Starting phenix.real_space_refine on Fri Jul 3 20:49:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l86_23223/07_2026/7l86_23223.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 99 5.16 5 C 9831 2.51 5 N 2650 2.21 5 O 3222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15802 Number of models: 1 Model: "" Number of chains: 47 Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3442 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 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: "I" 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: "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: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.62, per 1000 atoms: 0.23 Number of scatterers: 15802 At special positions: 0 Unit cell: (141.11, 149.35, 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 99 16.00 O 3222 8.00 N 2650 7.00 C 9831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA V 3 " - " MAN V 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA V 3 " - " MAN V 5 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " 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 n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 137 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 137 " " NAG C 607 " - " ASN C 355 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 448 " " NAG E 605 " - " ASN E 88 " " NAG E 606 " - " ASN E 355 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN E 156 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 276 " " NAG N 1 " - " ASN E 295 " " NAG O 1 " - " ASN E 301 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN E 392 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 234 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 301 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 392 " " NAG c 1 " - " ASN A 156 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 234 " " NAG f 1 " - " ASN A 262 " " NAG g 1 " - " ASN A 276 " " NAG h 1 " - " ASN A 295 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 392 " " NAG l 1 " - " ASN A 448 " " NAG m 1 " - " ASN A 88 " " NAG n 1 " - " ASN A 462 " " NAG o 1 " - " ASN A 355 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 594.7 milliseconds 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 41 sheets defined 27.9% alpha, 75.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.967A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.049A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.168A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.165A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.667A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.358A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.016A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.723A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.250A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.985A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.262A 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 425 through 429 removed outlier: 4.394A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.837A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.831A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.651A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA5, first strand: chain 'L' and resid 61 through 64 removed outlier: 3.683A pdb=" N UNK L 74 " --> pdb=" O UNK L 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.436A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.826A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AB2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.200A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.298A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.770A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.298A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.770A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.916A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.859A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AC5, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.913A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.329A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.255A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.496A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.255A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.497A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.255A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.329A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.496A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.675A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.255A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.956A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.792A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.896A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.995A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.619A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.698A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.995A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.619A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3830 1.32 - 1.46: 5006 1.46 - 1.60: 7100 1.60 - 1.74: 13 1.74 - 1.88: 122 Bond restraints: 16071 Sorted by residual: bond pdb=" CB ASN E 289 " pdb=" CG ASN E 289 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.93e+01 bond pdb=" CB LEU E 125 " pdb=" CG LEU E 125 " ideal model delta sigma weight residual 1.530 1.424 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CB ASN E 195 " pdb=" CG ASN E 195 " ideal model delta sigma weight residual 1.516 1.386 0.130 2.50e-02 1.60e+03 2.70e+01 bond pdb=" CB ILE E 201 " pdb=" CG1 ILE E 201 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB HIS C 66 " pdb=" CG HIS C 66 " ideal model delta sigma weight residual 1.497 1.567 -0.070 1.40e-02 5.10e+03 2.52e+01 ... (remaining 16066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 17514 1.99 - 3.98: 3585 3.98 - 5.97: 641 5.97 - 7.97: 109 7.97 - 9.96: 14 Bond angle restraints: 21863 Sorted by residual: angle pdb=" C CYS E 239 " pdb=" N PRO E 240 " pdb=" CA PRO E 240 " ideal model delta sigma weight residual 119.56 127.86 -8.30 1.02e+00 9.61e-01 6.62e+01 angle pdb=" CA ASN E 195 " pdb=" CB ASN E 195 " pdb=" CG ASN E 195 " ideal model delta sigma weight residual 112.60 104.63 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.39 -7.83 1.02e+00 9.61e-01 5.89e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 126.92 -7.36 1.02e+00 9.61e-01 5.21e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 126.86 -7.30 1.02e+00 9.61e-01 5.12e+01 ... (remaining 21858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 8586 17.64 - 35.28: 219 35.28 - 52.92: 66 52.92 - 70.56: 16 70.56 - 88.20: 8 Dihedral angle restraints: 8895 sinusoidal: 3354 harmonic: 5541 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.57 -63.57 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 149.26 -56.26 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.47 -54.47 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 8892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1798 0.101 - 0.202: 608 0.202 - 0.302: 224 0.302 - 0.403: 119 0.403 - 0.504: 59 Chirality restraints: 2808 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 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 -2.65 0.25 2.00e-02 2.50e+03 1.60e+02 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.60e+02 ... (remaining 2805 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG o 2 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG o 2 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG o 2 " -0.083 2.00e-02 2.50e+03 pdb=" N2 NAG o 2 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG o 2 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG n 2 " 0.344 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG n 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG n 2 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG n 2 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG n 2 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG n 1 " -0.323 2.00e-02 2.50e+03 2.76e-01 9.53e+02 pdb=" C7 NAG n 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG n 1 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG n 1 " 0.485 2.00e-02 2.50e+03 pdb=" O7 NAG n 1 " -0.070 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5305 2.87 - 3.38: 14060 3.38 - 3.88: 25410 3.88 - 4.39: 29588 4.39 - 4.90: 47106 Nonbonded interactions: 121469 Sorted by model distance: nonbonded pdb=" N UNK H 67 " pdb=" N UNK H 68 " model vdw 2.361 2.560 nonbonded pdb=" OD1 ASP C 107 " pdb=" NZ LYS D 574 " model vdw 2.389 3.120 nonbonded pdb=" NZ LYS C 490 " pdb=" OE2 GLU C 492 " model vdw 2.397 3.120 nonbonded pdb=" N VAL A 75 " pdb=" O VAL A 75 " model vdw 2.424 2.496 nonbonded pdb=" N THR C 139 " pdb=" O THR C 139 " model vdw 2.430 2.496 ... (remaining 121464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 397 or resid 412 through 458 or resid 463 throu \ gh 605)) selection = (chain 'C' and (resid 33 through 397 or resid 412 through 605)) selection = (chain 'E' and (resid 33 through 57 or resid 66 through 397 or resid 412 through \ 605)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } ncs_group { reference = (chain 'H' and resid 16 through 120) selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'V' selection = chain 'f' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.140 16203 Z= 1.237 Angle : 1.739 10.619 22226 Z= 1.085 Chirality : 0.144 0.504 2808 Planarity : 0.015 0.298 2673 Dihedral : 9.632 88.204 5188 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.19), residues: 1646 helix: 0.51 (0.24), residues: 407 sheet: 1.06 (0.24), residues: 396 loop : 0.67 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 192 TYR 0.049 0.008 TYR C 486 PHE 0.029 0.006 PHE A 383 TRP 0.061 0.009 TRP E 69 HIS 0.009 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02286 / 1.21 (16071) covalent geometry : angle 1.69670 / 1.08 (21863) SS BOND : bond 0.01022 / 0.52 ( 33) SS BOND : angle 3.06925 / 1.56 ( 66) hydrogen bonds : bond 0.18084 / 9.99 ( 606) hydrogen bonds : angle 7.84221 / 4.53 ( 2142) link_ALPHA1-3 : bond 0.08143 / 4.07 ( 3) link_ALPHA1-3 : angle 4.36200 / 2.13 ( 9) link_ALPHA1-6 : bond 0.06118 / 3.05 ( 3) link_ALPHA1-6 : angle 4.00177 / 1.92 ( 9) link_BETA1-4 : bond 0.06698 / 3.65 ( 36) link_BETA1-4 : angle 4.57830 / 2.38 ( 108) link_NAG-ASN : bond 0.07010 / 3.87 ( 57) link_NAG-ASN : angle 2.51570 / 1.28 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 195 ASN cc_start: 0.8418 (p0) cc_final: 0.8084 (p0) REVERT: F 617 ARG cc_start: 0.8639 (mtt-85) cc_final: 0.8213 (mtp85) REVERT: C 51 THR cc_start: 0.9397 (m) cc_final: 0.8989 (p) REVERT: C 150 MET cc_start: 0.8771 (mmm) cc_final: 0.8537 (mmt) REVERT: C 482 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 636 SER cc_start: 0.8916 (t) cc_final: 0.8693 (t) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1488 time to fit residues: 73.8029 Evaluate side-chains 170 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 ASN E 66 HIS E 246 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 428 GLN D 590 GLN A 67 ASN A 85 HIS A 280 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 618 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097470 restraints weight = 29102.188| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.80 r_work: 0.3058 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16203 Z= 0.166 Angle : 0.749 15.454 22226 Z= 0.365 Chirality : 0.046 0.266 2808 Planarity : 0.004 0.051 2673 Dihedral : 4.805 23.621 2005 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.73 % Allowed : 7.33 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.21), residues: 1646 helix: 2.13 (0.26), residues: 400 sheet: 0.91 (0.25), residues: 407 loop : 0.47 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 178 TYR 0.011 0.001 TYR C 173 PHE 0.015 0.002 PHE A 353 TRP 0.016 0.002 TRP E 96 HIS 0.005 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16071) covalent geometry : angle 0.69152 / 0.35 (21863) SS BOND : bond 0.00429 / 0.22 ( 33) SS BOND : angle 1.38394 / 0.66 ( 66) hydrogen bonds : bond 0.06506 / 3.54 ( 606) hydrogen bonds : angle 5.50208 / 3.10 ( 2142) link_ALPHA1-3 : bond 0.01128 / 0.56 ( 3) link_ALPHA1-3 : angle 1.26137 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00691 / 0.34 ( 3) link_ALPHA1-6 : angle 1.50234 / 0.80 ( 9) link_BETA1-4 : bond 0.00782 / 0.43 ( 36) link_BETA1-4 : angle 2.51281 / 1.29 ( 108) link_NAG-ASN : bond 0.00500 / 0.28 ( 57) link_NAG-ASN : angle 2.61253 / 1.33 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9100 (mt) cc_final: 0.8784 (tp) REVERT: E 475 MET cc_start: 0.8571 (mmm) cc_final: 0.8355 (mmp) REVERT: F 621 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 51 THR cc_start: 0.9439 (m) cc_final: 0.9219 (p) REVERT: C 482 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8346 (mm-30) REVERT: D 660 LEU cc_start: 0.8813 (mp) cc_final: 0.8180 (tt) REVERT: A 325 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8547 (t0) REVERT: B 640 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7989 (mp10) outliers start: 26 outliers final: 13 residues processed: 242 average time/residue: 0.1158 time to fit residues: 42.8496 Evaluate side-chains 190 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 640 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 148 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 ASN E 66 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN C 280 ASN C 422 GLN A 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.091942 restraints weight = 29795.312| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.78 r_work: 0.2972 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16203 Z= 0.259 Angle : 0.742 10.705 22226 Z= 0.361 Chirality : 0.047 0.298 2808 Planarity : 0.005 0.045 2673 Dihedral : 4.810 20.068 2005 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.07 % Allowed : 9.79 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.20), residues: 1646 helix: 1.74 (0.26), residues: 412 sheet: 0.87 (0.26), residues: 396 loop : -0.02 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 617 TYR 0.018 0.002 TYR F 586 PHE 0.024 0.003 PHE F 522 TRP 0.015 0.002 TRP C 45 HIS 0.006 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 (16071) covalent geometry : angle 0.70204 / 0.35 (21863) SS BOND : bond 0.00711 / 0.37 ( 33) SS BOND : angle 1.50592 / 0.70 ( 66) hydrogen bonds : bond 0.05780 / 3.15 ( 606) hydrogen bonds : angle 5.06433 / 2.87 ( 2142) link_ALPHA1-3 : bond 0.00690 / 0.35 ( 3) link_ALPHA1-3 : angle 1.73048 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00695 / 0.34 ( 3) link_ALPHA1-6 : angle 1.55308 / 0.79 ( 9) link_BETA1-4 : bond 0.00502 / 0.26 ( 36) link_BETA1-4 : angle 1.94789 / 1.00 ( 108) link_NAG-ASN : bond 0.00459 / 0.28 ( 57) link_NAG-ASN : angle 2.24216 / 1.17 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8721 (mmm) cc_final: 0.8305 (mmp) REVERT: C 51 THR cc_start: 0.9430 (m) cc_final: 0.9201 (p) REVERT: C 199 SER cc_start: 0.8672 (t) cc_final: 0.8303 (t) REVERT: C 482 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8435 (mm-30) REVERT: D 634 GLU cc_start: 0.8518 (tt0) cc_final: 0.8298 (tt0) REVERT: D 660 LEU cc_start: 0.8985 (mp) cc_final: 0.8399 (tt) REVERT: D 663 LEU cc_start: 0.7561 (mm) cc_final: 0.7139 (mm) REVERT: A 325 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8622 (t0) REVERT: A 485 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8467 (mtpt) REVERT: B 543 ASN cc_start: 0.8812 (m-40) cc_final: 0.8508 (t0) REVERT: B 571 TRP cc_start: 0.6759 (m100) cc_final: 0.6425 (m100) REVERT: B 584 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8259 (mt-10) outliers start: 31 outliers final: 19 residues processed: 205 average time/residue: 0.1136 time to fit residues: 35.2516 Evaluate side-chains 187 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 180 optimal weight: 0.2980 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 0.0670 chunk 158 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS C 377 ASN C 440 GLN A 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095922 restraints weight = 29160.838| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.79 r_work: 0.3038 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16203 Z= 0.108 Angle : 0.576 8.308 22226 Z= 0.281 Chirality : 0.042 0.209 2808 Planarity : 0.004 0.037 2673 Dihedral : 4.342 18.003 2005 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.27 % Allowed : 10.39 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.20), residues: 1646 helix: 2.31 (0.26), residues: 400 sheet: 0.96 (0.26), residues: 388 loop : 0.04 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 617 TYR 0.015 0.001 TYR F 586 PHE 0.009 0.001 PHE A 353 TRP 0.010 0.001 TRP E 96 HIS 0.004 0.000 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (16071) covalent geometry : angle 0.54147 / 0.27 (21863) SS BOND : bond 0.00381 / 0.19 ( 33) SS BOND : angle 0.99664 / 0.45 ( 66) hydrogen bonds : bond 0.04415 / 2.39 ( 606) hydrogen bonds : angle 4.52600 / 2.55 ( 2142) link_ALPHA1-3 : bond 0.00718 / 0.36 ( 3) link_ALPHA1-3 : angle 1.30780 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00633 / 0.31 ( 3) link_ALPHA1-6 : angle 1.53789 / 0.79 ( 9) link_BETA1-4 : bond 0.00489 / 0.26 ( 36) link_BETA1-4 : angle 1.57456 / 0.82 ( 108) link_NAG-ASN : bond 0.00240 / 0.13 ( 57) link_NAG-ASN : angle 1.85317 / 0.94 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 125 LEU cc_start: 0.8767 (tp) cc_final: 0.8532 (tp) REVERT: E 201 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8511 (mt) REVERT: E 368 ASP cc_start: 0.7236 (p0) cc_final: 0.6751 (p0) REVERT: E 370 GLU cc_start: 0.7723 (tt0) cc_final: 0.7490 (pt0) REVERT: E 475 MET cc_start: 0.8631 (mmm) cc_final: 0.8281 (mmp) REVERT: F 599 SER cc_start: 0.9042 (t) cc_final: 0.8815 (t) REVERT: F 621 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7192 (tm-30) REVERT: F 639 THR cc_start: 0.8922 (m) cc_final: 0.8669 (p) REVERT: C 51 THR cc_start: 0.9387 (m) cc_final: 0.9173 (p) REVERT: C 199 SER cc_start: 0.8479 (t) cc_final: 0.8138 (t) REVERT: C 482 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8339 (mm-30) REVERT: D 617 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8261 (mtt-85) REVERT: D 634 GLU cc_start: 0.8431 (tt0) cc_final: 0.7720 (tt0) REVERT: D 660 LEU cc_start: 0.8943 (mp) cc_final: 0.8486 (tt) REVERT: D 663 LEU cc_start: 0.7442 (mm) cc_final: 0.7024 (mm) REVERT: B 640 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8093 (mp10) outliers start: 19 outliers final: 8 residues processed: 206 average time/residue: 0.1155 time to fit residues: 35.8875 Evaluate side-chains 193 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 640 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092899 restraints weight = 29722.954| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.78 r_work: 0.2986 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16203 Z= 0.181 Angle : 0.621 7.598 22226 Z= 0.301 Chirality : 0.044 0.212 2808 Planarity : 0.004 0.044 2673 Dihedral : 4.360 16.892 2005 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.93 % Allowed : 10.33 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.21), residues: 1646 helix: 2.24 (0.26), residues: 400 sheet: 0.81 (0.26), residues: 403 loop : -0.10 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.018 0.001 TYR A 173 PHE 0.016 0.002 PHE C 53 TRP 0.011 0.001 TRP A 96 HIS 0.005 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (16071) covalent geometry : angle 0.58856 / 0.29 (21863) SS BOND : bond 0.00544 / 0.28 ( 33) SS BOND : angle 1.32907 / 0.57 ( 66) hydrogen bonds : bond 0.04819 / 2.61 ( 606) hydrogen bonds : angle 4.54057 / 2.57 ( 2142) link_ALPHA1-3 : bond 0.00687 / 0.35 ( 3) link_ALPHA1-3 : angle 1.59090 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00588 / 0.29 ( 3) link_ALPHA1-6 : angle 1.53391 / 0.79 ( 9) link_BETA1-4 : bond 0.00450 / 0.23 ( 36) link_BETA1-4 : angle 1.63490 / 0.84 ( 108) link_NAG-ASN : bond 0.00272 / 0.15 ( 57) link_NAG-ASN : angle 1.80988 / 0.93 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8549 (mt) REVERT: E 368 ASP cc_start: 0.7393 (p0) cc_final: 0.6534 (p0) REVERT: E 475 MET cc_start: 0.8706 (mmm) cc_final: 0.8364 (mmp) REVERT: F 621 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7478 (tm-30) REVERT: F 639 THR cc_start: 0.8975 (m) cc_final: 0.8685 (p) REVERT: C 51 THR cc_start: 0.9359 (m) cc_final: 0.9111 (p) REVERT: C 199 SER cc_start: 0.8545 (t) cc_final: 0.8165 (t) REVERT: C 482 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 617 ARG cc_start: 0.8787 (mtt-85) cc_final: 0.8316 (mtt-85) REVERT: D 634 GLU cc_start: 0.8487 (tt0) cc_final: 0.7752 (tt0) REVERT: D 660 LEU cc_start: 0.8977 (mp) cc_final: 0.8527 (tt) REVERT: D 663 LEU cc_start: 0.7475 (mm) cc_final: 0.7044 (mm) REVERT: B 640 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8179 (mp10) outliers start: 29 outliers final: 16 residues processed: 199 average time/residue: 0.1186 time to fit residues: 35.4667 Evaluate side-chains 198 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 640 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 182 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN B 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.092157 restraints weight = 29489.483| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.77 r_work: 0.2978 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16203 Z= 0.189 Angle : 0.620 10.919 22226 Z= 0.300 Chirality : 0.044 0.232 2808 Planarity : 0.004 0.044 2673 Dihedral : 4.380 17.750 2005 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.00 % Allowed : 10.79 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.21), residues: 1646 helix: 2.08 (0.26), residues: 402 sheet: 0.50 (0.25), residues: 434 loop : -0.20 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.019 0.001 TYR A 173 PHE 0.014 0.002 PHE E 53 TRP 0.011 0.001 TRP A 96 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (16071) covalent geometry : angle 0.59104 / 0.29 (21863) SS BOND : bond 0.00489 / 0.25 ( 33) SS BOND : angle 1.18868 / 0.52 ( 66) hydrogen bonds : bond 0.04758 / 2.58 ( 606) hydrogen bonds : angle 4.47381 / 2.54 ( 2142) link_ALPHA1-3 : bond 0.00737 / 0.38 ( 3) link_ALPHA1-3 : angle 1.49631 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00587 / 0.29 ( 3) link_ALPHA1-6 : angle 1.54228 / 0.80 ( 9) link_BETA1-4 : bond 0.00449 / 0.24 ( 36) link_BETA1-4 : angle 1.55256 / 0.80 ( 108) link_NAG-ASN : bond 0.00259 / 0.14 ( 57) link_NAG-ASN : angle 1.73102 / 0.89 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8680 (mmm) cc_final: 0.8281 (mmp) REVERT: F 617 ARG cc_start: 0.9003 (mtp85) cc_final: 0.8743 (mtp85) REVERT: F 621 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7725 (tm-30) REVERT: F 639 THR cc_start: 0.9020 (m) cc_final: 0.8713 (p) REVERT: C 42 VAL cc_start: 0.9121 (t) cc_final: 0.8873 (m) REVERT: C 199 SER cc_start: 0.8651 (t) cc_final: 0.8285 (t) REVERT: C 482 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8418 (mm-30) REVERT: D 542 ARG cc_start: 0.8906 (ptm160) cc_final: 0.8704 (ptm160) REVERT: D 617 ARG cc_start: 0.8811 (mtt-85) cc_final: 0.8287 (mtt-85) REVERT: D 634 GLU cc_start: 0.8530 (tt0) cc_final: 0.7790 (tt0) REVERT: D 660 LEU cc_start: 0.8968 (mp) cc_final: 0.8506 (tt) REVERT: B 584 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8199 (mt-10) REVERT: B 640 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8182 (mp10) outliers start: 30 outliers final: 19 residues processed: 208 average time/residue: 0.1226 time to fit residues: 37.4993 Evaluate side-chains 200 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS F 543 ASN C 440 GLN ** B 607 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 = 0.3357 r_free = 0.3357 target = 0.108571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.089865 restraints weight = 29608.651| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.76 r_work: 0.2940 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16203 Z= 0.269 Angle : 0.714 8.712 22226 Z= 0.342 Chirality : 0.046 0.222 2808 Planarity : 0.004 0.049 2673 Dihedral : 4.630 18.216 2005 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.87 % Allowed : 11.46 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.21), residues: 1646 helix: 1.78 (0.26), residues: 406 sheet: 0.38 (0.25), residues: 438 loop : -0.37 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 456 TYR 0.019 0.002 TYR A 173 PHE 0.019 0.002 PHE C 53 TRP 0.013 0.001 TRP A 96 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.27 (16071) covalent geometry : angle 0.68410 / 0.34 (21863) SS BOND : bond 0.00548 / 0.29 ( 33) SS BOND : angle 1.29501 / 0.60 ( 66) hydrogen bonds : bond 0.05427 / 2.94 ( 606) hydrogen bonds : angle 4.71976 / 2.68 ( 2142) link_ALPHA1-3 : bond 0.00649 / 0.34 ( 3) link_ALPHA1-3 : angle 1.69722 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00598 / 0.30 ( 3) link_ALPHA1-6 : angle 1.60647 / 0.83 ( 9) link_BETA1-4 : bond 0.00446 / 0.23 ( 36) link_BETA1-4 : angle 1.72742 / 0.89 ( 108) link_NAG-ASN : bond 0.00421 / 0.22 ( 57) link_NAG-ASN : angle 1.89007 / 0.98 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8704 (mmm) cc_final: 0.8315 (mmp) REVERT: F 617 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8625 (mtp85) REVERT: F 621 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7750 (tm-30) REVERT: F 639 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8768 (p) REVERT: C 42 VAL cc_start: 0.9170 (t) cc_final: 0.8926 (m) REVERT: C 199 SER cc_start: 0.8815 (t) cc_final: 0.8437 (t) REVERT: C 482 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8419 (mm-30) REVERT: D 617 ARG cc_start: 0.8820 (mtt-85) cc_final: 0.8321 (mtt-85) REVERT: D 634 GLU cc_start: 0.8560 (tt0) cc_final: 0.7835 (tt0) REVERT: D 660 LEU cc_start: 0.8985 (mp) cc_final: 0.8420 (tt) REVERT: B 543 ASN cc_start: 0.8710 (m-40) cc_final: 0.8399 (t0) REVERT: B 584 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8236 (mt-10) outliers start: 28 outliers final: 22 residues processed: 189 average time/residue: 0.1195 time to fit residues: 33.8666 Evaluate side-chains 195 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN ** B 607 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 = 0.3392 r_free = 0.3392 target = 0.110952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.092290 restraints weight = 29554.073| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.76 r_work: 0.2981 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16203 Z= 0.150 Angle : 0.596 8.432 22226 Z= 0.287 Chirality : 0.042 0.220 2808 Planarity : 0.004 0.044 2673 Dihedral : 4.358 16.647 2005 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.53 % Allowed : 11.73 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.21), residues: 1646 helix: 2.31 (0.27), residues: 393 sheet: 0.44 (0.25), residues: 430 loop : -0.32 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.020 0.001 TYR A 173 PHE 0.011 0.001 PHE E 53 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (16071) covalent geometry : angle 0.56677 / 0.28 (21863) SS BOND : bond 0.00505 / 0.26 ( 33) SS BOND : angle 1.18923 / 0.50 ( 66) hydrogen bonds : bond 0.04516 / 2.44 ( 606) hydrogen bonds : angle 4.38920 / 2.49 ( 2142) link_ALPHA1-3 : bond 0.00743 / 0.38 ( 3) link_ALPHA1-3 : angle 1.46065 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00566 / 0.28 ( 3) link_ALPHA1-6 : angle 1.55245 / 0.81 ( 9) link_BETA1-4 : bond 0.00443 / 0.23 ( 36) link_BETA1-4 : angle 1.49200 / 0.77 ( 108) link_NAG-ASN : bond 0.00218 / 0.12 ( 57) link_NAG-ASN : angle 1.68785 / 0.86 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8583 (mmm) cc_final: 0.8161 (mmp) REVERT: F 599 SER cc_start: 0.9089 (t) cc_final: 0.8817 (t) REVERT: F 617 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8613 (mtp85) REVERT: C 42 VAL cc_start: 0.9127 (t) cc_final: 0.8876 (m) REVERT: C 199 SER cc_start: 0.8730 (t) cc_final: 0.8370 (t) REVERT: C 482 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8325 (mm-30) REVERT: D 617 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.8238 (mtt-85) REVERT: D 634 GLU cc_start: 0.8522 (tt0) cc_final: 0.7857 (tt0) REVERT: D 660 LEU cc_start: 0.8949 (mp) cc_final: 0.8509 (tt) REVERT: B 543 ASN cc_start: 0.8705 (m-40) cc_final: 0.8473 (t0) REVERT: B 584 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 640 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8188 (mp10) outliers start: 23 outliers final: 17 residues processed: 204 average time/residue: 0.1239 time to fit residues: 37.3510 Evaluate side-chains 198 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 640 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS C 85 HIS C 440 GLN ** B 607 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 = 0.3418 r_free = 0.3418 target = 0.112644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094119 restraints weight = 29165.665| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.76 r_work: 0.3013 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16203 Z= 0.116 Angle : 0.560 8.746 22226 Z= 0.270 Chirality : 0.042 0.215 2808 Planarity : 0.004 0.040 2673 Dihedral : 4.143 18.833 2005 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.13 % Allowed : 12.33 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.21), residues: 1646 helix: 2.42 (0.27), residues: 396 sheet: 0.45 (0.25), residues: 434 loop : -0.20 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.020 0.001 TYR A 173 PHE 0.008 0.001 PHE C 53 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.000 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16071) covalent geometry : angle 0.53237 / 0.26 (21863) SS BOND : bond 0.00403 / 0.20 ( 33) SS BOND : angle 1.10298 / 0.49 ( 66) hydrogen bonds : bond 0.04046 / 2.19 ( 606) hydrogen bonds : angle 4.19517 / 2.38 ( 2142) link_ALPHA1-3 : bond 0.00694 / 0.36 ( 3) link_ALPHA1-3 : angle 1.44541 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00544 / 0.27 ( 3) link_ALPHA1-6 : angle 1.51669 / 0.80 ( 9) link_BETA1-4 : bond 0.00443 / 0.23 ( 36) link_BETA1-4 : angle 1.45726 / 0.75 ( 108) link_NAG-ASN : bond 0.00193 / 0.10 ( 57) link_NAG-ASN : angle 1.56367 / 0.79 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: E 475 MET cc_start: 0.8530 (mmm) cc_final: 0.8027 (mmp) REVERT: F 599 SER cc_start: 0.8976 (t) cc_final: 0.8700 (t) REVERT: C 42 VAL cc_start: 0.9095 (t) cc_final: 0.8828 (m) REVERT: C 112 TRP cc_start: 0.8700 (t-100) cc_final: 0.8158 (t-100) REVERT: C 121 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8658 (mttp) REVERT: C 199 SER cc_start: 0.8776 (t) cc_final: 0.8408 (t) REVERT: C 482 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8255 (mm-30) REVERT: D 617 ARG cc_start: 0.8785 (mtt-85) cc_final: 0.8077 (ttm110) REVERT: D 660 LEU cc_start: 0.8960 (mp) cc_final: 0.8510 (tt) REVERT: A 69 TRP cc_start: 0.7408 (m100) cc_final: 0.6965 (m100) REVERT: B 543 ASN cc_start: 0.8651 (m-40) cc_final: 0.8408 (t0) outliers start: 17 outliers final: 14 residues processed: 199 average time/residue: 0.1183 time to fit residues: 35.1422 Evaluate side-chains 199 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS F 640 GLN C 66 HIS C 440 GLN ** B 607 ASN ** 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 = 0.3401 r_free = 0.3401 target = 0.111381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092710 restraints weight = 29283.995| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.76 r_work: 0.2990 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16203 Z= 0.159 Angle : 0.593 11.685 22226 Z= 0.285 Chirality : 0.043 0.418 2808 Planarity : 0.004 0.047 2673 Dihedral : 4.182 19.334 2005 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.07 % Allowed : 12.79 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.21), residues: 1646 helix: 2.32 (0.27), residues: 402 sheet: 0.51 (0.25), residues: 428 loop : -0.22 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.020 0.001 TYR A 173 PHE 0.011 0.001 PHE C 53 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (16071) covalent geometry : angle 0.56014 / 0.28 (21863) SS BOND : bond 0.00430 / 0.22 ( 33) SS BOND : angle 1.19447 / 0.55 ( 66) hydrogen bonds : bond 0.04316 / 2.34 ( 606) hydrogen bonds : angle 4.23030 / 2.39 ( 2142) link_ALPHA1-3 : bond 0.00645 / 0.33 ( 3) link_ALPHA1-3 : angle 1.48527 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00517 / 0.26 ( 3) link_ALPHA1-6 : angle 1.50470 / 0.80 ( 9) link_BETA1-4 : bond 0.00426 / 0.22 ( 36) link_BETA1-4 : angle 1.49750 / 0.77 ( 108) link_NAG-ASN : bond 0.00259 / 0.15 ( 57) link_NAG-ASN : angle 1.84938 / 0.97 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8585 (mmm) cc_final: 0.8094 (mmp) REVERT: C 42 VAL cc_start: 0.9115 (t) cc_final: 0.8865 (m) REVERT: C 112 TRP cc_start: 0.8723 (t-100) cc_final: 0.8219 (t-100) REVERT: C 121 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8671 (mttp) REVERT: C 136 ASN cc_start: 0.7626 (p0) cc_final: 0.7396 (t0) REVERT: C 199 SER cc_start: 0.8794 (t) cc_final: 0.8407 (t) REVERT: C 482 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8273 (mm-30) REVERT: D 617 ARG cc_start: 0.8838 (mtt-85) cc_final: 0.8174 (ttm110) REVERT: D 660 LEU cc_start: 0.8941 (mp) cc_final: 0.8546 (tt) REVERT: A 69 TRP cc_start: 0.7458 (m100) cc_final: 0.7032 (m100) REVERT: B 584 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8149 (mt-10) outliers start: 16 outliers final: 13 residues processed: 192 average time/residue: 0.1304 time to fit residues: 37.2908 Evaluate side-chains 192 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 529 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 171 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 122 optimal weight: 0.0270 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS C 440 GLN B 543 ASN ** B 607 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 = 0.3426 r_free = 0.3426 target = 0.113148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094638 restraints weight = 29345.146| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.76 r_work: 0.3020 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16203 Z= 0.108 Angle : 0.544 9.409 22226 Z= 0.263 Chirality : 0.042 0.353 2808 Planarity : 0.004 0.040 2673 Dihedral : 4.036 18.997 2005 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.07 % Allowed : 12.79 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.21), residues: 1646 helix: 2.56 (0.27), residues: 396 sheet: 0.60 (0.26), residues: 419 loop : -0.15 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 617 TYR 0.021 0.001 TYR A 173 PHE 0.007 0.001 PHE C 53 TRP 0.013 0.001 TRP E 96 HIS 0.002 0.000 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16071) covalent geometry : angle 0.51482 / 0.26 (21863) SS BOND : bond 0.00363 / 0.18 ( 33) SS BOND : angle 0.99356 / 0.45 ( 66) hydrogen bonds : bond 0.03889 / 2.11 ( 606) hydrogen bonds : angle 4.07290 / 2.30 ( 2142) link_ALPHA1-3 : bond 0.00649 / 0.33 ( 3) link_ALPHA1-3 : angle 1.40822 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00506 / 0.25 ( 3) link_ALPHA1-6 : angle 1.48665 / 0.79 ( 9) link_BETA1-4 : bond 0.00428 / 0.23 ( 36) link_BETA1-4 : angle 1.41544 / 0.73 ( 108) link_NAG-ASN : bond 0.00204 / 0.12 ( 57) link_NAG-ASN : angle 1.63910 / 0.85 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.94 seconds wall clock time: 51 minutes 47.33 seconds (3107.33 seconds total)