Starting phenix.real_space_refine on Sun Sep 13 04:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vi0_21208/09_2026/6vi0_21208.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vi0_21208/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vi0_21208/09_2026/6vi0_21208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vi0_21208/09_2026/6vi0_21208.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vi0_21208/09_2026/6vi0_21208.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vi0_21208/09_2026/6vi0_21208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vi0_21208/09_2026/6vi0_21208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vi0_21208/09_2026/6vi0_21208.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 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 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 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 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 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 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 chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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 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 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 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 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 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 chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 4.93, per 1000 atoms: 0.24 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: 2.41 Conformation dependent library (CDL) restraints added in 813.2 milliseconds 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: 0.70 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: 3.93 Time building geometry restraints manager: 2.99 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 - 16.49: 10269 16.49 - 32.98: 1202 32.98 - 49.48: 208 49.48 - 65.97: 48 65.97 - 82.46: 15 Dihedral angle restraints: 11742 sinusoidal: 4800 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 11739 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: 0.01 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.800 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 13.991 82.459 7137 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/Z covalent geometry : bond 0.00850 / 0.41 (21252) covalent geometry : angle 1.11983 / 0.57 (28854) SS BOND : bond 0.00622 / 0.36 ( 45) SS BOND : angle 1.68388 / 1.08 ( 90) hydrogen bonds : bond 0.26357 / 17.50 ( 531) hydrogen bonds : angle 10.46124 / 7.08 ( 1386) link_ALPHA1-2 : bond 0.00123 / 0.06 ( 6) link_ALPHA1-2 : angle 3.98839 / 2.59 ( 18) link_ALPHA1-3 : bond 0.00624 / 0.35 ( 15) link_ALPHA1-3 : angle 3.30322 / 2.11 ( 45) link_ALPHA1-6 : bond 0.02991 / 1.79 ( 15) link_ALPHA1-6 : angle 14.65742 / 8.04 ( 45) link_BETA1-4 : bond 0.04759 / 2.66 ( 39) link_BETA1-4 : angle 17.09320 / 11.09 ( 117) link_NAG-ASN : bond 0.01080 / 0.68 ( 60) link_NAG-ASN : angle 3.15426 / 2.05 ( 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 : 0.832 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: 0.1749 time to fit residues: 78.5629 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 : 0.796 ------------------------------------------------------------------------------- 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... 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** F 590 GLN J 6 GLN K 3 GLN ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.102509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082647 restraints weight = 43740.676| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.92 r_work: 0.3203 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21432 Z= 0.133 Angle : 0.755 11.592 29349 Z= 0.346 Chirality : 0.046 0.308 3585 Planarity : 0.005 0.045 3498 Dihedral : 5.747 32.621 2614 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.70 % Allowed : 11.25 % Favored : 87.04 % 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: -4.29 (0.14), residues: 2376 helix: -3.11 (0.17), residues: 390 sheet: -2.55 (0.18), residues: 717 loop : -2.95 (0.15), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 54 TYR 0.016 0.001 TYR A 638 PHE 0.013 0.001 PHE I 53 TRP 0.013 0.001 TRP E 100B HIS 0.012 0.001 HIS K 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (21252) covalent geometry : angle 0.71168 / 0.34 (28854) SS BOND : bond 0.00230 / 0.13 ( 45) SS BOND : angle 1.46593 / 0.97 ( 90) hydrogen bonds : bond 0.04467 / 2.95 ( 531) hydrogen bonds : angle 6.07453 / 4.15 ( 1386) link_ALPHA1-2 : bond 0.01179 / 0.60 ( 6) link_ALPHA1-2 : angle 2.07741 / 1.38 ( 18) link_ALPHA1-3 : bond 0.00732 / 0.41 ( 15) link_ALPHA1-3 : angle 1.79833 / 1.19 ( 45) link_ALPHA1-6 : bond 0.00454 / 0.26 ( 15) link_ALPHA1-6 : angle 1.73593 / 1.14 ( 45) link_BETA1-4 : bond 0.00754 / 0.43 ( 39) link_BETA1-4 : angle 2.09893 / 1.38 ( 117) link_NAG-ASN : bond 0.00287 / 0.17 ( 60) link_NAG-ASN : angle 2.43765 / 1.58 ( 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 253 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8507 (t70) cc_final: 0.8210 (t0) REVERT: G 114 GLN cc_start: 0.8449 (tm130) cc_final: 0.8088 (tm-30) REVERT: G 166 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7205 (ttp-170) REVERT: H 76 ASP cc_start: 0.7752 (p0) cc_final: 0.7509 (p0) REVERT: H 87 THR cc_start: 0.9067 (m) cc_final: 0.8767 (p) REVERT: A 632 ASP cc_start: 0.8330 (t70) cc_final: 0.8052 (t0) REVERT: C 114 GLN cc_start: 0.8448 (tm130) cc_final: 0.8139 (tm-30) REVERT: C 166 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7192 (ttp-110) REVERT: E 75 GLN cc_start: 0.8861 (mt0) cc_final: 0.8653 (mt0) REVERT: F 616 ASN cc_start: 0.8540 (p0) cc_final: 0.8291 (p0) REVERT: F 632 ASP cc_start: 0.8599 (t70) cc_final: 0.8267 (t0) REVERT: F 655 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7442 (mmmt) REVERT: I 166 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7230 (ttp-110) REVERT: J 97 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6517 (pm20) REVERT: K 76 ASP cc_start: 0.7989 (p0) cc_final: 0.7688 (p0) REVERT: K 101 GLU cc_start: 0.8315 (tt0) cc_final: 0.8108 (tt0) outliers start: 36 outliers final: 22 residues processed: 248 average time/residue: 0.1432 time to fit residues: 56.5919 Evaluate side-chains 211 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 J residue 97 GLU 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: 6.9990 chunk 232 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.100379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079055 restraints weight = 46957.704| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.38 r_work: 0.3205 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1675 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= 0.131 Angle : 0.716 16.014 29349 Z= 0.329 Chirality : 0.046 0.314 3585 Planarity : 0.004 0.038 3498 Dihedral : 5.459 39.155 2607 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.74 % Allowed : 12.77 % Favored : 84.49 % 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: -3.42 (0.16), residues: 2376 helix: -1.87 (0.23), residues: 387 sheet: -2.00 (0.19), residues: 669 loop : -2.58 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 54 TYR 0.018 0.001 TYR A 638 PHE 0.010 0.001 PHE G 53 TRP 0.012 0.001 TRP H 100B HIS 0.008 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (21252) covalent geometry : angle 0.66864 / 0.32 (28854) SS BOND : bond 0.00268 / 0.15 ( 45) SS BOND : angle 2.55100 / 1.82 ( 90) hydrogen bonds : bond 0.03542 / 2.36 ( 531) hydrogen bonds : angle 5.21182 / 3.56 ( 1386) link_ALPHA1-2 : bond 0.00970 / 0.49 ( 6) link_ALPHA1-2 : angle 2.07699 / 1.40 ( 18) link_ALPHA1-3 : bond 0.00691 / 0.39 ( 15) link_ALPHA1-3 : angle 1.73813 / 1.15 ( 45) link_ALPHA1-6 : bond 0.00488 / 0.29 ( 15) link_ALPHA1-6 : angle 1.79381 / 1.14 ( 45) link_BETA1-4 : bond 0.00452 / 0.26 ( 39) link_BETA1-4 : angle 1.84293 / 1.24 ( 117) link_NAG-ASN : bond 0.00217 / 0.13 ( 60) link_NAG-ASN : angle 2.11452 / 1.39 ( 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 256 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8817 (mtp) cc_final: 0.8488 (mtp) REVERT: B 632 ASP cc_start: 0.8930 (t70) cc_final: 0.8615 (t0) REVERT: G 95 MET cc_start: 0.9128 (ptm) cc_final: 0.8922 (ttp) REVERT: G 114 GLN cc_start: 0.8432 (tm130) cc_final: 0.8110 (tm-30) REVERT: G 166 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7185 (ttp-110) REVERT: L 97 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: H 76 ASP cc_start: 0.8064 (p0) cc_final: 0.7854 (p0) REVERT: H 87 THR cc_start: 0.9045 (m) cc_final: 0.8835 (p) REVERT: A 616 ASN cc_start: 0.8734 (p0) cc_final: 0.8261 (p0) REVERT: A 632 ASP cc_start: 0.8817 (t70) cc_final: 0.8540 (t0) REVERT: C 114 GLN cc_start: 0.8466 (tm130) cc_final: 0.8195 (tm-30) REVERT: D 97 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: F 616 ASN cc_start: 0.8721 (p0) cc_final: 0.8469 (p0) REVERT: F 632 ASP cc_start: 0.8987 (t70) cc_final: 0.8641 (t0) REVERT: F 655 LYS cc_start: 0.8049 (pttt) cc_final: 0.7349 (mmmt) REVERT: I 166 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7107 (ttp-110) REVERT: J 42 GLN cc_start: 0.8093 (mt0) cc_final: 0.7670 (mp10) REVERT: J 97 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6618 (pm20) REVERT: K 76 ASP cc_start: 0.8193 (p0) cc_final: 0.7938 (p0) REVERT: K 96 LYS cc_start: 0.9135 (tttm) cc_final: 0.8829 (tttm) outliers start: 58 outliers final: 26 residues processed: 246 average time/residue: 0.1419 time to fit residues: 56.0028 Evaluate side-chains 206 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 120 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 L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 663 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 C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 187 optimal weight: 5.9990 chunk 211 optimal weight: 0.0270 chunk 140 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 229 optimal weight: 0.0170 chunk 233 optimal weight: 8.9990 chunk 206 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 85 optimal weight: 0.0000 overall best weight: 0.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN H 102 HIS A 540 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.102299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.081089 restraints weight = 46488.829| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.38 r_work: 0.3245 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 21432 Z= 0.100 Angle : 0.656 10.686 29349 Z= 0.299 Chirality : 0.044 0.299 3585 Planarity : 0.003 0.037 3498 Dihedral : 5.222 38.995 2606 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.70 % Allowed : 14.47 % Favored : 83.83 % 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: -2.87 (0.16), residues: 2376 helix: -1.06 (0.26), residues: 354 sheet: -1.72 (0.20), residues: 681 loop : -2.28 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 54 TYR 0.019 0.001 TYR A 638 PHE 0.007 0.001 PHE G 53 TRP 0.012 0.001 TRP I 112 HIS 0.004 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (21252) covalent geometry : angle 0.61882 / 0.29 (28854) SS BOND : bond 0.00186 / 0.11 ( 45) SS BOND : angle 1.90228 / 1.29 ( 90) hydrogen bonds : bond 0.03020 / 2.00 ( 531) hydrogen bonds : angle 4.71354 / 3.22 ( 1386) link_ALPHA1-2 : bond 0.01019 / 0.52 ( 6) link_ALPHA1-2 : angle 2.11567 / 1.43 ( 18) link_ALPHA1-3 : bond 0.00750 / 0.42 ( 15) link_ALPHA1-3 : angle 1.62502 / 1.08 ( 45) link_ALPHA1-6 : bond 0.00514 / 0.31 ( 15) link_ALPHA1-6 : angle 1.60142 / 1.02 ( 45) link_BETA1-4 : bond 0.00446 / 0.27 ( 39) link_BETA1-4 : angle 1.62065 / 1.10 ( 117) link_NAG-ASN : bond 0.00198 / 0.13 ( 60) link_NAG-ASN : angle 1.88872 / 1.24 ( 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 227 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8882 (t70) cc_final: 0.8586 (t0) REVERT: B 648 GLU cc_start: 0.8516 (pm20) cc_final: 0.8125 (pm20) REVERT: B 659 ASP cc_start: 0.8404 (m-30) cc_final: 0.8117 (t0) REVERT: G 114 GLN cc_start: 0.8401 (tm130) cc_final: 0.8090 (tm-30) REVERT: G 166 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7162 (ttp-110) REVERT: L 54 ARG cc_start: 0.7798 (ptp-110) cc_final: 0.7566 (mtm110) REVERT: L 97 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6960 (pt0) REVERT: H 76 ASP cc_start: 0.8529 (t0) cc_final: 0.8178 (t0) REVERT: A 584 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: A 616 ASN cc_start: 0.8694 (p0) cc_final: 0.8475 (p0) REVERT: A 632 ASP cc_start: 0.8770 (t70) cc_final: 0.8507 (t0) REVERT: C 114 GLN cc_start: 0.8432 (tm130) cc_final: 0.8166 (tm-30) REVERT: D 54 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7828 (mtm110) REVERT: D 97 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6859 (pt0) REVERT: E 76 ASP cc_start: 0.8599 (t0) cc_final: 0.8298 (t0) REVERT: F 632 ASP cc_start: 0.8965 (t70) cc_final: 0.8632 (t0) REVERT: F 655 LYS cc_start: 0.7996 (pttt) cc_final: 0.7287 (mmmt) REVERT: I 166 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7094 (ttp-110) REVERT: K 76 ASP cc_start: 0.8115 (p0) cc_final: 0.7857 (p0) REVERT: K 96 LYS cc_start: 0.9081 (tttm) cc_final: 0.8774 (ttpp) outliers start: 36 outliers final: 14 residues processed: 222 average time/residue: 0.1388 time to fit residues: 49.6869 Evaluate side-chains 193 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain K residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 130 optimal weight: 0.3980 chunk 156 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN G 246 GLN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN I 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.103611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.084326 restraints weight = 43830.097| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.84 r_work: 0.3250 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21432 Z= 0.138 Angle : 0.666 10.396 29349 Z= 0.304 Chirality : 0.045 0.341 3585 Planarity : 0.003 0.036 3498 Dihedral : 4.989 34.798 2603 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.65 % Allowed : 15.04 % Favored : 82.32 % 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: -2.66 (0.17), residues: 2376 helix: -0.76 (0.27), residues: 357 sheet: -1.52 (0.20), residues: 681 loop : -2.24 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 54 TYR 0.015 0.001 TYR A 638 PHE 0.009 0.001 PHE G 53 TRP 0.010 0.001 TRP E 50 HIS 0.014 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (21252) covalent geometry : angle 0.63009 / 0.29 (28854) SS BOND : bond 0.00236 / 0.12 ( 45) SS BOND : angle 1.71980 / 1.15 ( 90) hydrogen bonds : bond 0.02977 / 1.96 ( 531) hydrogen bonds : angle 4.59776 / 3.13 ( 1386) link_ALPHA1-2 : bond 0.00947 / 0.48 ( 6) link_ALPHA1-2 : angle 1.98766 / 1.33 ( 18) link_ALPHA1-3 : bond 0.00634 / 0.36 ( 15) link_ALPHA1-3 : angle 1.65165 / 1.07 ( 45) link_ALPHA1-6 : bond 0.00487 / 0.29 ( 15) link_ALPHA1-6 : angle 1.68644 / 1.09 ( 45) link_BETA1-4 : bond 0.00425 / 0.25 ( 39) link_BETA1-4 : angle 1.56115 / 1.05 ( 117) link_NAG-ASN : bond 0.00199 / 0.12 ( 60) link_NAG-ASN : angle 1.96306 / 1.30 ( 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 237 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.8848 (mtp) cc_final: 0.8383 (mtp) REVERT: B 632 ASP cc_start: 0.8603 (t70) cc_final: 0.8335 (t0) REVERT: B 648 GLU cc_start: 0.8280 (pm20) cc_final: 0.7912 (pm20) REVERT: G 114 GLN cc_start: 0.8397 (tm130) cc_final: 0.8089 (tm-30) REVERT: G 166 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7248 (ttp-110) REVERT: G 377 ASN cc_start: 0.8883 (p0) cc_final: 0.8650 (p0) REVERT: L 97 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: H 76 ASP cc_start: 0.8573 (t0) cc_final: 0.8356 (t0) REVERT: A 530 MET cc_start: 0.8647 (mtp) cc_final: 0.8287 (mtm) REVERT: A 584 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: A 616 ASN cc_start: 0.8354 (p0) cc_final: 0.8085 (p0) REVERT: A 632 ASP cc_start: 0.8441 (t70) cc_final: 0.8202 (t0) REVERT: C 114 GLN cc_start: 0.8421 (tm130) cc_final: 0.8098 (tm-30) REVERT: D 97 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7019 (pt0) REVERT: F 616 ASN cc_start: 0.8477 (p0) cc_final: 0.8215 (p0) REVERT: F 632 ASP cc_start: 0.8649 (t70) cc_final: 0.8333 (t0) REVERT: F 655 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7327 (mmmt) REVERT: I 166 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7201 (ttp-110) REVERT: J 97 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6976 (pt0) REVERT: K 76 ASP cc_start: 0.7790 (p0) cc_final: 0.7525 (p0) REVERT: K 96 LYS cc_start: 0.8847 (tttm) cc_final: 0.8615 (ttpp) outliers start: 56 outliers final: 34 residues processed: 228 average time/residue: 0.1446 time to fit residues: 53.2650 Evaluate side-chains 212 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 H residue 70 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 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 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 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 83 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.100480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081060 restraints weight = 44325.105| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.81 r_work: 0.3182 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21432 Z= 0.272 Angle : 0.781 11.065 29349 Z= 0.362 Chirality : 0.048 0.319 3585 Planarity : 0.004 0.072 3498 Dihedral : 5.395 35.776 2603 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.79 % Allowed : 15.13 % Favored : 82.08 % 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: -2.82 (0.17), residues: 2376 helix: -0.65 (0.27), residues: 360 sheet: -1.66 (0.20), residues: 708 loop : -2.40 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 54 TYR 0.021 0.002 TYR D 91 PHE 0.016 0.002 PHE G 53 TRP 0.017 0.002 TRP E 50 HIS 0.015 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.27 (21252) covalent geometry : angle 0.73947 / 0.35 (28854) SS BOND : bond 0.00380 / 0.23 ( 45) SS BOND : angle 2.12142 / 1.41 ( 90) hydrogen bonds : bond 0.03390 / 2.23 ( 531) hydrogen bonds : angle 4.94587 / 3.38 ( 1386) link_ALPHA1-2 : bond 0.00883 / 0.44 ( 6) link_ALPHA1-2 : angle 1.86422 / 1.22 ( 18) link_ALPHA1-3 : bond 0.00611 / 0.34 ( 15) link_ALPHA1-3 : angle 1.74574 / 1.10 ( 45) link_ALPHA1-6 : bond 0.00445 / 0.27 ( 15) link_ALPHA1-6 : angle 1.94275 / 1.29 ( 45) link_BETA1-4 : bond 0.00468 / 0.26 ( 39) link_BETA1-4 : angle 1.64653 / 1.09 ( 117) link_NAG-ASN : bond 0.00446 / 0.27 ( 60) link_NAG-ASN : angle 2.38382 / 1.60 ( 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 238 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8659 (t70) cc_final: 0.8368 (t0) REVERT: B 648 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: G 114 GLN cc_start: 0.8407 (tm130) cc_final: 0.8083 (tm-30) REVERT: G 166 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7294 (ttp-110) REVERT: H 76 ASP cc_start: 0.8597 (t0) cc_final: 0.8351 (t0) REVERT: A 584 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: A 616 ASN cc_start: 0.8370 (p0) cc_final: 0.8110 (p0) REVERT: A 632 ASP cc_start: 0.8538 (t70) cc_final: 0.8272 (t0) REVERT: C 114 GLN cc_start: 0.8470 (tm130) cc_final: 0.8131 (tm-30) REVERT: C 269 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: F 632 ASP cc_start: 0.8736 (t70) cc_final: 0.8410 (t0) REVERT: I 166 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7229 (ttp-110) REVERT: I 434 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7863 (ptm) REVERT: J 97 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: K 76 ASP cc_start: 0.7794 (p0) cc_final: 0.7520 (p0) outliers start: 59 outliers final: 40 residues processed: 227 average time/residue: 0.1375 time to fit residues: 50.3446 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 : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 648 GLU 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 85 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 70 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 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 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 68 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 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 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: 0.8980 chunk 210 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 377 ASN H 102 HIS F 540 GLN I 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.103136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.083657 restraints weight = 43934.400| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.86 r_work: 0.3209 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21432 Z= 0.120 Angle : 0.671 10.259 29349 Z= 0.307 Chirality : 0.045 0.358 3585 Planarity : 0.004 0.034 3498 Dihedral : 5.118 38.308 2603 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.55 % Allowed : 16.03 % Favored : 81.42 % 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: -2.51 (0.17), residues: 2376 helix: -0.18 (0.28), residues: 357 sheet: -1.30 (0.21), residues: 669 loop : -2.35 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 308 TYR 0.013 0.001 TYR A 638 PHE 0.009 0.001 PHE C 53 TRP 0.013 0.001 TRP H 100B HIS 0.012 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (21252) covalent geometry : angle 0.63694 / 0.30 (28854) SS BOND : bond 0.00187 / 0.10 ( 45) SS BOND : angle 1.66334 / 1.09 ( 90) hydrogen bonds : bond 0.02892 / 1.91 ( 531) hydrogen bonds : angle 4.60050 / 3.14 ( 1386) link_ALPHA1-2 : bond 0.00940 / 0.47 ( 6) link_ALPHA1-2 : angle 1.93091 / 1.30 ( 18) link_ALPHA1-3 : bond 0.00640 / 0.36 ( 15) link_ALPHA1-3 : angle 1.55622 / 1.00 ( 45) link_ALPHA1-6 : bond 0.00533 / 0.32 ( 15) link_ALPHA1-6 : angle 1.66992 / 1.10 ( 45) link_BETA1-4 : bond 0.00393 / 0.23 ( 39) link_BETA1-4 : angle 1.47681 / 1.00 ( 117) link_NAG-ASN : bond 0.00211 / 0.13 ( 60) link_NAG-ASN : angle 2.00221 / 1.34 ( 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 229 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: B 632 ASP cc_start: 0.8534 (t70) cc_final: 0.8281 (t0) REVERT: G 114 GLN cc_start: 0.8396 (tm130) cc_final: 0.8106 (tm-30) REVERT: G 166 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7235 (ttp-110) REVERT: L 97 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7024 (pt0) REVERT: A 584 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: A 616 ASN cc_start: 0.8333 (p0) cc_final: 0.8062 (p0) REVERT: A 632 ASP cc_start: 0.8374 (t70) cc_final: 0.8152 (t0) REVERT: C 114 GLN cc_start: 0.8449 (tm130) cc_final: 0.8125 (tm-30) REVERT: C 269 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: D 97 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6986 (pt0) REVERT: F 584 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: F 632 ASP cc_start: 0.8616 (t70) cc_final: 0.8317 (t0) REVERT: I 166 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7202 (ttp-110) REVERT: J 97 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: K 76 ASP cc_start: 0.7707 (p0) cc_final: 0.7454 (p0) outliers start: 54 outliers final: 32 residues processed: 220 average time/residue: 0.1289 time to fit residues: 46.6759 Evaluate side-chains 207 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 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 120 VAL 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 33 THR Chi-restraints excluded: chain E residue 68 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 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 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 98 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 176 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 173 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 193 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3679 r_free = 0.3679 target = 0.101510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081978 restraints weight = 43602.551| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.81 r_work: 0.3218 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21432 Z= 0.134 Angle : 0.675 10.340 29349 Z= 0.309 Chirality : 0.046 0.349 3585 Planarity : 0.004 0.033 3498 Dihedral : 5.033 39.355 2603 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.41 % Allowed : 16.17 % Favored : 81.42 % 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: -2.42 (0.17), residues: 2376 helix: -0.01 (0.28), residues: 357 sheet: -1.32 (0.20), residues: 696 loop : -2.28 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 308 TYR 0.012 0.001 TYR D 91 PHE 0.009 0.001 PHE G 53 TRP 0.011 0.001 TRP H 100B HIS 0.005 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (21252) covalent geometry : angle 0.64143 / 0.30 (28854) SS BOND : bond 0.00196 / 0.11 ( 45) SS BOND : angle 1.63628 / 1.09 ( 90) hydrogen bonds : bond 0.02825 / 1.87 ( 531) hydrogen bonds : angle 4.53027 / 3.09 ( 1386) link_ALPHA1-2 : bond 0.00917 / 0.46 ( 6) link_ALPHA1-2 : angle 1.87940 / 1.26 ( 18) link_ALPHA1-3 : bond 0.00606 / 0.35 ( 15) link_ALPHA1-3 : angle 1.57963 / 1.01 ( 45) link_ALPHA1-6 : bond 0.00505 / 0.30 ( 15) link_ALPHA1-6 : angle 1.66790 / 1.10 ( 45) link_BETA1-4 : bond 0.00407 / 0.24 ( 39) link_BETA1-4 : angle 1.43087 / 0.96 ( 117) link_NAG-ASN : bond 0.00213 / 0.13 ( 60) link_NAG-ASN : angle 1.97203 / 1.32 ( 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: 51 poor density : 172 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.8462 (mtp) cc_final: 0.8147 (mtm) REVERT: B 584 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: B 632 ASP cc_start: 0.8568 (t70) cc_final: 0.8309 (t0) REVERT: G 114 GLN cc_start: 0.8408 (tm130) cc_final: 0.8082 (tm-30) REVERT: G 166 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7323 (ttp-110) REVERT: L 97 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: A 584 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: A 616 ASN cc_start: 0.8332 (p0) cc_final: 0.7944 (p0) REVERT: A 632 ASP cc_start: 0.8458 (t70) cc_final: 0.8242 (t0) REVERT: C 114 GLN cc_start: 0.8423 (tm130) cc_final: 0.8109 (tm-30) REVERT: C 269 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: D 97 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: F 584 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: F 632 ASP cc_start: 0.8656 (t70) cc_final: 0.8332 (t0) REVERT: I 166 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7197 (ttp-110) REVERT: J 97 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: K 76 ASP cc_start: 0.7728 (p0) cc_final: 0.7480 (p0) outliers start: 51 outliers final: 36 residues processed: 213 average time/residue: 0.1311 time to fit residues: 46.3344 Evaluate side-chains 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 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 H residue 70 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 68 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN 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 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 98 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 181 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3699 r_free = 0.3699 target = 0.102259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.082854 restraints weight = 44055.413| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.84 r_work: 0.3193 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21432 Z= 0.177 Angle : 0.705 10.528 29349 Z= 0.324 Chirality : 0.047 0.431 3585 Planarity : 0.004 0.034 3498 Dihedral : 5.143 40.188 2603 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.36 % Allowed : 16.36 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.42 (0.17), residues: 2376 helix: 0.09 (0.28), residues: 357 sheet: -1.37 (0.20), residues: 696 loop : -2.28 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 308 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 0.005 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (21252) covalent geometry : angle 0.67021 / 0.31 (28854) SS BOND : bond 0.00244 / 0.14 ( 45) SS BOND : angle 1.86286 / 1.19 ( 90) hydrogen bonds : bond 0.02925 / 1.93 ( 531) hydrogen bonds : angle 4.60746 / 3.14 ( 1386) link_ALPHA1-2 : bond 0.00848 / 0.43 ( 6) link_ALPHA1-2 : angle 1.82754 / 1.21 ( 18) link_ALPHA1-3 : bond 0.00568 / 0.33 ( 15) link_ALPHA1-3 : angle 1.61072 / 1.02 ( 45) link_ALPHA1-6 : bond 0.00464 / 0.28 ( 15) link_ALPHA1-6 : angle 1.75061 / 1.16 ( 45) link_BETA1-4 : bond 0.00413 / 0.24 ( 39) link_BETA1-4 : angle 1.43549 / 0.96 ( 117) link_NAG-ASN : bond 0.00278 / 0.17 ( 60) link_NAG-ASN : angle 2.07876 / 1.39 ( 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 223 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7983 (pt0) REVERT: B 632 ASP cc_start: 0.8569 (t70) cc_final: 0.8314 (t0) REVERT: G 166 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7321 (ttp-110) REVERT: L 97 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: A 584 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: A 616 ASN cc_start: 0.8314 (p0) cc_final: 0.7939 (p0) REVERT: A 632 ASP cc_start: 0.8419 (t70) cc_final: 0.8206 (t0) REVERT: C 114 GLN cc_start: 0.8484 (tm130) cc_final: 0.8142 (tm-30) REVERT: C 269 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: D 97 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: F 584 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: F 632 ASP cc_start: 0.8640 (t70) cc_final: 0.8336 (t0) REVERT: I 166 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7200 (ttp-110) REVERT: J 97 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: K 76 ASP cc_start: 0.7749 (p0) cc_final: 0.7499 (p0) outliers start: 50 outliers final: 39 residues processed: 215 average time/residue: 0.1352 time to fit residues: 47.3872 Evaluate side-chains 212 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 H residue 70 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 68 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN 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 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 Chi-restraints excluded: chain K residue 98 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 8 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 108 optimal weight: 0.0170 chunk 173 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3699 r_free = 0.3699 target = 0.102261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082970 restraints weight = 44185.582| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.81 r_work: 0.3186 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21432 Z= 0.185 Angle : 0.716 10.530 29349 Z= 0.329 Chirality : 0.047 0.429 3585 Planarity : 0.004 0.033 3498 Dihedral : 5.210 41.788 2603 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.32 % Allowed : 16.41 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.42 (0.17), residues: 2376 helix: -0.07 (0.28), residues: 378 sheet: -1.39 (0.20), residues: 696 loop : -2.25 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 308 TYR 0.015 0.001 TYR D 91 PHE 0.012 0.001 PHE G 53 TRP 0.014 0.001 TRP B 628 HIS 0.005 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (21252) covalent geometry : angle 0.68203 / 0.32 (28854) SS BOND : bond 0.00233 / 0.13 ( 45) SS BOND : angle 1.74190 / 1.15 ( 90) hydrogen bonds : bond 0.02970 / 1.97 ( 531) hydrogen bonds : angle 4.62468 / 3.16 ( 1386) link_ALPHA1-2 : bond 0.00882 / 0.45 ( 6) link_ALPHA1-2 : angle 1.81153 / 1.19 ( 18) link_ALPHA1-3 : bond 0.00566 / 0.32 ( 15) link_ALPHA1-3 : angle 1.59783 / 1.01 ( 45) link_ALPHA1-6 : bond 0.00460 / 0.28 ( 15) link_ALPHA1-6 : angle 1.77327 / 1.18 ( 45) link_BETA1-4 : bond 0.00403 / 0.23 ( 39) link_BETA1-4 : angle 1.42006 / 0.95 ( 117) link_NAG-ASN : bond 0.00287 / 0.17 ( 60) link_NAG-ASN : angle 2.09789 / 1.41 ( 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 225 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7983 (pt0) REVERT: B 632 ASP cc_start: 0.8557 (t70) cc_final: 0.8309 (t0) REVERT: G 166 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7309 (ttp-110) REVERT: L 97 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: A 584 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: A 616 ASN cc_start: 0.8319 (p0) cc_final: 0.7942 (p0) REVERT: A 632 ASP cc_start: 0.8433 (t70) cc_final: 0.8217 (t0) REVERT: C 114 GLN cc_start: 0.8426 (tm130) cc_final: 0.8088 (tm-30) REVERT: C 269 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: D 97 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: F 584 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: F 632 ASP cc_start: 0.8628 (t70) cc_final: 0.8305 (t0) REVERT: I 166 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.7204 (ttp-110) REVERT: J 97 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: K 76 ASP cc_start: 0.7737 (p0) cc_final: 0.7483 (p0) outliers start: 49 outliers final: 41 residues processed: 216 average time/residue: 0.1410 time to fit residues: 49.4976 Evaluate side-chains 216 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 H residue 70 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 18 MET Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN 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 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 Chi-restraints excluded: chain K residue 98 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 15 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 230 optimal weight: 0.6980 chunk 138 optimal weight: 0.1980 chunk 198 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.103878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.084724 restraints weight = 43756.883| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.81 r_work: 0.3216 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21432 Z= 0.115 Angle : 0.684 10.223 29349 Z= 0.313 Chirality : 0.046 0.408 3585 Planarity : 0.004 0.083 3498 Dihedral : 5.107 45.703 2603 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.89 % Allowed : 17.21 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.27 (0.17), residues: 2376 helix: 0.29 (0.29), residues: 357 sheet: -1.26 (0.20), residues: 699 loop : -2.22 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L 54 TYR 0.011 0.001 TYR D 91 PHE 0.013 0.001 PHE G 376 TRP 0.023 0.001 TRP C 112 HIS 0.005 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (21252) covalent geometry : angle 0.65386 / 0.31 (28854) SS BOND : bond 0.00191 / 0.12 ( 45) SS BOND : angle 1.55380 / 0.97 ( 90) hydrogen bonds : bond 0.02735 / 1.82 ( 531) hydrogen bonds : angle 4.45951 / 3.04 ( 1386) link_ALPHA1-2 : bond 0.00936 / 0.47 ( 6) link_ALPHA1-2 : angle 1.84079 / 1.23 ( 18) link_ALPHA1-3 : bond 0.00613 / 0.35 ( 15) link_ALPHA1-3 : angle 1.51244 / 0.97 ( 45) link_ALPHA1-6 : bond 0.00556 / 0.33 ( 15) link_ALPHA1-6 : angle 1.60459 / 1.05 ( 45) link_BETA1-4 : bond 0.00392 / 0.23 ( 39) link_BETA1-4 : angle 1.38278 / 0.94 ( 117) link_NAG-ASN : bond 0.00192 / 0.13 ( 60) link_NAG-ASN : angle 1.91165 / 1.27 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3863.84 seconds wall clock time: 67 minutes 54.90 seconds (4074.90 seconds total)