Starting phenix.real_space_refine on Thu Mar 5 09:05:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vi0_21208/03_2026/6vi0_21208.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vi0_21208/03_2026/6vi0_21208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vi0_21208/03_2026/6vi0_21208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vi0_21208/03_2026/6vi0_21208.map" model { file = "/net/cci-nas-00/data/ceres_data/6vi0_21208/03_2026/6vi0_21208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vi0_21208/03_2026/6vi0_21208.cif" } resolution = 3.43 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= 0.013 sd= 0.094 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 138 5.16 5 C 12987 2.51 5 N 3447 2.21 5 O 4251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 20823 Number of models: 1 Model: "" Number of chains: 45 Chain: "B" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "A" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "E" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "F" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "K" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.11, per 1000 atoms: 0.25 Number of scatterers: 20823 At special positions: 0 Unit cell: (148.109, 143.816, 123.424, 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 138 16.00 O 4251 8.00 N 3447 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.01 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 32 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 98 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN P 4 " - " MAN P 5 " " MAN W 4 " - " MAN W 5 " " MAN X 4 " - " MAN X 5 " " MAN e 4 " - " MAN e 5 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA Z 3 " - " MAN Z 6 " " MAN Z 4 " - " MAN Z 5 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA h 3 " - " MAN h 6 " " MAN h 4 " - " MAN h 5 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 6 " " BMA P 3 " - " MAN P 6 " " MAN P 6 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 6 " " BMA f 3 " - " MAN f 6 " " MAN f 6 " - " MAN f 8 " " BMA h 3 " - " MAN h 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1611 " - " ASN A 611 " " NAG A1637 " - " ASN A 637 " " NAG B1611 " - " ASN B 611 " " NAG B1637 " - " ASN B 637 " " NAG C1088 " - " ASN C 88 " " NAG C1133 " - " ASN C 133 " " NAG C1156 " - " ASN C 156 " " NAG C1234 " - " ASN C 234 " " NAG C1301 " - " ASN C 301 " " NAG C1332 " - " ASN C 332 " " NAG C1339 " - " ASN C 339 " " NAG C1355 " - " ASN C 355 " " NAG C1392 " - " ASN C 392 " " NAG D1072 " - " ASN D 72 " " NAG F1611 " - " ASN F 611 " " NAG F1637 " - " ASN F 637 " " NAG G1088 " - " ASN G 88 " " NAG G1133 " - " ASN G 133 " " NAG G1156 " - " ASN G 156 " " NAG G1234 " - " ASN G 234 " " NAG G1301 " - " ASN G 301 " " NAG G1332 " - " ASN G 332 " " NAG G1339 " - " ASN G 339 " " NAG G1355 " - " ASN G 355 " " NAG G1392 " - " ASN G 392 " " NAG I1088 " - " ASN I 88 " " NAG I1133 " - " ASN I 133 " " NAG I1156 " - " ASN I 156 " " NAG I1234 " - " ASN I 234 " " NAG I1301 " - " ASN I 301 " " NAG I1332 " - " ASN I 332 " " NAG I1339 " - " ASN I 339 " " NAG I1355 " - " ASN I 355 " " NAG I1392 " - " ASN I 392 " " NAG J1072 " - " ASN J 72 " " NAG L1072 " - " ASN L 72 " " NAG M 1 " - " ASN G 160 " " NAG N 1 " - " ASN G 197 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 276 " " NAG Q 1 " - " ASN G 295 " " NAG R 1 " - " ASN G 363 " " NAG S 1 " - " ASN G 386 " " NAG T 1 " - " ASN G 448 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 276 " " NAG Y 1 " - " ASN C 295 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN I 160 " " NAG d 1 " - " ASN I 197 " " NAG e 1 " - " ASN I 262 " " NAG f 1 " - " ASN I 276 " " NAG g 1 " - " ASN I 295 " " NAG h 1 " - " ASN I 363 " " NAG i 1 " - " ASN I 386 " " NAG j 1 " - " ASN I 448 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 48 sheets defined 18.2% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.255A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 593 removed outlier: 3.684A pdb=" N TRP B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 removed outlier: 4.032A pdb=" N GLY B 597 " --> pdb=" O GLY B 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 594 through 597' Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR B 639 " --> pdb=" O SER B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 639' Processing helix chain 'B' and resid 641 through 658 removed outlier: 4.293A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 354 removed outlier: 3.701A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 482 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.865A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.733A pdb=" N GLN H 64 " --> pdb=" O ARG H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.254A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 593 removed outlier: 3.682A pdb=" N TRP A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 removed outlier: 4.032A pdb=" N GLY A 597 " --> pdb=" O GLY A 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR A 639 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 641 through 664 removed outlier: 4.293A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.699A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.865A pdb=" N ASP D 82 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.732A pdb=" N GLN E 64 " --> pdb=" O ARG E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.256A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 593 removed outlier: 3.683A pdb=" N TRP F 571 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 removed outlier: 4.033A pdb=" N GLY F 597 " --> pdb=" O GLY F 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 594 through 597' Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR F 639 " --> pdb=" O SER F 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 636 through 639' Processing helix chain 'F' and resid 641 through 658 removed outlier: 4.293A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 63 Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.701A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 482 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.866A pdb=" N ASP J 82 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.733A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.347A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.586A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.119A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 466 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 302 through 308 removed outlier: 6.643A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 423 through 424 removed outlier: 4.271A pdb=" N ILE G 424 " --> pdb=" O MET G 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER L 65 " --> pdb=" O ASN L 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.811A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.572A pdb=" N GLN H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'H' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN H 58 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.346A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.692A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC5, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.587A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.120A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.254A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 466 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.643A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.168A pdb=" N ILE C 424 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 65 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.813A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.571A pdb=" N GLN E 72 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'E' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP E 50 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN E 58 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 603 through 609 removed outlier: 7.347A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.692A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AE2, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AE3, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.585A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.118A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 466 " --> pdb=" O ILE I 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 302 through 308 removed outlier: 6.645A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 423 through 424 removed outlier: 4.089A pdb=" N ILE I 424 " --> pdb=" O MET I 434 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER J 65 " --> pdb=" O ASN J 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.812A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.571A pdb=" N GLN K 72 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'K' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3554 1.32 - 1.45: 5923 1.45 - 1.57: 11589 1.57 - 1.69: 0 1.69 - 1.82: 186 Bond restraints: 21252 Sorted by residual: bond pdb=" N CYS G 201 " pdb=" CA CYS G 201 " ideal model delta sigma weight residual 1.463 1.392 0.071 1.27e-02 6.20e+03 3.11e+01 bond pdb=" CA SER I 199 " pdb=" CB SER I 199 " ideal model delta sigma weight residual 1.532 1.450 0.081 1.56e-02 4.11e+03 2.71e+01 bond pdb=" N CYS I 201 " pdb=" CA CYS I 201 " ideal model delta sigma weight residual 1.460 1.402 0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" CA SER C 199 " pdb=" CB SER C 199 " ideal model delta sigma weight residual 1.532 1.451 0.081 1.68e-02 3.54e+03 2.35e+01 bond pdb=" CA SER G 199 " pdb=" CB SER G 199 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.69e-02 3.50e+03 2.05e+01 ... (remaining 21247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 27156 2.18 - 4.36: 1402 4.36 - 6.53: 217 6.53 - 8.71: 60 8.71 - 10.89: 19 Bond angle restraints: 28854 Sorted by residual: angle pdb=" C ASN I 156 " pdb=" CA ASN I 156 " pdb=" CB ASN I 156 " ideal model delta sigma weight residual 111.68 100.79 10.89 1.67e+00 3.59e-01 4.25e+01 angle pdb=" C ASN C 156 " pdb=" CA ASN C 156 " pdb=" CB ASN C 156 " ideal model delta sigma weight residual 111.68 100.85 10.83 1.67e+00 3.59e-01 4.20e+01 angle pdb=" C ASN G 156 " pdb=" CA ASN G 156 " pdb=" CB ASN G 156 " ideal model delta sigma weight residual 111.68 100.86 10.82 1.67e+00 3.59e-01 4.19e+01 angle pdb=" CA ALA I 200 " pdb=" C ALA I 200 " pdb=" O ALA I 200 " ideal model delta sigma weight residual 121.11 115.25 5.86 1.13e+00 7.83e-01 2.69e+01 angle pdb=" N LEU A 663 " pdb=" CA LEU A 663 " pdb=" C LEU A 663 " ideal model delta sigma weight residual 111.28 105.83 5.45 1.09e+00 8.42e-01 2.50e+01 ... (remaining 28849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 13242 21.87 - 43.74: 935 43.74 - 65.60: 142 65.60 - 87.47: 96 87.47 - 109.34: 60 Dihedral angle restraints: 14475 sinusoidal: 7533 harmonic: 6942 Sorted by residual: dihedral pdb=" CB CYS K 32 " pdb=" SG CYS K 32 " pdb=" SG CYS K 98 " pdb=" CB CYS K 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.56 -72.44 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS H 32 " pdb=" SG CYS H 32 " pdb=" SG CYS H 98 " pdb=" CB CYS H 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.57 -72.43 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS E 32 " pdb=" SG CYS E 32 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.60 -72.40 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 14472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.288: 3518 0.288 - 0.576: 55 0.576 - 0.864: 6 0.864 - 1.152: 3 1.152 - 1.441: 3 Chirality restraints: 3585 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.19e+03 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.16e+03 chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-02 2.50e+03 5.13e+03 ... (remaining 3582 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " 0.308 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG h 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.308 2.00e-02 2.50e+03 2.59e-01 8.40e+02 pdb=" C7 NAG R 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.444 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.307 2.00e-02 2.50e+03 2.59e-01 8.39e+02 pdb=" C7 NAG Z 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.030 2.00e-02 2.50e+03 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4427 2.77 - 3.30: 17738 3.30 - 3.84: 32644 3.84 - 4.37: 37378 4.37 - 4.90: 66247 Nonbonded interactions: 158434 Sorted by model distance: nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.241 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.241 3.040 nonbonded pdb=" OG SER J 63 " pdb=" OG1 THR J 74 " model vdw 2.241 3.040 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.306 3.040 nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.307 3.040 ... (remaining 158429 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' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'N' selection = chain 'V' selection = chain 'd' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'W' selection = chain 'Z' selection = chain 'e' selection = chain 'h' } ncs_group { reference = chain 'P' selection = chain 'X' selection = chain 'f' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } 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: 3.150 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.580 Find NCS groups from input model: 0.340 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.009 0.081 21432 Z= 0.428 Angle : 1.680 52.335 29349 Z= 0.704 Chirality : 0.103 1.441 3585 Planarity : 0.015 0.259 3498 Dihedral : 17.431 109.340 9870 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.79 % Favored : 92.05 % Rotamer: Outliers : 1.23 % Allowed : 8.13 % Favored : 90.64 % Cbeta Deviations : 0.13 % 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: -5.43 (0.13), residues: 2376 helix: -4.82 (0.08), residues: 390 sheet: -3.18 (0.16), residues: 720 loop : -3.48 (0.13), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 71 TYR 0.028 0.002 TYR G 435 PHE 0.018 0.002 PHE G 53 TRP 0.021 0.002 TRP K 50 HIS 0.011 0.002 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00850 (21252) covalent geometry : angle 1.11983 (28854) SS BOND : bond 0.00622 ( 45) SS BOND : angle 1.68388 ( 90) hydrogen bonds : bond 0.26357 ( 531) hydrogen bonds : angle 10.46124 ( 1386) link_ALPHA1-2 : bond 0.00123 ( 6) link_ALPHA1-2 : angle 3.98839 ( 18) link_ALPHA1-3 : bond 0.00624 ( 15) link_ALPHA1-3 : angle 3.30322 ( 45) link_ALPHA1-6 : bond 0.02991 ( 15) link_ALPHA1-6 : angle 14.65742 ( 45) link_BETA1-4 : bond 0.04759 ( 39) link_BETA1-4 : angle 17.09320 ( 117) link_NAG-ASN : bond 0.01080 ( 60) link_NAG-ASN : angle 3.15426 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 603 ILE cc_start: 0.8994 (mt) cc_final: 0.8700 (tt) REVERT: B 632 ASP cc_start: 0.8695 (t70) cc_final: 0.8336 (t0) REVERT: B 651 ASN cc_start: 0.8180 (t0) cc_final: 0.7492 (p0) REVERT: G 166 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7112 (ttp-170) REVERT: L 17 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7906 (mt-10) REVERT: L 54 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7780 (ptp-110) REVERT: H 76 ASP cc_start: 0.7987 (p0) cc_final: 0.7764 (p0) REVERT: A 603 ILE cc_start: 0.8960 (mt) cc_final: 0.8661 (tt) REVERT: A 632 ASP cc_start: 0.8629 (t70) cc_final: 0.8316 (t0) REVERT: A 633 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8850 (mtmm) REVERT: A 651 ASN cc_start: 0.8059 (t0) cc_final: 0.7439 (p0) REVERT: C 114 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 166 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7159 (ttp-110) REVERT: C 426 MET cc_start: 0.8615 (tpp) cc_final: 0.8397 (tpt) REVERT: D 17 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7775 (mt-10) REVERT: D 42 GLN cc_start: 0.8356 (mt0) cc_final: 0.8062 (mt0) REVERT: D 75 ILE cc_start: 0.7683 (mt) cc_final: 0.7459 (tt) REVERT: F 603 ILE cc_start: 0.8980 (mt) cc_final: 0.8614 (tt) REVERT: F 632 ASP cc_start: 0.8873 (t70) cc_final: 0.8520 (t0) REVERT: F 651 ASN cc_start: 0.8177 (t0) cc_final: 0.7600 (p0) REVERT: I 100 MET cc_start: 0.9090 (mtp) cc_final: 0.8804 (mtt) REVERT: I 166 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7096 (ttp-110) REVERT: I 424 ILE cc_start: 0.8563 (pt) cc_final: 0.8299 (pt) REVERT: I 426 MET cc_start: 0.8697 (tpp) cc_final: 0.8477 (tpt) REVERT: J 17 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7709 (mt-10) REVERT: J 24 ARG cc_start: 0.7936 (tpt90) cc_final: 0.7622 (tpt170) REVERT: J 42 GLN cc_start: 0.8357 (mt0) cc_final: 0.7945 (mp10) REVERT: J 60 ASP cc_start: 0.8413 (m-30) cc_final: 0.8202 (m-30) REVERT: K 76 ASP cc_start: 0.8102 (p0) cc_final: 0.7857 (p0) REVERT: K 96 LYS cc_start: 0.9229 (tttm) cc_final: 0.8810 (tttm) outliers start: 26 outliers final: 10 residues processed: 302 average time/residue: 0.1793 time to fit residues: 79.9015 Evaluate side-chains 198 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 430 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN L 6 GLN H 3 GLN C 114 GLN D 6 GLN E 3 GLN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN K 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.103133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.083854 restraints weight = 43753.636| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.83 r_work: 0.3206 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21432 Z= 0.140 Angle : 0.782 11.526 29349 Z= 0.354 Chirality : 0.047 0.325 3585 Planarity : 0.005 0.046 3498 Dihedral : 13.388 76.631 5347 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.70 % Allowed : 11.21 % Favored : 87.09 % 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: -4.41 (0.14), residues: 2376 helix: -3.34 (0.16), residues: 408 sheet: -2.57 (0.18), residues: 717 loop : -3.00 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 54 TYR 0.015 0.001 TYR A 638 PHE 0.013 0.001 PHE I 382 TRP 0.013 0.001 TRP E 100B HIS 0.010 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00316 (21252) covalent geometry : angle 0.72786 (28854) SS BOND : bond 0.00196 ( 45) SS BOND : angle 1.60130 ( 90) hydrogen bonds : bond 0.04978 ( 531) hydrogen bonds : angle 6.14801 ( 1386) link_ALPHA1-2 : bond 0.01005 ( 6) link_ALPHA1-2 : angle 2.39539 ( 18) link_ALPHA1-3 : bond 0.00883 ( 15) link_ALPHA1-3 : angle 1.67454 ( 45) link_ALPHA1-6 : bond 0.00372 ( 15) link_ALPHA1-6 : angle 2.13253 ( 45) link_BETA1-4 : bond 0.00611 ( 39) link_BETA1-4 : angle 2.69700 ( 117) link_NAG-ASN : bond 0.00303 ( 60) link_NAG-ASN : angle 2.50399 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8436 (t70) cc_final: 0.8170 (t0) REVERT: G 114 GLN cc_start: 0.8448 (tm130) cc_final: 0.8087 (tm-30) REVERT: G 166 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7209 (ttp-170) REVERT: H 76 ASP cc_start: 0.7678 (p0) cc_final: 0.7436 (p0) REVERT: H 87 THR cc_start: 0.9044 (m) cc_final: 0.8737 (p) REVERT: A 632 ASP cc_start: 0.8247 (t70) cc_final: 0.7989 (t0) REVERT: C 114 GLN cc_start: 0.8441 (tm130) cc_final: 0.8131 (tm-30) REVERT: C 166 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7205 (ttp-110) REVERT: F 616 ASN cc_start: 0.8467 (p0) cc_final: 0.8223 (p0) REVERT: F 632 ASP cc_start: 0.8553 (t70) cc_final: 0.8224 (t0) REVERT: F 655 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7474 (mmmt) REVERT: I 166 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7242 (ttp-110) REVERT: K 76 ASP cc_start: 0.7917 (p0) cc_final: 0.7607 (p0) outliers start: 36 outliers final: 23 residues processed: 246 average time/residue: 0.1469 time to fit residues: 57.3691 Evaluate side-chains 210 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 58 optimal weight: 7.9990 chunk 232 optimal weight: 0.1980 chunk 68 optimal weight: 0.0670 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.098455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.076992 restraints weight = 47249.742| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.38 r_work: 0.3160 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21432 Z= 0.197 Angle : 0.779 16.695 29349 Z= 0.355 Chirality : 0.049 0.370 3585 Planarity : 0.004 0.040 3498 Dihedral : 11.340 64.104 5340 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.88 % Allowed : 12.67 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.49 (0.16), residues: 2376 helix: -1.71 (0.24), residues: 369 sheet: -2.09 (0.19), residues: 675 loop : -2.67 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.020 0.001 TYR A 638 PHE 0.013 0.001 PHE G 53 TRP 0.014 0.001 TRP E 50 HIS 0.005 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00459 (21252) covalent geometry : angle 0.72500 (28854) SS BOND : bond 0.00270 ( 45) SS BOND : angle 2.63965 ( 90) hydrogen bonds : bond 0.03782 ( 531) hydrogen bonds : angle 5.34865 ( 1386) link_ALPHA1-2 : bond 0.00929 ( 6) link_ALPHA1-2 : angle 2.20751 ( 18) link_ALPHA1-3 : bond 0.00868 ( 15) link_ALPHA1-3 : angle 1.74814 ( 45) link_ALPHA1-6 : bond 0.00609 ( 15) link_ALPHA1-6 : angle 2.01761 ( 45) link_BETA1-4 : bond 0.00486 ( 39) link_BETA1-4 : angle 2.18916 ( 117) link_NAG-ASN : bond 0.00317 ( 60) link_NAG-ASN : angle 2.39033 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8963 (t70) cc_final: 0.8638 (t0) REVERT: G 114 GLN cc_start: 0.8430 (tm130) cc_final: 0.8129 (tm-30) REVERT: G 166 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7238 (ttp-170) REVERT: L 54 ARG cc_start: 0.8298 (mtm110) cc_final: 0.8016 (mtm110) REVERT: L 60 ASP cc_start: 0.8623 (m-30) cc_final: 0.8419 (m-30) REVERT: H 76 ASP cc_start: 0.8090 (p0) cc_final: 0.7881 (p0) REVERT: A 616 ASN cc_start: 0.8743 (p0) cc_final: 0.8278 (p0) REVERT: A 632 ASP cc_start: 0.8866 (t70) cc_final: 0.8572 (t0) REVERT: C 114 GLN cc_start: 0.8501 (tm130) cc_final: 0.8220 (tm-30) REVERT: F 616 ASN cc_start: 0.8737 (p0) cc_final: 0.8488 (p0) REVERT: F 632 ASP cc_start: 0.9024 (t70) cc_final: 0.8692 (t0) REVERT: F 655 LYS cc_start: 0.8068 (pttt) cc_final: 0.7357 (mmmt) REVERT: I 166 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7128 (ttp-110) REVERT: I 426 MET cc_start: 0.8772 (tpt) cc_final: 0.8553 (tpt) REVERT: K 76 ASP cc_start: 0.8218 (p0) cc_final: 0.7953 (p0) REVERT: K 96 LYS cc_start: 0.9200 (tttm) cc_final: 0.8854 (tttm) outliers start: 61 outliers final: 32 residues processed: 239 average time/residue: 0.1290 time to fit residues: 49.5162 Evaluate side-chains 202 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 187 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 134 optimal weight: 0.0070 chunk 85 optimal weight: 0.0370 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN H 3 GLN A 540 GLN F 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.101596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080380 restraints weight = 46582.717| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.38 r_work: 0.3230 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21432 Z= 0.106 Angle : 0.687 10.243 29349 Z= 0.309 Chirality : 0.048 0.349 3585 Planarity : 0.003 0.036 3498 Dihedral : 9.670 59.950 5337 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.17 % Allowed : 14.61 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.91 (0.16), residues: 2376 helix: -1.02 (0.26), residues: 354 sheet: -1.71 (0.20), residues: 672 loop : -2.36 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 54 TYR 0.019 0.001 TYR A 638 PHE 0.007 0.001 PHE I 53 TRP 0.013 0.001 TRP I 112 HIS 0.006 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00241 (21252) covalent geometry : angle 0.64519 (28854) SS BOND : bond 0.00297 ( 45) SS BOND : angle 1.69522 ( 90) hydrogen bonds : bond 0.03078 ( 531) hydrogen bonds : angle 4.75761 ( 1386) link_ALPHA1-2 : bond 0.00964 ( 6) link_ALPHA1-2 : angle 2.35261 ( 18) link_ALPHA1-3 : bond 0.01052 ( 15) link_ALPHA1-3 : angle 1.60255 ( 45) link_ALPHA1-6 : bond 0.00860 ( 15) link_ALPHA1-6 : angle 1.72411 ( 45) link_BETA1-4 : bond 0.00445 ( 39) link_BETA1-4 : angle 1.95806 ( 117) link_NAG-ASN : bond 0.00203 ( 60) link_NAG-ASN : angle 2.08416 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8899 (t70) cc_final: 0.8608 (t0) REVERT: B 648 GLU cc_start: 0.8561 (pm20) cc_final: 0.8173 (pm20) REVERT: B 659 ASP cc_start: 0.8369 (m-30) cc_final: 0.8140 (t0) REVERT: G 114 GLN cc_start: 0.8424 (tm130) cc_final: 0.8116 (tm-30) REVERT: G 166 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7161 (ttp-110) REVERT: L 97 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6986 (pt0) REVERT: H 76 ASP cc_start: 0.8562 (t0) cc_final: 0.8197 (t0) REVERT: A 584 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: A 616 ASN cc_start: 0.8693 (p0) cc_final: 0.8475 (p0) REVERT: A 632 ASP cc_start: 0.8789 (t70) cc_final: 0.8530 (t0) REVERT: C 114 GLN cc_start: 0.8478 (tm130) cc_final: 0.8205 (tm-30) REVERT: D 97 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: E 76 ASP cc_start: 0.8596 (t0) cc_final: 0.8366 (t0) REVERT: F 632 ASP cc_start: 0.8975 (t70) cc_final: 0.8667 (t0) REVERT: F 655 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7299 (mmmt) REVERT: I 166 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7096 (ttp-110) REVERT: J 97 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: K 76 ASP cc_start: 0.8137 (p0) cc_final: 0.7879 (p0) REVERT: K 96 LYS cc_start: 0.9120 (tttm) cc_final: 0.8829 (tttm) outliers start: 46 outliers final: 21 residues processed: 229 average time/residue: 0.1348 time to fit residues: 49.8745 Evaluate side-chains 200 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 33 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.083014 restraints weight = 43949.407| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.82 r_work: 0.3192 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21432 Z= 0.176 Angle : 0.708 10.693 29349 Z= 0.321 Chirality : 0.048 0.377 3585 Planarity : 0.004 0.048 3498 Dihedral : 9.259 59.964 5336 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.55 % Allowed : 15.22 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.73 (0.17), residues: 2376 helix: -0.52 (0.28), residues: 339 sheet: -1.54 (0.20), residues: 669 loop : -2.36 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 54 TYR 0.014 0.001 TYR A 638 PHE 0.011 0.001 PHE G 53 TRP 0.012 0.001 TRP E 50 HIS 0.004 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00415 (21252) covalent geometry : angle 0.66510 (28854) SS BOND : bond 0.00237 ( 45) SS BOND : angle 1.75401 ( 90) hydrogen bonds : bond 0.03167 ( 531) hydrogen bonds : angle 4.71874 ( 1386) link_ALPHA1-2 : bond 0.00930 ( 6) link_ALPHA1-2 : angle 2.14033 ( 18) link_ALPHA1-3 : bond 0.00886 ( 15) link_ALPHA1-3 : angle 1.72173 ( 45) link_ALPHA1-6 : bond 0.00835 ( 15) link_ALPHA1-6 : angle 1.86257 ( 45) link_BETA1-4 : bond 0.00456 ( 39) link_BETA1-4 : angle 1.86913 ( 117) link_NAG-ASN : bond 0.00253 ( 60) link_NAG-ASN : angle 2.21575 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.761 Fit side-chains REVERT: B 530 MET cc_start: 0.8679 (mtp) cc_final: 0.8031 (mtm) REVERT: B 632 ASP cc_start: 0.8563 (t70) cc_final: 0.8313 (t0) REVERT: B 648 GLU cc_start: 0.8254 (pm20) cc_final: 0.8005 (pm20) REVERT: G 114 GLN cc_start: 0.8451 (tm130) cc_final: 0.8134 (tm-30) REVERT: G 166 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7311 (ttp-110) REVERT: G 269 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: G 377 ASN cc_start: 0.8863 (p0) cc_final: 0.8631 (p0) REVERT: L 97 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: A 530 MET cc_start: 0.8697 (mtp) cc_final: 0.8338 (mtm) REVERT: A 584 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: A 616 ASN cc_start: 0.8305 (p0) cc_final: 0.8031 (p0) REVERT: A 632 ASP cc_start: 0.8413 (t70) cc_final: 0.8186 (t0) REVERT: C 114 GLN cc_start: 0.8488 (tm130) cc_final: 0.8150 (tm-30) REVERT: D 97 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: F 616 ASN cc_start: 0.8419 (p0) cc_final: 0.8141 (p0) REVERT: F 632 ASP cc_start: 0.8609 (t70) cc_final: 0.8311 (t0) REVERT: F 655 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7373 (mmmt) REVERT: I 125 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8300 (tt) REVERT: I 166 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7247 (ttp-110) REVERT: J 97 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: K 76 ASP cc_start: 0.7743 (p0) cc_final: 0.7504 (p0) outliers start: 54 outliers final: 30 residues processed: 224 average time/residue: 0.1366 time to fit residues: 49.3900 Evaluate side-chains 206 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 83 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 GLN I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.102528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083159 restraints weight = 43673.404| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.84 r_work: 0.3203 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21432 Z= 0.145 Angle : 0.688 10.532 29349 Z= 0.313 Chirality : 0.048 0.372 3585 Planarity : 0.004 0.061 3498 Dihedral : 8.905 59.995 5336 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.93 % Allowed : 15.18 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.58 (0.17), residues: 2376 helix: -0.20 (0.28), residues: 339 sheet: -1.49 (0.20), residues: 696 loop : -2.31 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 54 TYR 0.015 0.001 TYR A 638 PHE 0.010 0.001 PHE C 53 TRP 0.011 0.001 TRP E 50 HIS 0.007 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00339 (21252) covalent geometry : angle 0.64728 (28854) SS BOND : bond 0.00224 ( 45) SS BOND : angle 1.71536 ( 90) hydrogen bonds : bond 0.02993 ( 531) hydrogen bonds : angle 4.60971 ( 1386) link_ALPHA1-2 : bond 0.00964 ( 6) link_ALPHA1-2 : angle 2.14158 ( 18) link_ALPHA1-3 : bond 0.00920 ( 15) link_ALPHA1-3 : angle 1.67517 ( 45) link_ALPHA1-6 : bond 0.00888 ( 15) link_ALPHA1-6 : angle 1.80255 ( 45) link_BETA1-4 : bond 0.00445 ( 39) link_BETA1-4 : angle 1.73137 ( 117) link_NAG-ASN : bond 0.00222 ( 60) link_NAG-ASN : angle 2.16545 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8553 (t70) cc_final: 0.8305 (t0) REVERT: G 114 GLN cc_start: 0.8469 (tm130) cc_final: 0.8123 (tm-30) REVERT: G 166 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7284 (ttp-110) REVERT: L 97 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6889 (pt0) REVERT: A 530 MET cc_start: 0.8766 (mtp) cc_final: 0.8414 (mtm) REVERT: A 584 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: A 616 ASN cc_start: 0.8305 (p0) cc_final: 0.8029 (p0) REVERT: A 632 ASP cc_start: 0.8407 (t70) cc_final: 0.8180 (t0) REVERT: C 114 GLN cc_start: 0.8450 (tm130) cc_final: 0.8114 (tm-30) REVERT: C 269 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6483 (pm20) REVERT: D 97 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: F 616 ASN cc_start: 0.8446 (p0) cc_final: 0.8163 (p0) REVERT: F 632 ASP cc_start: 0.8617 (t70) cc_final: 0.8305 (t0) REVERT: F 655 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7374 (mmmt) REVERT: I 125 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8246 (tt) REVERT: I 166 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7211 (ttp-110) REVERT: I 269 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: J 97 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7115 (pt0) REVERT: K 76 ASP cc_start: 0.7733 (p0) cc_final: 0.7491 (p0) outliers start: 62 outliers final: 36 residues processed: 234 average time/residue: 0.1457 time to fit residues: 54.3769 Evaluate side-chains 215 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 49 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.102071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.082637 restraints weight = 44125.863| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.85 r_work: 0.3171 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21432 Z= 0.185 Angle : 0.711 10.642 29349 Z= 0.325 Chirality : 0.048 0.419 3585 Planarity : 0.004 0.070 3498 Dihedral : 8.818 59.887 5336 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.51 % Allowed : 16.12 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.59 (0.17), residues: 2376 helix: -0.32 (0.28), residues: 357 sheet: -1.45 (0.20), residues: 696 loop : -2.32 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 54 TYR 0.015 0.001 TYR D 91 PHE 0.012 0.001 PHE G 53 TRP 0.012 0.001 TRP E 50 HIS 0.004 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00434 (21252) covalent geometry : angle 0.66844 (28854) SS BOND : bond 0.00345 ( 45) SS BOND : angle 1.91967 ( 90) hydrogen bonds : bond 0.03066 ( 531) hydrogen bonds : angle 4.68522 ( 1386) link_ALPHA1-2 : bond 0.00929 ( 6) link_ALPHA1-2 : angle 2.03569 ( 18) link_ALPHA1-3 : bond 0.00839 ( 15) link_ALPHA1-3 : angle 1.71885 ( 45) link_ALPHA1-6 : bond 0.00843 ( 15) link_ALPHA1-6 : angle 1.89595 ( 45) link_BETA1-4 : bond 0.00444 ( 39) link_BETA1-4 : angle 1.68928 ( 117) link_NAG-ASN : bond 0.00278 ( 60) link_NAG-ASN : angle 2.25801 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8579 (t70) cc_final: 0.8317 (t0) REVERT: G 114 GLN cc_start: 0.8418 (tm130) cc_final: 0.8125 (tm-30) REVERT: G 166 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7291 (ttp-110) REVERT: L 97 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: A 584 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: A 616 ASN cc_start: 0.8303 (p0) cc_final: 0.8042 (p0) REVERT: A 632 ASP cc_start: 0.8465 (t70) cc_final: 0.8251 (t0) REVERT: C 95 MET cc_start: 0.8925 (ptm) cc_final: 0.8622 (ttp) REVERT: C 114 GLN cc_start: 0.8454 (tm130) cc_final: 0.8112 (tm-30) REVERT: C 269 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6875 (pm20) REVERT: D 97 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: F 616 ASN cc_start: 0.8433 (p0) cc_final: 0.8019 (p0) REVERT: F 632 ASP cc_start: 0.8638 (t70) cc_final: 0.8343 (t0) REVERT: F 655 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7395 (mmmt) REVERT: I 125 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8355 (tt) REVERT: I 166 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7231 (ttp-110) REVERT: I 269 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: K 76 ASP cc_start: 0.7756 (p0) cc_final: 0.7512 (p0) outliers start: 53 outliers final: 38 residues processed: 218 average time/residue: 0.1374 time to fit residues: 48.2507 Evaluate side-chains 213 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 176 optimal weight: 5.9990 chunk 68 optimal weight: 0.2980 chunk 173 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.102290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082985 restraints weight = 43401.753| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.81 r_work: 0.3205 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21432 Z= 0.125 Angle : 0.679 10.365 29349 Z= 0.308 Chirality : 0.047 0.443 3585 Planarity : 0.003 0.032 3498 Dihedral : 8.522 59.763 5336 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.17 % Allowed : 16.69 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.44 (0.17), residues: 2376 helix: -0.07 (0.28), residues: 357 sheet: -1.35 (0.20), residues: 696 loop : -2.27 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 617 TYR 0.012 0.001 TYR J 91 PHE 0.009 0.001 PHE G 53 TRP 0.013 0.001 TRP B 628 HIS 0.005 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00292 (21252) covalent geometry : angle 0.64075 (28854) SS BOND : bond 0.00181 ( 45) SS BOND : angle 1.60652 ( 90) hydrogen bonds : bond 0.02835 ( 531) hydrogen bonds : angle 4.51523 ( 1386) link_ALPHA1-2 : bond 0.00956 ( 6) link_ALPHA1-2 : angle 2.10332 ( 18) link_ALPHA1-3 : bond 0.00921 ( 15) link_ALPHA1-3 : angle 1.61444 ( 45) link_ALPHA1-6 : bond 0.00901 ( 15) link_ALPHA1-6 : angle 1.75981 ( 45) link_BETA1-4 : bond 0.00438 ( 39) link_BETA1-4 : angle 1.61712 ( 117) link_NAG-ASN : bond 0.00197 ( 60) link_NAG-ASN : angle 2.09892 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: B 632 ASP cc_start: 0.8619 (t70) cc_final: 0.8370 (t0) REVERT: G 166 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7250 (ttp-110) REVERT: L 97 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7046 (pt0) REVERT: A 584 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: A 616 ASN cc_start: 0.8351 (p0) cc_final: 0.7897 (p0) REVERT: C 95 MET cc_start: 0.8966 (ptm) cc_final: 0.8761 (ttp) REVERT: C 114 GLN cc_start: 0.8423 (tm130) cc_final: 0.8100 (tm-30) REVERT: C 269 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6645 (pm20) REVERT: D 97 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: F 584 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: F 616 ASN cc_start: 0.8487 (p0) cc_final: 0.8089 (p0) REVERT: F 632 ASP cc_start: 0.8701 (t70) cc_final: 0.8384 (t0) REVERT: F 655 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7388 (mmmt) REVERT: I 125 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8321 (tt) REVERT: I 166 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7168 (ttp-110) REVERT: I 269 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: J 97 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: K 76 ASP cc_start: 0.7805 (p0) cc_final: 0.7547 (p0) outliers start: 46 outliers final: 31 residues processed: 213 average time/residue: 0.1366 time to fit residues: 47.8284 Evaluate side-chains 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080713 restraints weight = 44062.407| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.91 r_work: 0.3154 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21432 Z= 0.217 Angle : 0.728 10.759 29349 Z= 0.334 Chirality : 0.049 0.433 3585 Planarity : 0.004 0.037 3498 Dihedral : 8.578 59.554 5336 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.41 % Allowed : 16.83 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.54 (0.17), residues: 2376 helix: -0.34 (0.27), residues: 378 sheet: -1.48 (0.20), residues: 705 loop : -2.26 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.016 0.001 TYR D 91 PHE 0.013 0.002 PHE G 53 TRP 0.014 0.001 TRP E 50 HIS 0.005 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00512 (21252) covalent geometry : angle 0.68770 (28854) SS BOND : bond 0.00244 ( 45) SS BOND : angle 1.71560 ( 90) hydrogen bonds : bond 0.03083 ( 531) hydrogen bonds : angle 4.70164 ( 1386) link_ALPHA1-2 : bond 0.00903 ( 6) link_ALPHA1-2 : angle 1.94928 ( 18) link_ALPHA1-3 : bond 0.00775 ( 15) link_ALPHA1-3 : angle 1.72151 ( 45) link_ALPHA1-6 : bond 0.00826 ( 15) link_ALPHA1-6 : angle 1.97708 ( 45) link_BETA1-4 : bond 0.00462 ( 39) link_BETA1-4 : angle 1.64179 ( 117) link_NAG-ASN : bond 0.00330 ( 60) link_NAG-ASN : angle 2.31284 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: B 632 ASP cc_start: 0.8630 (t70) cc_final: 0.8372 (t0) REVERT: G 166 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7295 (ttp-110) REVERT: A 584 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8069 (pt0) REVERT: A 616 ASN cc_start: 0.8352 (p0) cc_final: 0.7922 (p0) REVERT: C 95 MET cc_start: 0.8923 (ptm) cc_final: 0.8637 (ttp) REVERT: C 114 GLN cc_start: 0.8513 (tm130) cc_final: 0.8168 (tm-30) REVERT: C 269 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: F 616 ASN cc_start: 0.8549 (p0) cc_final: 0.8237 (p0) REVERT: F 632 ASP cc_start: 0.8699 (t70) cc_final: 0.8382 (t0) REVERT: I 125 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8420 (tt) REVERT: I 166 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7182 (ttp-110) REVERT: I 269 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6828 (pm20) REVERT: K 76 ASP cc_start: 0.7814 (p0) cc_final: 0.7558 (p0) outliers start: 51 outliers final: 35 residues processed: 215 average time/residue: 0.1339 time to fit residues: 47.0585 Evaluate side-chains 209 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 8 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.103467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084212 restraints weight = 43731.080| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.83 r_work: 0.3232 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21432 Z= 0.122 Angle : 0.682 10.320 29349 Z= 0.311 Chirality : 0.047 0.423 3585 Planarity : 0.004 0.034 3498 Dihedral : 8.279 59.463 5336 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.89 % Allowed : 17.54 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.33 (0.17), residues: 2376 helix: -0.17 (0.28), residues: 378 sheet: -1.18 (0.21), residues: 666 loop : -2.21 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 350 TYR 0.013 0.001 TYR J 91 PHE 0.008 0.001 PHE C 382 TRP 0.014 0.001 TRP H 100B HIS 0.004 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00287 (21252) covalent geometry : angle 0.64365 (28854) SS BOND : bond 0.00156 ( 45) SS BOND : angle 1.73425 ( 90) hydrogen bonds : bond 0.02786 ( 531) hydrogen bonds : angle 4.48895 ( 1386) link_ALPHA1-2 : bond 0.00946 ( 6) link_ALPHA1-2 : angle 2.04960 ( 18) link_ALPHA1-3 : bond 0.00893 ( 15) link_ALPHA1-3 : angle 1.56171 ( 45) link_ALPHA1-6 : bond 0.00904 ( 15) link_ALPHA1-6 : angle 1.76766 ( 45) link_BETA1-4 : bond 0.00427 ( 39) link_BETA1-4 : angle 1.57162 ( 117) link_NAG-ASN : bond 0.00199 ( 60) link_NAG-ASN : angle 2.09700 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: B 632 ASP cc_start: 0.8585 (t70) cc_final: 0.8336 (t0) REVERT: G 166 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7258 (ttp-110) REVERT: G 334 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8132 (p) REVERT: L 97 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7042 (pt0) REVERT: A 584 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: A 616 ASN cc_start: 0.8388 (p0) cc_final: 0.7916 (p0) REVERT: C 114 GLN cc_start: 0.8465 (tm130) cc_final: 0.8125 (tm-30) REVERT: C 269 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: D 97 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7049 (pt0) REVERT: F 584 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7471 (pt0) REVERT: F 616 ASN cc_start: 0.8508 (p0) cc_final: 0.8222 (p0) REVERT: F 632 ASP cc_start: 0.8649 (t70) cc_final: 0.8349 (t0) REVERT: I 125 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8309 (tt) REVERT: I 166 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7161 (ttp-110) REVERT: I 269 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: J 97 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7095 (pt0) REVERT: K 76 ASP cc_start: 0.7757 (p0) cc_final: 0.7506 (p0) outliers start: 40 outliers final: 28 residues processed: 211 average time/residue: 0.1373 time to fit residues: 46.5060 Evaluate side-chains 206 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 15 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 230 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 0.0040 chunk 67 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN A 618 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.104652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.085445 restraints weight = 43508.798| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.83 r_work: 0.3225 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 21432 Z= 0.110 Angle : 0.666 10.235 29349 Z= 0.304 Chirality : 0.047 0.428 3585 Planarity : 0.004 0.036 3498 Dihedral : 8.006 59.835 5336 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.56 % Allowed : 17.78 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.22 (0.17), residues: 2376 helix: -0.02 (0.28), residues: 375 sheet: -1.21 (0.20), residues: 714 loop : -2.12 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.010 0.001 TYR D 91 PHE 0.026 0.001 PHE G 376 TRP 0.011 0.001 TRP B 628 HIS 0.004 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00255 (21252) covalent geometry : angle 0.63294 (28854) SS BOND : bond 0.00145 ( 45) SS BOND : angle 1.41469 ( 90) hydrogen bonds : bond 0.02637 ( 531) hydrogen bonds : angle 4.37805 ( 1386) link_ALPHA1-2 : bond 0.00925 ( 6) link_ALPHA1-2 : angle 2.05966 ( 18) link_ALPHA1-3 : bond 0.00890 ( 15) link_ALPHA1-3 : angle 1.52502 ( 45) link_ALPHA1-6 : bond 0.00924 ( 15) link_ALPHA1-6 : angle 1.66937 ( 45) link_BETA1-4 : bond 0.00451 ( 39) link_BETA1-4 : angle 1.53502 ( 117) link_NAG-ASN : bond 0.00181 ( 60) link_NAG-ASN : angle 1.99135 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.52 seconds wall clock time: 67 minutes 51.89 seconds (4071.89 seconds total)