-30) REVERT: D 136 ASN cc_start: 0.8498 (m-40) cc_final: 0.8224 (m110) REVERT: D 173 TYR cc_start: 0.8273 (p90) cc_final: 0.7860 (p90) REVERT: D 256 SER cc_start: 0.8523 (m) cc_final: 0.8315 (m) REVERT: D 260 LEU cc_start: 0.9272 (mt) cc_final: 0.8879 (mp) REVERT: D 435 TYR cc_start: 0.8432 (t80) cc_final: 0.7704 (t80) REVERT: F 530 MET cc_start: 0.9190 (mtp) cc_final: 0.8805 (mtp) REVERT: F 621 GLU cc_start: 0.8292 (tp30) cc_final: 0.7839 (tp30) REVERT: I 34 MET cc_start: 0.8964 (mmm) cc_final: 0.8621 (mmm) REVERT: I 61 ASP cc_start: 0.8994 (p0) cc_final: 0.8458 (t70) REVERT: I 100 TYR cc_start: 0.8402 (t80) cc_final: 0.8153 (t80) REVERT: K 2 VAL cc_start: 0.8973 (t) cc_final: 0.8710 (t) REVERT: K 37 GLN cc_start: 0.8923 (pp30) cc_final: 0.8655 (pp30) REVERT: K 55 ILE cc_start: 0.9428 (pt) cc_final: 0.9224 (pt) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1088 time to fit residues: 83.2871 Evaluate side-chains 366 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 143 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.053568 restraints weight = 79016.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055649 restraints weight = 43534.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057087 restraints weight = 28773.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058144 restraints weight = 21369.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058898 restraints weight = 17084.566| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 20520 Z= 0.200 Angle : 0.766 13.086 28050 Z= 0.373 Chirality : 0.047 0.249 3387 Planarity : 0.005 0.072 3375 Dihedral : 5.230 26.072 2520 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.71 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.23 (0.18), residues: 2310 helix: 0.20 (0.26), residues: 441 sheet: 0.45 (0.19), residues: 696 loop : -0.61 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 66 TYR 0.024 0.002 TYR A 435 PHE 0.027 0.002 PHE A 53 TRP 0.019 0.002 TRP A 96 HIS 0.010 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (20376) covalent geometry : angle 0.73029 / 0.37 (27657) SS BOND : bond 0.00609 / 0.34 ( 39) SS BOND : angle 1.22290 / 0.85 ( 78) hydrogen bonds : bond 0.04484 / 3.04 ( 747) hydrogen bonds : angle 5.68988 / 3.93 ( 1980) link_ALPHA1-2 : bond 0.00410 / 0.21 ( 3) link_ALPHA1-2 : angle 1.58331 / 1.14 ( 9) link_ALPHA1-3 : bond 0.00556 / 0.33 ( 6) link_ALPHA1-3 : angle 1.63932 / 1.08 ( 18) link_ALPHA1-6 : bond 0.00550 / 0.28 ( 3) link_ALPHA1-6 : angle 1.98829 / 1.39 ( 9) link_BETA1-4 : bond 0.00268 / 0.17 ( 39) link_BETA1-4 : angle 1.50420 / 1.06 ( 117) link_NAG-ASN : bond 0.00460 / 0.31 ( 54) link_NAG-ASN : angle 2.75433 / 1.76 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8775 (m-40) cc_final: 0.8484 (p0) REVERT: A 116 LEU cc_start: 0.8947 (mt) cc_final: 0.8312 (mt) REVERT: A 136 ASN cc_start: 0.8724 (m-40) cc_final: 0.8392 (m110) REVERT: A 256 SER cc_start: 0.8638 (p) cc_final: 0.8200 (p) REVERT: A 435 TYR cc_start: 0.8668 (t80) cc_final: 0.8301 (t80) REVERT: B 543 ASN cc_start: 0.9238 (t0) cc_final: 0.8929 (t0) REVERT: B 626 MET cc_start: 0.9257 (mmp) cc_final: 0.8714 (mmm) REVERT: B 653 GLN cc_start: 0.9299 (tt0) cc_final: 0.8926 (mt0) REVERT: L 21 ILE cc_start: 0.9474 (pt) cc_final: 0.9097 (mm) REVERT: L 33 LEU cc_start: 0.8455 (tp) cc_final: 0.8191 (tp) REVERT: L 37 GLN cc_start: 0.9120 (pp30) cc_final: 0.8798 (pp30) REVERT: L 47 LEU cc_start: 0.9729 (mm) cc_final: 0.9526 (mm) REVERT: L 53 GLN cc_start: 0.9038 (tp40) cc_final: 0.8648 (tp-100) REVERT: L 73 LEU cc_start: 0.9236 (tp) cc_final: 0.8977 (tp) REVERT: C 67 ASN cc_start: 0.8912 (m-40) cc_final: 0.8561 (p0) REVERT: C 136 ASN cc_start: 0.8811 (m110) cc_final: 0.8521 (m110) REVERT: C 256 SER cc_start: 0.8279 (m) cc_final: 0.8007 (t) REVERT: C 427 TRP cc_start: 0.7937 (m-10) cc_final: 0.7135 (m-90) REVERT: C 435 TYR cc_start: 0.8570 (t80) cc_final: 0.8095 (t80) REVERT: C 475 MET cc_start: 0.8721 (pmm) cc_final: 0.8517 (pmm) REVERT: E 543 ASN cc_start: 0.9208 (t0) cc_final: 0.8938 (t0) REVERT: E 548 ILE cc_start: 0.8942 (tp) cc_final: 0.8468 (pt) REVERT: E 584 GLU cc_start: 0.9316 (tt0) cc_final: 0.9055 (tt0) REVERT: E 589 ASP cc_start: 0.9267 (m-30) cc_final: 0.8984 (m-30) REVERT: E 591 GLN cc_start: 0.9542 (tp40) cc_final: 0.9085 (tp40) REVERT: E 626 MET cc_start: 0.9153 (mmp) cc_final: 0.8878 (mmm) REVERT: G 33 ASP cc_start: 0.8078 (p0) cc_final: 0.7373 (p0) REVERT: G 35 HIS cc_start: 0.9046 (m-70) cc_final: 0.8784 (m-70) REVERT: G 61 ASP cc_start: 0.9113 (p0) cc_final: 0.8496 (t0) REVERT: J 37 GLN cc_start: 0.9083 (pp30) cc_final: 0.8821 (pp30) REVERT: J 53 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8533 (tp-100) REVERT: J 55 ILE cc_start: 0.9424 (pt) cc_final: 0.9165 (pt) REVERT: J 71 PHE cc_start: 0.9118 (m-80) cc_final: 0.8855 (m-10) REVERT: D 95 MET cc_start: 0.9260 (pmm) cc_final: 0.9037 (pmm) REVERT: D 104 MET cc_start: 0.9783 (ttt) cc_final: 0.9470 (ttt) REVERT: D 173 TYR cc_start: 0.8309 (p90) cc_final: 0.7824 (p90) REVERT: D 305 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7781 (mtmm) REVERT: D 435 TYR cc_start: 0.8571 (t80) cc_final: 0.8110 (t80) REVERT: F 543 ASN cc_start: 0.9168 (t0) cc_final: 0.8891 (t0) REVERT: F 621 GLU cc_start: 0.8282 (tp30) cc_final: 0.7823 (tp30) REVERT: I 34 MET cc_start: 0.9039 (mmm) cc_final: 0.8729 (mmp) REVERT: I 61 ASP cc_start: 0.9084 (p0) cc_final: 0.8412 (t0) REVERT: I 80 LEU cc_start: 0.9014 (tp) cc_final: 0.8322 (tp) REVERT: I 100 TYR cc_start: 0.8570 (t80) cc_final: 0.8352 (t80) REVERT: I 107 THR cc_start: 0.9108 (m) cc_final: 0.8855 (p) REVERT: K 37 GLN cc_start: 0.8939 (pp30) cc_final: 0.8694 (pp30) REVERT: K 53 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8598 (tp-100) REVERT: K 71 PHE cc_start: 0.8999 (m-80) cc_final: 0.8551 (m-10) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.1091 time to fit residues: 79.5240 Evaluate side-chains 343 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 151 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS L 6 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN D 67 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.054837 restraints weight = 76077.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.057004 restraints weight = 41220.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.058542 restraints weight = 27029.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059611 restraints weight = 19864.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060426 restraints weight = 15859.880| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20520 Z= 0.131 Angle : 0.709 12.595 28050 Z= 0.343 Chirality : 0.047 0.584 3387 Planarity : 0.004 0.066 3375 Dihedral : 5.065 24.093 2520 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.89 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.08 (0.18), residues: 2310 helix: 0.71 (0.27), residues: 411 sheet: 0.47 (0.19), residues: 693 loop : -0.60 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 617 TYR 0.016 0.001 TYR A 435 PHE 0.028 0.002 PHE F 519 TRP 0.042 0.002 TRP A 427 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (20376) covalent geometry : angle 0.67369 / 0.34 (27657) SS BOND : bond 0.00392 / 0.22 ( 39) SS BOND : angle 1.04677 / 0.71 ( 78) hydrogen bonds : bond 0.04064 / 2.76 ( 747) hydrogen bonds : angle 5.61705 / 3.88 ( 1980) link_ALPHA1-2 : bond 0.00484 / 0.24 ( 3) link_ALPHA1-2 : angle 1.60500 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00494 / 0.28 ( 6) link_ALPHA1-3 : angle 1.58067 / 1.04 ( 18) link_ALPHA1-6 : bond 0.00777 / 0.39 ( 3) link_ALPHA1-6 : angle 1.68919 / 1.18 ( 9) link_BETA1-4 : bond 0.00374 / 0.24 ( 39) link_BETA1-4 : angle 1.40997 / 0.98 ( 117) link_NAG-ASN : bond 0.00447 / 0.32 ( 54) link_NAG-ASN : angle 2.65605 / 1.69 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8719 (mp0) cc_final: 0.8423 (mm-30) REVERT: A 67 ASN cc_start: 0.8788 (m-40) cc_final: 0.8516 (p0) REVERT: A 94 ASN cc_start: 0.9437 (t0) cc_final: 0.9181 (t0) REVERT: A 116 LEU cc_start: 0.8949 (mt) cc_final: 0.8091 (mt) REVERT: A 136 ASN cc_start: 0.8707 (m-40) cc_final: 0.8456 (m110) REVERT: A 435 TYR cc_start: 0.8664 (t80) cc_final: 0.8284 (t80) REVERT: A 475 MET cc_start: 0.8575 (mpp) cc_final: 0.8234 (mmt) REVERT: B 543 ASN cc_start: 0.9241 (t0) cc_final: 0.8960 (t0) REVERT: B 626 MET cc_start: 0.9129 (mmp) cc_final: 0.8685 (mmm) REVERT: B 653 GLN cc_start: 0.9265 (tt0) cc_final: 0.8896 (mt0) REVERT: H 61 ASP cc_start: 0.9049 (p0) cc_final: 0.8373 (t0) REVERT: H 80 LEU cc_start: 0.8536 (tt) cc_final: 0.7596 (tp) REVERT: H 82 LEU cc_start: 0.8740 (mt) cc_final: 0.8462 (mt) REVERT: L 17 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8824 (mt-10) REVERT: L 18 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8904 (mmmt) REVERT: L 21 ILE cc_start: 0.9471 (pt) cc_final: 0.9067 (mm) REVERT: L 37 GLN cc_start: 0.9126 (pp30) cc_final: 0.8815 (pp30) REVERT: L 73 LEU cc_start: 0.9278 (tp) cc_final: 0.9000 (tp) REVERT: C 49 GLU cc_start: 0.8657 (mp0) cc_final: 0.8350 (mm-30) REVERT: C 66 HIS cc_start: 0.8160 (m-70) cc_final: 0.7948 (m-70) REVERT: C 67 ASN cc_start: 0.8950 (m-40) cc_final: 0.8523 (p0) REVERT: C 136 ASN cc_start: 0.8821 (m110) cc_final: 0.8619 (m110) REVERT: C 256 SER cc_start: 0.8318 (m) cc_final: 0.7982 (m) REVERT: C 435 TYR cc_start: 0.8587 (t80) cc_final: 0.8057 (t80) REVERT: E 584 GLU cc_start: 0.9332 (tt0) cc_final: 0.9064 (tt0) REVERT: E 589 ASP cc_start: 0.9208 (m-30) cc_final: 0.8929 (m-30) REVERT: E 591 GLN cc_start: 0.9539 (tp40) cc_final: 0.9017 (tp40) REVERT: E 598 CYS cc_start: 0.7000 (m) cc_final: 0.6707 (m) REVERT: E 626 MET cc_start: 0.9025 (mmp) cc_final: 0.8803 (mmm) REVERT: E 634 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8898 (tt0) REVERT: G 33 ASP cc_start: 0.8050 (p0) cc_final: 0.7417 (p0) REVERT: G 35 HIS cc_start: 0.9015 (m-70) cc_final: 0.8305 (m-70) REVERT: G 61 ASP cc_start: 0.9133 (p0) cc_final: 0.8545 (t0) REVERT: J 37 GLN cc_start: 0.9068 (pp30) cc_final: 0.8793 (pp30) REVERT: D 49 GLU cc_start: 0.8591 (mp0) cc_final: 0.8087 (mm-30) REVERT: D 95 MET cc_start: 0.9180 (pmm) cc_final: 0.8923 (pmm) REVERT: D 99 ASN cc_start: 0.9006 (p0) cc_final: 0.8576 (p0) REVERT: D 104 MET cc_start: 0.9780 (ttt) cc_final: 0.9498 (ttt) REVERT: D 173 TYR cc_start: 0.8254 (p90) cc_final: 0.7901 (p90) REVERT: D 201 ILE cc_start: 0.9109 (mp) cc_final: 0.8745 (tp) REVERT: D 256 SER cc_start: 0.8448 (m) cc_final: 0.8178 (m) REVERT: D 305 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7641 (mtmm) REVERT: D 435 TYR cc_start: 0.8543 (t80) cc_final: 0.7804 (t80) REVERT: F 621 GLU cc_start: 0.8295 (tp30) cc_final: 0.7781 (tp30) REVERT: I 34 MET cc_start: 0.9052 (mmm) cc_final: 0.8726 (mmp) REVERT: I 61 ASP cc_start: 0.9060 (p0) cc_final: 0.8461 (t0) REVERT: I 80 LEU cc_start: 0.9035 (tp) cc_final: 0.8491 (tp) REVERT: I 82 MET cc_start: 0.8930 (pmm) cc_final: 0.8460 (pmm) REVERT: I 100 TYR cc_start: 0.8505 (t80) cc_final: 0.8274 (t80) REVERT: I 107 THR cc_start: 0.9113 (m) cc_final: 0.8796 (p) REVERT: K 37 GLN cc_start: 0.8902 (pp30) cc_final: 0.8653 (pp30) REVERT: K 53 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8566 (tp-100) REVERT: K 71 PHE cc_start: 0.8943 (m-80) cc_final: 0.8553 (m-10) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1091 time to fit residues: 82.1449 Evaluate side-chains 360 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 40 optimal weight: 0.4980 chunk 78 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.054144 restraints weight = 77984.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.056273 restraints weight = 42698.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057796 restraints weight = 28159.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058854 restraints weight = 20774.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059650 restraints weight = 16638.007| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20520 Z= 0.152 Angle : 0.719 13.177 28050 Z= 0.349 Chirality : 0.049 0.622 3387 Planarity : 0.004 0.056 3375 Dihedral : 5.024 24.200 2520 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.49 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.16 (0.18), residues: 2310 helix: 0.72 (0.27), residues: 411 sheet: 0.45 (0.19), residues: 705 loop : -0.71 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 480 TYR 0.018 0.001 TYR A 435 PHE 0.042 0.002 PHE J 71 TRP 0.029 0.002 TRP A 96 HIS 0.010 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (20376) covalent geometry : angle 0.68403 / 0.34 (27657) SS BOND : bond 0.00362 / 0.22 ( 39) SS BOND : angle 1.19890 / 0.85 ( 78) hydrogen bonds : bond 0.04039 / 2.78 ( 747) hydrogen bonds : angle 5.61775 / 3.87 ( 1980) link_ALPHA1-2 : bond 0.00365 / 0.19 ( 3) link_ALPHA1-2 : angle 1.54864 / 1.12 ( 9) link_ALPHA1-3 : bond 0.00457 / 0.27 ( 6) link_ALPHA1-3 : angle 1.55043 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00674 / 0.34 ( 3) link_ALPHA1-6 : angle 1.83004 / 1.26 ( 9) link_BETA1-4 : bond 0.00328 / 0.22 ( 39) link_BETA1-4 : angle 1.42237 / 1.00 ( 117) link_NAG-ASN : bond 0.00408 / 0.30 ( 54) link_NAG-ASN : angle 2.61767 / 1.68 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8819 (m-40) cc_final: 0.8510 (p0) REVERT: A 94 ASN cc_start: 0.9454 (t0) cc_final: 0.9186 (t0) REVERT: A 95 MET cc_start: 0.9079 (ptm) cc_final: 0.8282 (ppp) REVERT: A 103 GLN cc_start: 0.9439 (mm110) cc_final: 0.9115 (tp40) REVERT: A 116 LEU cc_start: 0.8809 (mt) cc_final: 0.8526 (mt) REVERT: A 136 ASN cc_start: 0.8759 (m-40) cc_final: 0.8435 (m110) REVERT: A 256 SER cc_start: 0.8811 (p) cc_final: 0.8407 (p) REVERT: A 435 TYR cc_start: 0.8803 (t80) cc_final: 0.8438 (t80) REVERT: B 520 LEU cc_start: 0.8591 (mm) cc_final: 0.8043 (mt) REVERT: B 626 MET cc_start: 0.9052 (mmp) cc_final: 0.8665 (mmm) REVERT: B 653 GLN cc_start: 0.9324 (tt0) cc_final: 0.8918 (mt0) REVERT: H 61 ASP cc_start: 0.9062 (p0) cc_final: 0.8272 (t0) REVERT: H 82 MET cc_start: 0.8993 (pmm) cc_final: 0.8658 (pmm) REVERT: L 17 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8921 (mt-10) REVERT: L 18 LYS cc_start: 0.9283 (mmtt) cc_final: 0.8922 (mmmt) REVERT: L 21 ILE cc_start: 0.9488 (pt) cc_final: 0.9096 (mm) REVERT: L 37 GLN cc_start: 0.9086 (pp30) cc_final: 0.8730 (pp30) REVERT: L 73 LEU cc_start: 0.9289 (tp) cc_final: 0.9055 (tp) REVERT: C 49 GLU cc_start: 0.8685 (mp0) cc_final: 0.8372 (mm-30) REVERT: C 67 ASN cc_start: 0.8941 (m-40) cc_final: 0.8510 (p0) REVERT: C 256 SER cc_start: 0.8298 (m) cc_final: 0.7942 (t) REVERT: C 271 MET cc_start: 0.8595 (mmm) cc_final: 0.8086 (mmm) REVERT: C 381 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 426 MET cc_start: 0.9083 (ttp) cc_final: 0.8244 (ttm) REVERT: C 427 TRP cc_start: 0.7908 (m-10) cc_final: 0.6934 (m-90) REVERT: C 435 TYR cc_start: 0.8617 (t80) cc_final: 0.8030 (t80) REVERT: E 584 GLU cc_start: 0.9323 (tt0) cc_final: 0.9112 (tt0) REVERT: E 589 ASP cc_start: 0.9217 (m-30) cc_final: 0.8926 (m-30) REVERT: E 591 GLN cc_start: 0.9548 (tp40) cc_final: 0.9034 (tp40) REVERT: E 598 CYS cc_start: 0.7146 (m) cc_final: 0.6823 (m) REVERT: E 626 MET cc_start: 0.9015 (mmp) cc_final: 0.8680 (mmm) REVERT: E 634 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8923 (tt0) REVERT: G 33 ASP cc_start: 0.8155 (p0) cc_final: 0.7244 (p0) REVERT: G 61 ASP cc_start: 0.9127 (p0) cc_final: 0.8499 (t0) REVERT: J 23 CYS cc_start: 0.2940 (m) cc_final: 0.2728 (m) REVERT: J 27 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8312 (tm-30) REVERT: J 29 ILE cc_start: 0.9115 (tt) cc_final: 0.8845 (mm) REVERT: J 35 TRP cc_start: 0.8702 (m100) cc_final: 0.8394 (m100) REVERT: J 37 GLN cc_start: 0.9061 (pp30) cc_final: 0.8735 (pp30) REVERT: J 53 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8543 (tp-100) REVERT: J 78 LEU cc_start: 0.9505 (tp) cc_final: 0.9279 (tp) REVERT: J 92 ASN cc_start: 0.9172 (t0) cc_final: 0.8787 (m-40) REVERT: D 95 MET cc_start: 0.9255 (pmm) cc_final: 0.8959 (pmm) REVERT: D 104 MET cc_start: 0.9787 (ttt) cc_final: 0.9530 (ttt) REVERT: D 107 ASP cc_start: 0.9118 (m-30) cc_final: 0.8835 (m-30) REVERT: D 173 TYR cc_start: 0.8213 (p90) cc_final: 0.7870 (p90) REVERT: D 201 ILE cc_start: 0.9117 (mp) cc_final: 0.8783 (tp) REVERT: D 435 TYR cc_start: 0.8610 (t80) cc_final: 0.8164 (t80) REVERT: F 626 MET cc_start: 0.8930 (mmp) cc_final: 0.8698 (mmm) REVERT: I 34 MET cc_start: 0.9094 (mmm) cc_final: 0.8771 (mmp) REVERT: I 61 ASP cc_start: 0.9083 (p0) cc_final: 0.8441 (t0) REVERT: I 80 LEU cc_start: 0.8973 (tp) cc_final: 0.8305 (tp) REVERT: I 82 MET cc_start: 0.8893 (pmm) cc_final: 0.8397 (pmm) REVERT: I 100 TYR cc_start: 0.8543 (t80) cc_final: 0.8341 (t80) REVERT: I 107 THR cc_start: 0.9152 (m) cc_final: 0.8869 (p) REVERT: K 18 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8949 (mmmt) REVERT: K 37 GLN cc_start: 0.8895 (pp30) cc_final: 0.8657 (pp30) REVERT: K 53 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8552 (tp-100) REVERT: K 71 PHE cc_start: 0.8949 (m-80) cc_final: 0.8694 (m-10) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1088 time to fit residues: 82.3027 Evaluate side-chains 359 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 167 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.053849 restraints weight = 77774.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055998 restraints weight = 42298.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.057532 restraints weight = 27775.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058628 restraints weight = 20427.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059395 restraints weight = 16245.338| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20520 Z= 0.166 Angle : 0.720 13.088 28050 Z= 0.350 Chirality : 0.048 0.471 3387 Planarity : 0.004 0.052 3375 Dihedral : 5.001 25.281 2520 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.62 % Favored : 93.07 % Rotamer: Outliers : 0.05 % Allowed : 0.68 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.18), residues: 2310 helix: 0.48 (0.26), residues: 438 sheet: 0.42 (0.19), residues: 684 loop : -0.81 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 304 TYR 0.016 0.001 TYR H 100A PHE 0.021 0.002 PHE A 53 TRP 0.029 0.002 TRP A 96 HIS 0.009 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (20376) covalent geometry : angle 0.68426 / 0.34 (27657) SS BOND : bond 0.00362 / 0.21 ( 39) SS BOND : angle 1.17712 / 0.81 ( 78) hydrogen bonds : bond 0.04018 / 2.76 ( 747) hydrogen bonds : angle 5.56440 / 3.85 ( 1980) link_ALPHA1-2 : bond 0.00446 / 0.22 ( 3) link_ALPHA1-2 : angle 1.61186 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00473 / 0.27 ( 6) link_ALPHA1-3 : angle 1.57654 / 1.04 ( 18) link_ALPHA1-6 : bond 0.00591 / 0.30 ( 3) link_ALPHA1-6 : angle 1.83541 / 1.28 ( 9) link_BETA1-4 : bond 0.00305 / 0.19 ( 39) link_BETA1-4 : angle 1.42379 / 1.00 ( 117) link_NAG-ASN : bond 0.00451 / 0.31 ( 54) link_NAG-ASN : angle 2.64885 / 1.68 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 439 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8833 (m-40) cc_final: 0.8486 (p0) REVERT: A 94 ASN cc_start: 0.9451 (t0) cc_final: 0.9221 (t0) REVERT: A 95 MET cc_start: 0.9125 (ptm) cc_final: 0.8139 (ppp) REVERT: A 103 GLN cc_start: 0.9388 (mm110) cc_final: 0.9124 (tp40) REVERT: A 136 ASN cc_start: 0.8770 (m-40) cc_final: 0.8460 (m110) REVERT: A 161 MET cc_start: 0.8745 (tpp) cc_final: 0.8449 (tpp) REVERT: A 435 TYR cc_start: 0.8783 (t80) cc_final: 0.8416 (t80) REVERT: B 520 LEU cc_start: 0.8641 (mm) cc_final: 0.8092 (mt) REVERT: B 543 ASN cc_start: 0.9212 (t0) cc_final: 0.8989 (t0) REVERT: B 626 MET cc_start: 0.9022 (mmp) cc_final: 0.8661 (mmm) REVERT: B 653 GLN cc_start: 0.9323 (tt0) cc_final: 0.8854 (mt0) REVERT: H 61 ASP cc_start: 0.9068 (p0) cc_final: 0.8269 (t0) REVERT: H 80 LEU cc_start: 0.8908 (tp) cc_final: 0.8478 (tp) REVERT: H 82 MET cc_start: 0.8960 (pmm) cc_final: 0.8606 (pmm) REVERT: L 17 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8932 (mt-10) REVERT: L 18 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8800 (mmmt) REVERT: L 21 ILE cc_start: 0.9482 (pt) cc_final: 0.9064 (mm) REVERT: L 37 GLN cc_start: 0.9128 (pp30) cc_final: 0.8774 (pp30) REVERT: L 53 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8413 (tp-100) REVERT: L 73 LEU cc_start: 0.9251 (tp) cc_final: 0.8940 (tp) REVERT: C 49 GLU cc_start: 0.8612 (mp0) cc_final: 0.8299 (mm-30) REVERT: C 67 ASN cc_start: 0.8979 (m-40) cc_final: 0.8761 (m110) REVERT: C 136 ASN cc_start: 0.8818 (m110) cc_final: 0.8581 (m110) REVERT: C 161 MET cc_start: 0.8923 (tpp) cc_final: 0.8693 (tpp) REVERT: C 256 SER cc_start: 0.8353 (m) cc_final: 0.7980 (t) REVERT: C 435 TYR cc_start: 0.8626 (t80) cc_final: 0.7926 (t80) REVERT: E 584 GLU cc_start: 0.9306 (tt0) cc_final: 0.9101 (tt0) REVERT: E 589 ASP cc_start: 0.9201 (m-30) cc_final: 0.8906 (m-30) REVERT: E 591 GLN cc_start: 0.9532 (tp40) cc_final: 0.8963 (tp40) REVERT: E 598 CYS cc_start: 0.7093 (m) cc_final: 0.6807 (m) REVERT: E 626 MET cc_start: 0.9051 (mmp) cc_final: 0.8692 (mmm) REVERT: E 634 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8974 (tt0) REVERT: G 33 ASP cc_start: 0.8188 (p0) cc_final: 0.7346 (p0) REVERT: G 61 ASP cc_start: 0.9115 (p0) cc_final: 0.8451 (t0) REVERT: J 4 MET cc_start: 0.7906 (tpt) cc_final: 0.7587 (tpp) REVERT: J 27 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8361 (tm-30) REVERT: J 29 ILE cc_start: 0.9141 (tt) cc_final: 0.8867 (mm) REVERT: J 37 GLN cc_start: 0.9078 (pp30) cc_final: 0.8764 (pp30) REVERT: J 53 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8514 (tp-100) REVERT: J 78 LEU cc_start: 0.9572 (tp) cc_final: 0.9319 (tp) REVERT: J 92 ASN cc_start: 0.9061 (t0) cc_final: 0.8717 (t0) REVERT: D 95 MET cc_start: 0.9240 (pmm) cc_final: 0.8997 (pmm) REVERT: D 107 ASP cc_start: 0.9093 (m-30) cc_final: 0.8831 (m-30) REVERT: D 173 TYR cc_start: 0.8132 (p90) cc_final: 0.7846 (p90) REVERT: D 435 TYR cc_start: 0.8601 (t80) cc_final: 0.8173 (t80) REVERT: F 626 MET cc_start: 0.9302 (mmp) cc_final: 0.8541 (mmm) REVERT: I 61 ASP cc_start: 0.9072 (p0) cc_final: 0.8438 (t0) REVERT: I 80 LEU cc_start: 0.8970 (tp) cc_final: 0.8314 (tp) REVERT: I 82 MET cc_start: 0.8794 (pmm) cc_final: 0.8379 (pmm) REVERT: K 16 LYS cc_start: 0.9386 (tppt) cc_final: 0.9186 (mmmt) REVERT: K 18 LYS cc_start: 0.9243 (mmtt) cc_final: 0.8940 (mmmt) REVERT: K 37 GLN cc_start: 0.8911 (pp30) cc_final: 0.8669 (pp30) REVERT: K 53 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8559 (tp-100) REVERT: K 71 PHE cc_start: 0.8993 (m-80) cc_final: 0.8761 (m-10) outliers start: 1 outliers final: 0 residues processed: 440 average time/residue: 0.1056 time to fit residues: 78.0970 Evaluate side-chains 350 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 141 optimal weight: 0.0570 chunk 11 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** 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 = 0.3091 r_free = 0.3091 target = 0.066047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.053088 restraints weight = 79197.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055187 restraints weight = 42995.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056696 restraints weight = 28328.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057769 restraints weight = 20892.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058563 restraints weight = 16680.409| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20520 Z= 0.183 Angle : 0.743 13.255 28050 Z= 0.362 Chirality : 0.048 0.416 3387 Planarity : 0.004 0.050 3375 Dihedral : 5.081 26.132 2520 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.06 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.45 (0.17), residues: 2310 helix: 0.37 (0.25), residues: 438 sheet: 0.34 (0.18), residues: 702 loop : -0.93 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 476 TYR 0.019 0.002 TYR H 100A PHE 0.021 0.002 PHE A 53 TRP 0.040 0.002 TRP K 35 HIS 0.004 0.001 HIS J 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20376) covalent geometry : angle 0.70828 / 0.36 (27657) SS BOND : bond 0.00565 / 0.33 ( 39) SS BOND : angle 1.27649 / 0.85 ( 78) hydrogen bonds : bond 0.04166 / 2.85 ( 747) hydrogen bonds : angle 5.60523 / 3.89 ( 1980) link_ALPHA1-2 : bond 0.00359 / 0.18 ( 3) link_ALPHA1-2 : angle 1.60977 / 1.17 ( 9) link_ALPHA1-3 : bond 0.00480 / 0.28 ( 6) link_ALPHA1-3 : angle 1.60794 / 1.06 ( 18) link_ALPHA1-6 : bond 0.00483 / 0.24 ( 3) link_ALPHA1-6 : angle 1.83086 / 1.28 ( 9) link_BETA1-4 : bond 0.00299 / 0.20 ( 39) link_BETA1-4 : angle 1.45543 / 1.02 ( 117) link_NAG-ASN : bond 0.00444 / 0.30 ( 54) link_NAG-ASN : angle 2.66422 / 1.69 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8836 (m-40) cc_final: 0.8485 (p0) REVERT: A 94 ASN cc_start: 0.9452 (t0) cc_final: 0.9246 (t0) REVERT: A 95 MET cc_start: 0.9231 (ptm) cc_final: 0.8069 (ppp) REVERT: A 103 GLN cc_start: 0.9336 (mm110) cc_final: 0.8921 (tp-100) REVERT: A 161 MET cc_start: 0.8646 (tpp) cc_final: 0.8358 (tpp) REVERT: A 256 SER cc_start: 0.8821 (p) cc_final: 0.8404 (p) REVERT: A 271 MET cc_start: 0.9067 (mmp) cc_final: 0.8721 (mmm) REVERT: A 435 TYR cc_start: 0.8789 (t80) cc_final: 0.8330 (t80) REVERT: B 543 ASN cc_start: 0.9268 (t0) cc_final: 0.8974 (t0) REVERT: B 626 MET cc_start: 0.9082 (mmp) cc_final: 0.8663 (mmm) REVERT: B 653 GLN cc_start: 0.9303 (tt0) cc_final: 0.8845 (mt0) REVERT: B 657 GLU cc_start: 0.8874 (pp20) cc_final: 0.8549 (pp20) REVERT: H 61 ASP cc_start: 0.9064 (p0) cc_final: 0.8194 (t0) REVERT: L 18 LYS cc_start: 0.9257 (mmtt) cc_final: 0.8908 (mmmt) REVERT: L 21 ILE cc_start: 0.9477 (pt) cc_final: 0.9041 (mm) REVERT: L 37 GLN cc_start: 0.9143 (pp30) cc_final: 0.8776 (pp30) REVERT: L 53 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8415 (tp-100) REVERT: L 73 LEU cc_start: 0.9263 (tp) cc_final: 0.8963 (tp) REVERT: C 67 ASN cc_start: 0.8907 (m-40) cc_final: 0.8619 (m-40) REVERT: C 256 SER cc_start: 0.8349 (m) cc_final: 0.8095 (m) REVERT: C 271 MET cc_start: 0.8517 (mmm) cc_final: 0.8066 (mmm) REVERT: C 427 TRP cc_start: 0.7807 (m-10) cc_final: 0.7136 (m-90) REVERT: C 435 TYR cc_start: 0.8646 (t80) cc_final: 0.7916 (t80) REVERT: E 520 LEU cc_start: 0.8645 (mm) cc_final: 0.8076 (mt) REVERT: E 543 ASN cc_start: 0.9215 (t0) cc_final: 0.8958 (t0) REVERT: E 584 GLU cc_start: 0.9338 (tt0) cc_final: 0.9107 (tt0) REVERT: E 589 ASP cc_start: 0.9207 (m-30) cc_final: 0.8918 (m-30) REVERT: E 591 GLN cc_start: 0.9534 (tp40) cc_final: 0.8916 (tp40) REVERT: E 598 CYS cc_start: 0.7237 (m) cc_final: 0.6950 (m) REVERT: E 626 MET cc_start: 0.9086 (mmp) cc_final: 0.8763 (mmm) REVERT: G 61 ASP cc_start: 0.9159 (p0) cc_final: 0.8455 (t0) REVERT: G 78 LEU cc_start: 0.8942 (mt) cc_final: 0.8669 (mt) REVERT: J 37 GLN cc_start: 0.9085 (pp30) cc_final: 0.8776 (pp30) REVERT: J 53 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8542 (tp-100) REVERT: J 78 LEU cc_start: 0.9549 (tp) cc_final: 0.9319 (tp) REVERT: D 95 MET cc_start: 0.9230 (pmm) cc_final: 0.8939 (pmm) REVERT: D 107 ASP cc_start: 0.9143 (m-30) cc_final: 0.8883 (m-30) REVERT: D 173 TYR cc_start: 0.8136 (p90) cc_final: 0.7893 (p90) REVERT: D 435 TYR cc_start: 0.8647 (t80) cc_final: 0.8218 (t80) REVERT: D 475 MET cc_start: 0.8113 (mmt) cc_final: 0.7811 (mmt) REVERT: F 543 ASN cc_start: 0.9045 (t0) cc_final: 0.8813 (t0) REVERT: F 621 GLU cc_start: 0.8191 (tp30) cc_final: 0.7674 (tp30) REVERT: F 626 MET cc_start: 0.9330 (mmp) cc_final: 0.8602 (mmm) REVERT: I 61 ASP cc_start: 0.9057 (p0) cc_final: 0.8432 (t0) REVERT: I 80 LEU cc_start: 0.8975 (tp) cc_final: 0.8769 (tt) REVERT: K 16 LYS cc_start: 0.9402 (tppt) cc_final: 0.9170 (mmmt) REVERT: K 17 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8860 (mt-10) REVERT: K 18 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8903 (mmmt) REVERT: K 37 GLN cc_start: 0.8910 (pp30) cc_final: 0.8674 (pp30) REVERT: K 53 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8583 (tp-100) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1074 time to fit residues: 77.6878 Evaluate side-chains 349 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** 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 = 0.3081 r_free = 0.3081 target = 0.065624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.052653 restraints weight = 80394.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054751 restraints weight = 44100.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.056232 restraints weight = 29123.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.057285 restraints weight = 21531.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058058 restraints weight = 17277.861| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20520 Z= 0.183 Angle : 0.748 13.272 28050 Z= 0.367 Chirality : 0.049 0.389 3387 Planarity : 0.004 0.049 3375 Dihedral : 5.168 25.976 2520 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.45 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.51 (0.17), residues: 2310 helix: 0.41 (0.26), residues: 435 sheet: 0.27 (0.19), residues: 705 loop : -0.99 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 66 TYR 0.021 0.002 TYR H 100A PHE 0.019 0.002 PHE A 53 TRP 0.054 0.002 TRP K 35 HIS 0.012 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20376) covalent geometry : angle 0.71397 / 0.36 (27657) SS BOND : bond 0.00380 / 0.22 ( 39) SS BOND : angle 1.35473 / 0.89 ( 78) hydrogen bonds : bond 0.04194 / 2.84 ( 747) hydrogen bonds : angle 5.59150 / 3.86 ( 1980) link_ALPHA1-2 : bond 0.00332 / 0.17 ( 3) link_ALPHA1-2 : angle 1.62257 / 1.18 ( 9) link_ALPHA1-3 : bond 0.00464 / 0.27 ( 6) link_ALPHA1-3 : angle 1.59350 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00471 / 0.24 ( 3) link_ALPHA1-6 : angle 1.80273 / 1.26 ( 9) link_BETA1-4 : bond 0.00303 / 0.20 ( 39) link_BETA1-4 : angle 1.46109 / 1.03 ( 117) link_NAG-ASN : bond 0.00468 / 0.33 ( 54) link_NAG-ASN : angle 2.61759 / 1.64 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.59 seconds wall clock time: 54 minutes 5.01 seconds (3245.01 seconds total)