Starting phenix.real_space_refine on Wed Mar 4 20:24:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l86_23223/03_2026/7l86_23223.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l86_23223/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7l86_23223/03_2026/7l86_23223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l86_23223/03_2026/7l86_23223.map" model { file = "/net/cci-nas-00/data/ceres_data/7l86_23223/03_2026/7l86_23223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l86_23223/03_2026/7l86_23223.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.32, per 1000 atoms: 0.21 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: 1.39 Conformation dependent library (CDL) restraints added in 565.2 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: 0.89 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: 2.95 Time building geometry restraints manager: 1.78 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 - 21.26: 10630 21.26 - 42.52: 227 42.52 - 63.77: 58 63.77 - 85.03: 28 85.03 - 106.29: 13 Dihedral angle restraints: 10956 sinusoidal: 5415 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 10953 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:1.270 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 10.850 106.288 7249 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 covalent geometry : bond 0.02286 (16071) covalent geometry : angle 1.69670 (21863) SS BOND : bond 0.01022 ( 33) SS BOND : angle 3.06925 ( 66) hydrogen bonds : bond 0.18084 ( 606) hydrogen bonds : angle 7.84221 ( 2142) link_ALPHA1-3 : bond 0.08143 ( 3) link_ALPHA1-3 : angle 4.36200 ( 9) link_ALPHA1-6 : bond 0.06118 ( 3) link_ALPHA1-6 : angle 4.00177 ( 9) link_BETA1-4 : bond 0.06698 ( 36) link_BETA1-4 : angle 4.57830 ( 108) link_NAG-ASN : bond 0.07010 ( 57) link_NAG-ASN : angle 2.51570 ( 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 : 0.400 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: 0.1491 time to fit residues: 73.4444 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 : 0.534 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3472 r_free = 0.3472 target = 0.116288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097493 restraints weight = 29106.270| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.80 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16203 Z= 0.172 Angle : 0.744 16.016 22226 Z= 0.363 Chirality : 0.047 0.252 2808 Planarity : 0.004 0.057 2673 Dihedral : 8.534 84.487 4066 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.67 % Allowed : 7.40 % 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 : 0.46 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 617 TYR 0.012 0.001 TYR D 643 PHE 0.016 0.002 PHE A 383 TRP 0.015 0.002 TRP E 96 HIS 0.005 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00378 (16071) covalent geometry : angle 0.68465 (21863) SS BOND : bond 0.00332 ( 33) SS BOND : angle 1.46011 ( 66) hydrogen bonds : bond 0.06376 ( 606) hydrogen bonds : angle 5.46678 ( 2142) link_ALPHA1-3 : bond 0.01558 ( 3) link_ALPHA1-3 : angle 1.58339 ( 9) link_ALPHA1-6 : bond 0.00712 ( 3) link_ALPHA1-6 : angle 1.88382 ( 9) link_BETA1-4 : bond 0.00797 ( 36) link_BETA1-4 : angle 2.56874 ( 108) link_NAG-ASN : bond 0.00509 ( 57) link_NAG-ASN : angle 2.57577 ( 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 257 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9113 (mt) cc_final: 0.8812 (tp) REVERT: E 475 MET cc_start: 0.8569 (mmm) cc_final: 0.8323 (mmp) REVERT: F 621 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6726 (tm-30) REVERT: C 51 THR cc_start: 0.9438 (m) cc_final: 0.9225 (p) REVERT: C 150 MET cc_start: 0.8818 (mmm) cc_final: 0.8588 (mmt) REVERT: C 482 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8347 (mm-30) REVERT: D 633 LYS cc_start: 0.8897 (mttm) cc_final: 0.8636 (mptt) REVERT: D 634 GLU cc_start: 0.8537 (tt0) cc_final: 0.8085 (tt0) REVERT: D 654 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: D 660 LEU cc_start: 0.8817 (mp) cc_final: 0.8179 (tt) REVERT: A 302 ASN cc_start: 0.8110 (m110) cc_final: 0.7817 (p0) REVERT: A 325 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (t0) REVERT: A 439 ILE cc_start: 0.8758 (mt) cc_final: 0.8233 (mt) REVERT: B 640 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8007 (mp10) outliers start: 25 outliers final: 10 residues processed: 249 average time/residue: 0.1135 time to fit residues: 43.0007 Evaluate side-chains 186 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 184 ILE 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 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: 0.9990 chunk 95 optimal weight: 0.4980 chunk 176 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093363 restraints weight = 29599.776| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.82 r_work: 0.2992 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16203 Z= 0.218 Angle : 0.701 10.925 22226 Z= 0.342 Chirality : 0.046 0.224 2808 Planarity : 0.004 0.042 2673 Dihedral : 7.772 72.713 4066 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.00 % Allowed : 9.79 % Favored : 88.21 % 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: 1.12 (0.20), residues: 1646 helix: 2.08 (0.26), residues: 400 sheet: 0.91 (0.26), residues: 396 loop : 0.08 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 298 TYR 0.017 0.002 TYR F 586 PHE 0.022 0.002 PHE F 522 TRP 0.013 0.001 TRP C 45 HIS 0.006 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00520 (16071) covalent geometry : angle 0.65559 (21863) SS BOND : bond 0.00520 ( 33) SS BOND : angle 1.53345 ( 66) hydrogen bonds : bond 0.05538 ( 606) hydrogen bonds : angle 4.98719 ( 2142) link_ALPHA1-3 : bond 0.01286 ( 3) link_ALPHA1-3 : angle 1.31825 ( 9) link_ALPHA1-6 : bond 0.00811 ( 3) link_ALPHA1-6 : angle 1.86175 ( 9) link_BETA1-4 : bond 0.00553 ( 36) link_BETA1-4 : angle 2.02705 ( 108) link_NAG-ASN : bond 0.00317 ( 57) link_NAG-ASN : angle 2.24924 ( 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 209 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8622 (mmm) cc_final: 0.8162 (mmp) REVERT: F 617 ARG cc_start: 0.9045 (mtp85) cc_final: 0.8797 (mtp85) REVERT: C 51 THR cc_start: 0.9432 (m) cc_final: 0.9207 (p) REVERT: C 199 SER cc_start: 0.8564 (t) cc_final: 0.8164 (t) REVERT: C 482 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8389 (mm-30) REVERT: D 660 LEU cc_start: 0.9004 (mp) cc_final: 0.8417 (tt) REVERT: D 663 LEU cc_start: 0.7500 (mm) cc_final: 0.7094 (mm) REVERT: A 325 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8606 (t0) REVERT: B 543 ASN cc_start: 0.8771 (m-40) cc_final: 0.8474 (t0) outliers start: 30 outliers final: 21 residues processed: 198 average time/residue: 0.1281 time to fit residues: 37.8105 Evaluate side-chains 187 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 C residue 434 MET Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 325 ASP 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: 2.9990 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS C 377 ASN C 440 GLN ** A 302 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 = 0.3446 r_free = 0.3446 target = 0.114547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095857 restraints weight = 29182.722| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.78 r_work: 0.3037 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16203 Z= 0.118 Angle : 0.582 8.320 22226 Z= 0.283 Chirality : 0.043 0.236 2808 Planarity : 0.004 0.038 2673 Dihedral : 6.846 62.187 4066 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.60 % Allowed : 9.99 % Favored : 88.41 % 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 (0.21), residues: 1646 helix: 2.25 (0.26), residues: 406 sheet: 0.93 (0.26), residues: 393 loop : 0.07 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.014 0.001 TYR F 586 PHE 0.010 0.001 PHE A 353 TRP 0.009 0.001 TRP E 96 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00258 (16071) covalent geometry : angle 0.54364 (21863) SS BOND : bond 0.00396 ( 33) SS BOND : angle 1.01433 ( 66) hydrogen bonds : bond 0.04504 ( 606) hydrogen bonds : angle 4.55410 ( 2142) link_ALPHA1-3 : bond 0.01322 ( 3) link_ALPHA1-3 : angle 1.32655 ( 9) link_ALPHA1-6 : bond 0.00850 ( 3) link_ALPHA1-6 : angle 1.87350 ( 9) link_BETA1-4 : bond 0.00519 ( 36) link_BETA1-4 : angle 1.75471 ( 108) link_NAG-ASN : bond 0.00245 ( 57) link_NAG-ASN : angle 1.91367 ( 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 217 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 125 LEU cc_start: 0.8805 (tp) cc_final: 0.8582 (tp) REVERT: E 201 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8499 (mt) REVERT: E 368 ASP cc_start: 0.7260 (p0) cc_final: 0.6751 (p0) REVERT: E 370 GLU cc_start: 0.7697 (tt0) cc_final: 0.7462 (pt0) REVERT: E 475 MET cc_start: 0.8628 (mmm) cc_final: 0.8281 (mmp) REVERT: F 599 SER cc_start: 0.9011 (t) cc_final: 0.8765 (t) REVERT: F 617 ARG cc_start: 0.9012 (mtp85) cc_final: 0.8806 (mtp85) REVERT: F 621 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7235 (tm-30) REVERT: F 639 THR cc_start: 0.8931 (m) cc_final: 0.8665 (p) REVERT: C 51 THR cc_start: 0.9397 (m) cc_final: 0.9176 (p) REVERT: C 95 MET cc_start: 0.9050 (ptt) cc_final: 0.8847 (ptt) REVERT: C 199 SER cc_start: 0.8456 (t) cc_final: 0.8103 (t) REVERT: C 482 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8342 (mm-30) REVERT: D 660 LEU cc_start: 0.8950 (mp) cc_final: 0.8490 (tt) REVERT: D 663 LEU cc_start: 0.7360 (mm) cc_final: 0.6922 (mm) REVERT: B 640 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8104 (mp10) outliers start: 24 outliers final: 12 residues processed: 207 average time/residue: 0.1185 time to fit residues: 36.6603 Evaluate side-chains 190 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 C residue 434 MET Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 450 THR 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: 0.8980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS F 543 ASN A 195 ASN ** A 302 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 = 0.3393 r_free = 0.3393 target = 0.110909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.092164 restraints weight = 29753.620| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.78 r_work: 0.2975 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16203 Z= 0.202 Angle : 0.646 7.573 22226 Z= 0.312 Chirality : 0.045 0.247 2808 Planarity : 0.004 0.046 2673 Dihedral : 6.653 54.184 4066 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.13 % Allowed : 10.46 % Favored : 87.41 % 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: 0.99 (0.21), residues: 1646 helix: 2.17 (0.26), residues: 400 sheet: 0.80 (0.26), residues: 405 loop : -0.12 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 327 TYR 0.018 0.002 TYR A 173 PHE 0.016 0.002 PHE C 53 TRP 0.013 0.001 TRP A 96 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00480 (16071) covalent geometry : angle 0.61058 (21863) SS BOND : bond 0.00455 ( 33) SS BOND : angle 1.16573 ( 66) hydrogen bonds : bond 0.05002 ( 606) hydrogen bonds : angle 4.59817 ( 2142) link_ALPHA1-3 : bond 0.01236 ( 3) link_ALPHA1-3 : angle 1.36692 ( 9) link_ALPHA1-6 : bond 0.00863 ( 3) link_ALPHA1-6 : angle 1.88527 ( 9) link_BETA1-4 : bond 0.00473 ( 36) link_BETA1-4 : angle 1.79942 ( 108) link_NAG-ASN : bond 0.00302 ( 57) link_NAG-ASN : angle 1.91934 ( 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 216 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 201 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8531 (mt) REVERT: E 368 ASP cc_start: 0.7366 (p0) cc_final: 0.6526 (p0) REVERT: E 475 MET cc_start: 0.8718 (mmm) cc_final: 0.8382 (mmp) REVERT: F 617 ARG cc_start: 0.9016 (mtp85) cc_final: 0.8708 (mtp85) REVERT: F 621 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7597 (tm-30) REVERT: F 639 THR cc_start: 0.8969 (m) cc_final: 0.8667 (p) REVERT: C 42 VAL cc_start: 0.9105 (t) cc_final: 0.8811 (m) REVERT: C 199 SER cc_start: 0.8462 (t) cc_final: 0.8056 (t) REVERT: C 482 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8442 (mm-30) REVERT: D 617 ARG cc_start: 0.8704 (mtt-85) cc_final: 0.8331 (mtt-85) REVERT: D 633 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8544 (mmtp) REVERT: D 634 GLU cc_start: 0.8376 (tt0) cc_final: 0.7901 (tt0) REVERT: D 660 LEU cc_start: 0.8976 (mp) cc_final: 0.8526 (tt) REVERT: D 663 LEU cc_start: 0.7504 (mm) cc_final: 0.7050 (mm) REVERT: B 543 ASN cc_start: 0.8644 (m-40) cc_final: 0.8423 (t0) REVERT: B 584 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8187 (mt-10) outliers start: 32 outliers final: 20 residues processed: 202 average time/residue: 0.1240 time to fit residues: 37.6566 Evaluate side-chains 199 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 167 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 534 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 182 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS F 543 ASN ** A 302 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 = 0.3348 r_free = 0.3348 target = 0.107890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089183 restraints weight = 29849.616| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.75 r_work: 0.2929 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 16203 Z= 0.310 Angle : 0.765 11.285 22226 Z= 0.366 Chirality : 0.049 0.375 2808 Planarity : 0.005 0.051 2673 Dihedral : 7.197 55.111 4066 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.80 % Allowed : 10.73 % Favored : 86.48 % 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: 0.46 (0.20), residues: 1646 helix: 1.65 (0.26), residues: 406 sheet: 0.52 (0.26), residues: 404 loop : -0.44 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 588 TYR 0.019 0.002 TYR E 177 PHE 0.021 0.003 PHE C 53 TRP 0.013 0.002 TRP A 96 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00746 (16071) covalent geometry : angle 0.72711 (21863) SS BOND : bond 0.00614 ( 33) SS BOND : angle 1.41838 ( 66) hydrogen bonds : bond 0.05766 ( 606) hydrogen bonds : angle 4.89912 ( 2142) link_ALPHA1-3 : bond 0.01274 ( 3) link_ALPHA1-3 : angle 1.47878 ( 9) link_ALPHA1-6 : bond 0.00912 ( 3) link_ALPHA1-6 : angle 1.98908 ( 9) link_BETA1-4 : bond 0.00478 ( 36) link_BETA1-4 : angle 1.91025 ( 108) link_NAG-ASN : bond 0.00451 ( 57) link_NAG-ASN : angle 2.25597 ( 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 219 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 617 ARG cc_start: 0.9052 (mtp85) cc_final: 0.8844 (mtp85) REVERT: C 42 VAL cc_start: 0.9182 (t) cc_final: 0.8912 (m) REVERT: C 482 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8457 (mm-30) REVERT: D 617 ARG cc_start: 0.8744 (mtt-85) cc_final: 0.8156 (mtt-85) REVERT: D 633 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8573 (mmtp) REVERT: D 634 GLU cc_start: 0.8537 (tt0) cc_final: 0.8080 (tt0) REVERT: D 660 LEU cc_start: 0.8995 (mp) cc_final: 0.8484 (tt) REVERT: B 543 ASN cc_start: 0.8825 (m-40) cc_final: 0.8521 (t0) REVERT: B 584 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 640 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8204 (mp10) outliers start: 42 outliers final: 31 residues processed: 202 average time/residue: 0.1283 time to fit residues: 38.5545 Evaluate side-chains 199 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 E residue 244 THR 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 51 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 534 SER 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 612 SER Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL 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 Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 640 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS C 440 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3394 r_free = 0.3394 target = 0.111059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.092296 restraints weight = 29324.330| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.78 r_work: 0.2982 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16203 Z= 0.147 Angle : 0.605 10.277 22226 Z= 0.291 Chirality : 0.044 0.332 2808 Planarity : 0.004 0.045 2673 Dihedral : 6.490 55.826 4066 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.67 % Allowed : 12.13 % Favored : 86.21 % 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: 0.72 (0.21), residues: 1646 helix: 2.24 (0.26), residues: 393 sheet: 0.42 (0.25), residues: 432 loop : -0.32 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 588 TYR 0.018 0.001 TYR A 173 PHE 0.009 0.001 PHE C 53 TRP 0.011 0.001 TRP B 571 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00340 (16071) covalent geometry : angle 0.56709 (21863) SS BOND : bond 0.00457 ( 33) SS BOND : angle 1.10447 ( 66) hydrogen bonds : bond 0.04599 ( 606) hydrogen bonds : angle 4.46437 ( 2142) link_ALPHA1-3 : bond 0.01343 ( 3) link_ALPHA1-3 : angle 1.12708 ( 9) link_ALPHA1-6 : bond 0.00959 ( 3) link_ALPHA1-6 : angle 1.77466 ( 9) link_BETA1-4 : bond 0.00480 ( 36) link_BETA1-4 : angle 1.65984 ( 108) link_NAG-ASN : bond 0.00269 ( 57) link_NAG-ASN : angle 1.99159 ( 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 212 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8591 (mmm) cc_final: 0.8168 (mmp) REVERT: F 617 ARG cc_start: 0.9146 (mtp85) cc_final: 0.8828 (mtp85) REVERT: F 621 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7635 (tm-30) REVERT: F 639 THR cc_start: 0.8993 (m) cc_final: 0.8735 (p) REVERT: C 42 VAL cc_start: 0.9121 (t) cc_final: 0.8848 (m) REVERT: C 482 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8372 (mm-30) REVERT: D 617 ARG cc_start: 0.8624 (mtt-85) cc_final: 0.8181 (mtt-85) REVERT: D 633 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8628 (mmtp) REVERT: D 634 GLU cc_start: 0.8492 (tt0) cc_final: 0.7884 (tt0) REVERT: D 660 LEU cc_start: 0.8964 (mp) cc_final: 0.8509 (tt) REVERT: B 584 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 640 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8184 (mp10) outliers start: 25 outliers final: 18 residues processed: 199 average time/residue: 0.1269 time to fit residues: 37.3562 Evaluate side-chains 196 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET 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 534 SER 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 625 ASN Chi-restraints excluded: chain A residue 68 VAL 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 634 GLU Chi-restraints excluded: chain B residue 640 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 78 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS F 543 ASN C 440 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** 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 = 0.3351 r_free = 0.3351 target = 0.108127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.089282 restraints weight = 29846.759| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.78 r_work: 0.2928 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16203 Z= 0.294 Angle : 0.746 10.929 22226 Z= 0.356 Chirality : 0.048 0.391 2808 Planarity : 0.004 0.050 2673 Dihedral : 7.070 55.049 4066 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.73 % Allowed : 12.72 % Favored : 85.54 % 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: 0.36 (0.21), residues: 1646 helix: 1.58 (0.26), residues: 411 sheet: 0.45 (0.26), residues: 425 loop : -0.55 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.015 0.002 TYR A 173 PHE 0.016 0.002 PHE C 53 TRP 0.014 0.002 TRP A 96 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00709 (16071) covalent geometry : angle 0.70732 (21863) SS BOND : bond 0.00629 ( 33) SS BOND : angle 1.56665 ( 66) hydrogen bonds : bond 0.05573 ( 606) hydrogen bonds : angle 4.81522 ( 2142) link_ALPHA1-3 : bond 0.01209 ( 3) link_ALPHA1-3 : angle 1.41563 ( 9) link_ALPHA1-6 : bond 0.00850 ( 3) link_ALPHA1-6 : angle 1.90141 ( 9) link_BETA1-4 : bond 0.00484 ( 36) link_BETA1-4 : angle 1.90877 ( 108) link_NAG-ASN : bond 0.00477 ( 57) link_NAG-ASN : angle 2.19682 ( 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 197 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 639 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8780 (p) REVERT: C 482 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8402 (mm-30) REVERT: D 617 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.8256 (mtt-85) REVERT: D 633 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8632 (mmtp) REVERT: D 634 GLU cc_start: 0.8558 (tt0) cc_final: 0.7986 (tt0) REVERT: D 660 LEU cc_start: 0.8920 (mp) cc_final: 0.8439 (tt) REVERT: B 584 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8229 (mt-10) outliers start: 26 outliers final: 23 residues processed: 184 average time/residue: 0.1332 time to fit residues: 36.1532 Evaluate side-chains 193 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 534 SER 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 612 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 439 ILE 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 543 ASN 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: 1.9990 chunk 181 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS C 66 HIS A 302 ASN B 543 ASN ** 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 = 0.3405 r_free = 0.3405 target = 0.111876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093257 restraints weight = 29132.918| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.76 r_work: 0.2997 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16203 Z= 0.119 Angle : 0.581 8.286 22226 Z= 0.282 Chirality : 0.043 0.338 2808 Planarity : 0.004 0.042 2673 Dihedral : 6.359 55.557 4066 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.27 % Allowed : 13.39 % Favored : 85.34 % 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: 0.69 (0.21), residues: 1646 helix: 2.20 (0.27), residues: 399 sheet: 0.47 (0.25), residues: 420 loop : -0.39 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 542 TYR 0.019 0.001 TYR A 173 PHE 0.009 0.001 PHE C 391 TRP 0.014 0.001 TRP B 571 HIS 0.002 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00267 (16071) covalent geometry : angle 0.54553 (21863) SS BOND : bond 0.00437 ( 33) SS BOND : angle 1.14314 ( 66) hydrogen bonds : bond 0.04296 ( 606) hydrogen bonds : angle 4.33083 ( 2142) link_ALPHA1-3 : bond 0.01304 ( 3) link_ALPHA1-3 : angle 0.99879 ( 9) link_ALPHA1-6 : bond 0.00937 ( 3) link_ALPHA1-6 : angle 1.63960 ( 9) link_BETA1-4 : bond 0.00499 ( 36) link_BETA1-4 : angle 1.61256 ( 108) link_NAG-ASN : bond 0.00215 ( 57) link_NAG-ASN : angle 1.86490 ( 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 201 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8554 (mmm) cc_final: 0.8109 (mmp) REVERT: F 599 SER cc_start: 0.8958 (t) cc_final: 0.8706 (t) REVERT: F 617 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8776 (mtp85) REVERT: C 42 VAL cc_start: 0.9114 (t) cc_final: 0.8854 (m) REVERT: C 482 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8312 (mm-30) REVERT: D 617 ARG cc_start: 0.8670 (mtt-85) cc_final: 0.8246 (mtt-85) REVERT: D 633 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8664 (mmtp) REVERT: D 634 GLU cc_start: 0.8487 (tt0) cc_final: 0.7941 (tt0) REVERT: D 660 LEU cc_start: 0.8938 (mp) cc_final: 0.8441 (tt) REVERT: B 640 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8121 (mp10) outliers start: 19 outliers final: 12 residues processed: 193 average time/residue: 0.1324 time to fit residues: 37.5637 Evaluate side-chains 188 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET 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 595 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 182 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS F 543 ASN C 85 HIS ** 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 = 0.3373 r_free = 0.3373 target = 0.109678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.090926 restraints weight = 29316.832| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.76 r_work: 0.2958 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16203 Z= 0.208 Angle : 0.643 8.693 22226 Z= 0.309 Chirality : 0.045 0.368 2808 Planarity : 0.004 0.046 2673 Dihedral : 6.558 55.024 4066 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.00 % Allowed : 13.79 % Favored : 85.21 % 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: 0.59 (0.21), residues: 1646 helix: 2.02 (0.27), residues: 401 sheet: 0.43 (0.25), residues: 435 loop : -0.43 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 456 TYR 0.015 0.001 TYR A 173 PHE 0.015 0.002 PHE C 53 TRP 0.012 0.001 TRP B 571 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00499 (16071) covalent geometry : angle 0.60696 (21863) SS BOND : bond 0.00524 ( 33) SS BOND : angle 1.32098 ( 66) hydrogen bonds : bond 0.04844 ( 606) hydrogen bonds : angle 4.49105 ( 2142) link_ALPHA1-3 : bond 0.01235 ( 3) link_ALPHA1-3 : angle 1.22920 ( 9) link_ALPHA1-6 : bond 0.00820 ( 3) link_ALPHA1-6 : angle 1.70929 ( 9) link_BETA1-4 : bond 0.00460 ( 36) link_BETA1-4 : angle 1.76113 ( 108) link_NAG-ASN : bond 0.00320 ( 57) link_NAG-ASN : angle 1.96227 ( 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 192 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: E 475 MET cc_start: 0.8646 (mmm) cc_final: 0.8220 (mmp) REVERT: F 617 ARG cc_start: 0.9037 (mtp85) cc_final: 0.8671 (mtp85) REVERT: C 42 VAL cc_start: 0.9139 (t) cc_final: 0.8891 (m) REVERT: C 482 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 617 ARG cc_start: 0.8710 (mtt-85) cc_final: 0.8295 (mtt-85) REVERT: D 633 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8653 (mmtp) REVERT: D 634 GLU cc_start: 0.8489 (tt0) cc_final: 0.7932 (tt0) REVERT: D 660 LEU cc_start: 0.8953 (mp) cc_final: 0.8448 (tt) REVERT: B 584 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8199 (mt-10) REVERT: B 617 ARG cc_start: 0.8303 (mtp180) cc_final: 0.7621 (ptm160) outliers start: 15 outliers final: 14 residues processed: 185 average time/residue: 0.1304 time to fit residues: 35.7259 Evaluate side-chains 190 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 MET 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 434 MET Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain A residue 182 VAL 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: 0.8980 chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 144 optimal weight: 0.0050 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.093661 restraints weight = 29249.059| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.77 r_work: 0.3007 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4117 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 : 0.559 8.215 22226 Z= 0.271 Chirality : 0.042 0.300 2808 Planarity : 0.004 0.042 2673 Dihedral : 6.037 54.902 4066 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.93 % Allowed : 13.92 % Favored : 85.14 % 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: 0.86 (0.21), residues: 1646 helix: 2.39 (0.27), residues: 395 sheet: 0.55 (0.26), residues: 415 loop : -0.27 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 456 TYR 0.018 0.001 TYR A 173 PHE 0.008 0.001 PHE E 53 TRP 0.013 0.001 TRP B 571 HIS 0.003 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00260 (16071) covalent geometry : angle 0.52638 (21863) SS BOND : bond 0.00425 ( 33) SS BOND : angle 1.03730 ( 66) hydrogen bonds : bond 0.04065 ( 606) hydrogen bonds : angle 4.21788 ( 2142) link_ALPHA1-3 : bond 0.01250 ( 3) link_ALPHA1-3 : angle 1.03108 ( 9) link_ALPHA1-6 : bond 0.00818 ( 3) link_ALPHA1-6 : angle 1.42808 ( 9) link_BETA1-4 : bond 0.00486 ( 36) link_BETA1-4 : angle 1.59117 ( 108) link_NAG-ASN : bond 0.00236 ( 57) link_NAG-ASN : angle 1.75342 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.22 seconds wall clock time: 52 minutes 30.11 seconds (3150.11 seconds total)