Starting phenix.real_space_refine on Thu Feb 5 21:47:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyf_46042/02_2026/9cyf_46042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyf_46042/02_2026/9cyf_46042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cyf_46042/02_2026/9cyf_46042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyf_46042/02_2026/9cyf_46042.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyf_46042/02_2026/9cyf_46042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyf_46042/02_2026/9cyf_46042.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 C 12444 2.51 5 N 3388 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20020 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.23, per 1000 atoms: 0.21 Number of scatterers: 20020 At special positions: 0 Unit cell: (128.325, 128.325, 89.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 120 16.00 O 4064 8.00 N 3388 7.00 C 12444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN R 4 " - " MAN R 5 " " MAN V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA R 3 " - " MAN R 6 " " MAN R 6 " - " MAN R 8 " " BMA V 3 " - " MAN V 6 " " MAN V 6 " - " MAN V 8 " " BMA Z 3 " - " MAN Z 6 " " MAN Z 6 " - " MAN Z 8 " 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 P 1 " - " NAG P 2 " " 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A 502 " - " ASN A 86 " " NAG A 503 " - " ASN A 234 " " NAG B 502 " - " ASN B 86 " " NAG B 503 " - " ASN B 234 " " NAG C 502 " - " ASN C 86 " " NAG C 503 " - " ASN C 234 " " NAG D 502 " - " ASN D 86 " " NAG D 503 " - " ASN D 234 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 200 " " NAG O 1 " - " ASN A 245 " " NAG P 1 " - " ASN A 367 " " NAG Q 1 " - " ASN B 146 " " NAG R 1 " - " ASN B 200 " " NAG S 1 " - " ASN B 245 " " NAG T 1 " - " ASN B 367 " " NAG U 1 " - " ASN C 146 " " NAG V 1 " - " ASN C 200 " " NAG W 1 " - " ASN C 245 " " NAG X 1 " - " ASN C 367 " " NAG Y 1 " - " ASN D 146 " " NAG Z 1 " - " ASN D 200 " " NAG a 1 " - " ASN D 245 " " NAG b 1 " - " ASN D 367 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 914.6 milliseconds 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4472 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 56 sheets defined 2.7% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.605A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.154A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.604A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.155A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.604A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 4.155A pdb=" N ASN C 146 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.604A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.155A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 5.323A pdb=" N PHE A 97 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR A 449 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N CYS A 447 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.662A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.535A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 225 removed outlier: 4.232A pdb=" N ILE A 222 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 244 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 225 removed outlier: 4.232A pdb=" N ILE A 222 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 244 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.495A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.259A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 16.136A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.284A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG H 94 " --> pdb=" O MET H 100I" (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET H 100I" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP H 96 " --> pdb=" O TYR H 100G" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.728A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.643A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.323A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.662A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.534A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 222 through 225 removed outlier: 4.232A pdb=" N ILE B 222 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 244 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 222 through 225 removed outlier: 4.232A pdb=" N ILE B 222 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 244 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 279 through 281 Processing sheet with id=AC3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.495A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.259A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 16.136A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.284A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP E 35A" --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.941A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS E 92 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL E 102 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG E 94 " --> pdb=" O MET E 100I" (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET E 100I" --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP E 96 " --> pdb=" O TYR E 100G" (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.728A pdb=" N THR I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'I' and resid 19 through 22 removed outlier: 3.643A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 96 through 102 removed outlier: 5.323A pdb=" N PHE C 97 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR C 449 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N CYS C 447 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.663A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.532A pdb=" N ASP C 213 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 222 through 225 removed outlier: 4.232A pdb=" N ILE C 222 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY C 244 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 222 through 225 removed outlier: 4.232A pdb=" N ILE C 222 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY C 244 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AD8, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.495A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP C 402 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N GLU C 375 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N ARG C 400 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N PHE C 377 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 13.259A pdb=" N VAL C 398 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 16.136A pdb=" N VAL C 379 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 16.285A pdb=" N VAL C 396 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP F 35A" --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N CYS F 92 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL F 102 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG F 94 " --> pdb=" O MET F 100I" (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET F 100I" --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP F 96 " --> pdb=" O TYR F 100G" (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 19 through 21 Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.728A pdb=" N THR J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AE6, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.642A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 96 through 102 removed outlier: 5.322A pdb=" N PHE D 97 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR D 449 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N CYS D 447 " --> pdb=" O PRO D 99 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.663A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.532A pdb=" N ASP D 213 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 222 through 225 removed outlier: 4.231A pdb=" N ILE D 222 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY D 244 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 222 through 225 removed outlier: 4.231A pdb=" N ILE D 222 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY D 244 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 279 through 281 Processing sheet with id=AF4, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.495A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.258A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 16.134A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.283A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AF6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.941A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.784A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS G 92 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG G 94 " --> pdb=" O MET G 100I" (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET G 100I" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP G 96 " --> pdb=" O TYR G 100G" (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 19 through 21 Processing sheet with id=AF9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.728A pdb=" N THR K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AG2, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.642A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1596 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: 3.65 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6384 1.35 - 1.47: 5538 1.47 - 1.59: 8390 1.59 - 1.72: 4 1.72 - 1.84: 152 Bond restraints: 20468 Sorted by residual: bond pdb=" CA ILE C 469 " pdb=" CB ILE C 469 " ideal model delta sigma weight residual 1.540 1.605 -0.065 2.70e-02 1.37e+03 5.88e+00 bond pdb=" CA ILE A 469 " pdb=" CB ILE A 469 " ideal model delta sigma weight residual 1.540 1.605 -0.065 2.70e-02 1.37e+03 5.88e+00 bond pdb=" CA ILE D 469 " pdb=" CB ILE D 469 " ideal model delta sigma weight residual 1.540 1.605 -0.065 2.70e-02 1.37e+03 5.88e+00 bond pdb=" CA ILE B 469 " pdb=" CB ILE B 469 " ideal model delta sigma weight residual 1.540 1.605 -0.065 2.70e-02 1.37e+03 5.79e+00 bond pdb=" C2 BMA N 3 " pdb=" C3 BMA N 3 " ideal model delta sigma weight residual 1.544 1.505 0.039 2.00e-02 2.50e+03 3.81e+00 ... (remaining 20463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 26923 2.39 - 4.79: 742 4.79 - 7.18: 103 7.18 - 9.57: 8 9.57 - 11.96: 4 Bond angle restraints: 27780 Sorted by residual: angle pdb=" C HIS A 468 " pdb=" N ILE A 469 " pdb=" CA ILE A 469 " ideal model delta sigma weight residual 121.70 133.66 -11.96 1.80e+00 3.09e-01 4.42e+01 angle pdb=" C HIS B 468 " pdb=" N ILE B 469 " pdb=" CA ILE B 469 " ideal model delta sigma weight residual 121.70 133.65 -11.95 1.80e+00 3.09e-01 4.41e+01 angle pdb=" C HIS C 468 " pdb=" N ILE C 469 " pdb=" CA ILE C 469 " ideal model delta sigma weight residual 121.70 133.65 -11.95 1.80e+00 3.09e-01 4.40e+01 angle pdb=" C HIS D 468 " pdb=" N ILE D 469 " pdb=" CA ILE D 469 " ideal model delta sigma weight residual 121.70 133.65 -11.95 1.80e+00 3.09e-01 4.40e+01 angle pdb=" CA ILE B 469 " pdb=" CB ILE B 469 " pdb=" CG1 ILE B 469 " ideal model delta sigma weight residual 110.40 118.48 -8.08 1.70e+00 3.46e-01 2.26e+01 ... (remaining 27775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.84: 11567 20.84 - 41.68: 993 41.68 - 62.53: 262 62.53 - 83.37: 42 83.37 - 104.21: 24 Dihedral angle restraints: 12888 sinusoidal: 5836 harmonic: 7052 Sorted by residual: dihedral pdb=" CD ARG G 66 " pdb=" NE ARG G 66 " pdb=" CZ ARG G 66 " pdb=" NH1 ARG G 66 " ideal model delta sinusoidal sigma weight residual 0.00 61.75 -61.75 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CD ARG E 66 " pdb=" NE ARG E 66 " pdb=" CZ ARG E 66 " pdb=" NH1 ARG E 66 " ideal model delta sinusoidal sigma weight residual 0.00 61.74 -61.74 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CD ARG F 66 " pdb=" NE ARG F 66 " pdb=" CZ ARG F 66 " pdb=" NH1 ARG F 66 " ideal model delta sinusoidal sigma weight residual 0.00 61.74 -61.74 1 1.00e+01 1.00e-02 5.05e+01 ... (remaining 12885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2120 0.047 - 0.095: 776 0.095 - 0.142: 260 0.142 - 0.189: 36 0.189 - 0.237: 12 Chirality restraints: 3204 Sorted by residual: chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3201 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 66 " -0.819 9.50e-02 1.11e+02 3.68e-01 9.03e+01 pdb=" NE ARG E 66 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG E 66 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG E 66 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG E 66 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 66 " 0.819 9.50e-02 1.11e+02 3.68e-01 9.03e+01 pdb=" NE ARG H 66 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG H 66 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG H 66 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG H 66 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 66 " -0.819 9.50e-02 1.11e+02 3.68e-01 9.03e+01 pdb=" NE ARG F 66 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG F 66 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG F 66 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 66 " -0.006 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 844 2.69 - 3.24: 18628 3.24 - 3.80: 32695 3.80 - 4.35: 46267 4.35 - 4.90: 78365 Nonbonded interactions: 176799 Sorted by model distance: nonbonded pdb=" O3 NAG U 1 " pdb=" O5 NAG U 2 " model vdw 2.141 3.040 nonbonded pdb=" O3 NAG Y 1 " pdb=" O5 NAG Y 2 " model vdw 2.141 3.040 nonbonded pdb=" O3 NAG M 1 " pdb=" O5 NAG M 2 " model vdw 2.141 3.040 nonbonded pdb=" O3 NAG Q 1 " pdb=" O5 NAG Q 2 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLN F 39 " pdb=" NE2 GLN J 38 " model vdw 2.341 3.120 ... (remaining 176794 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' selection = chain 'Z' } 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: 11.440 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.640 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.006 0.065 20576 Z= 0.270 Angle : 0.966 11.964 28060 Z= 0.479 Chirality : 0.055 0.237 3204 Planarity : 0.018 0.368 3468 Dihedral : 16.620 104.211 8284 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.19 % Allowed : 21.01 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.15), residues: 2468 helix: -1.70 (0.83), residues: 24 sheet: -1.05 (0.17), residues: 884 loop : -1.40 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.003 ARG G 66 TYR 0.019 0.002 TYR F 53 PHE 0.018 0.002 PHE C 410 TRP 0.016 0.002 TRP F 36 HIS 0.008 0.002 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00624 (20468) covalent geometry : angle 0.93317 (27780) SS BOND : bond 0.00656 ( 44) SS BOND : angle 2.52446 ( 88) hydrogen bonds : bond 0.23271 ( 568) hydrogen bonds : angle 10.69751 ( 1596) link_ALPHA1-2 : bond 0.00685 ( 4) link_ALPHA1-2 : angle 0.95881 ( 12) link_ALPHA1-3 : bond 0.00363 ( 8) link_ALPHA1-3 : angle 1.63645 ( 24) link_ALPHA1-6 : bond 0.00290 ( 8) link_ALPHA1-6 : angle 2.00570 ( 24) link_BETA1-4 : bond 0.00448 ( 20) link_BETA1-4 : angle 2.29757 ( 60) link_NAG-ASN : bond 0.00619 ( 24) link_NAG-ASN : angle 3.65997 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8405 (p0) REVERT: C 146 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (p0) REVERT: D 146 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8408 (p0) outliers start: 4 outliers final: 0 residues processed: 272 average time/residue: 0.4881 time to fit residues: 154.8428 Evaluate side-chains 238 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 235 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain D residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.0470 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.4980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 294 ASN C 294 ASN D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.168305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119475 restraints weight = 21404.129| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.93 r_work: 0.3149 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20576 Z= 0.141 Angle : 0.662 9.954 28060 Z= 0.332 Chirality : 0.049 0.216 3204 Planarity : 0.005 0.047 3468 Dihedral : 9.336 74.777 4006 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.38 % Allowed : 20.72 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2468 helix: -1.13 (0.89), residues: 24 sheet: -0.32 (0.17), residues: 972 loop : -0.99 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 66 TYR 0.015 0.002 TYR B 121 PHE 0.014 0.002 PHE A 354 TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00310 (20468) covalent geometry : angle 0.63123 (27780) SS BOND : bond 0.00357 ( 44) SS BOND : angle 1.72193 ( 88) hydrogen bonds : bond 0.04259 ( 568) hydrogen bonds : angle 7.36137 ( 1596) link_ALPHA1-2 : bond 0.00530 ( 4) link_ALPHA1-2 : angle 1.59776 ( 12) link_ALPHA1-3 : bond 0.00895 ( 8) link_ALPHA1-3 : angle 2.03573 ( 24) link_ALPHA1-6 : bond 0.00554 ( 8) link_ALPHA1-6 : angle 1.43012 ( 24) link_BETA1-4 : bond 0.00611 ( 20) link_BETA1-4 : angle 2.22207 ( 60) link_NAG-ASN : bond 0.00352 ( 24) link_NAG-ASN : angle 2.60252 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 243 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.9131 (ptm) cc_final: 0.8771 (ptp) REVERT: A 368 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: A 417 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7197 (t) REVERT: H 52 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5382 (mp) REVERT: B 362 MET cc_start: 0.9126 (ptm) cc_final: 0.8769 (ptp) REVERT: B 368 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 417 CYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7198 (t) REVERT: E 52 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5382 (mp) REVERT: C 362 MET cc_start: 0.9140 (ptm) cc_final: 0.8770 (ptp) REVERT: C 368 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: C 417 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7205 (t) REVERT: F 52 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5379 (mp) REVERT: D 362 MET cc_start: 0.9132 (ptm) cc_final: 0.8760 (ptp) REVERT: D 368 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: D 417 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7183 (t) REVERT: G 52 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5376 (mp) outliers start: 72 outliers final: 20 residues processed: 286 average time/residue: 0.4400 time to fit residues: 147.5265 Evaluate side-chains 249 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 53 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 151 optimal weight: 0.2980 chunk 128 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 441 ASN H 39 GLN B 294 ASN B 441 ASN C 294 ASN C 441 ASN D 294 ASN D 441 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.167778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116846 restraints weight = 21462.785| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.97 r_work: 0.3128 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20576 Z= 0.132 Angle : 0.611 9.792 28060 Z= 0.305 Chirality : 0.047 0.224 3204 Planarity : 0.004 0.046 3468 Dihedral : 8.403 61.501 4000 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.87 % Allowed : 23.26 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2468 helix: -0.77 (0.96), residues: 24 sheet: -0.09 (0.18), residues: 884 loop : -0.82 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.011 0.001 TYR A 121 PHE 0.013 0.002 PHE B 410 TRP 0.012 0.001 TRP A 178 HIS 0.006 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00294 (20468) covalent geometry : angle 0.58632 (27780) SS BOND : bond 0.00236 ( 44) SS BOND : angle 1.26158 ( 88) hydrogen bonds : bond 0.03928 ( 568) hydrogen bonds : angle 6.54573 ( 1596) link_ALPHA1-2 : bond 0.00398 ( 4) link_ALPHA1-2 : angle 1.51955 ( 12) link_ALPHA1-3 : bond 0.00866 ( 8) link_ALPHA1-3 : angle 1.65965 ( 24) link_ALPHA1-6 : bond 0.00516 ( 8) link_ALPHA1-6 : angle 1.45574 ( 24) link_BETA1-4 : bond 0.00523 ( 20) link_BETA1-4 : angle 1.92577 ( 60) link_NAG-ASN : bond 0.00332 ( 24) link_NAG-ASN : angle 2.40869 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8397 (mttt) cc_final: 0.8046 (mmpt) REVERT: A 362 MET cc_start: 0.9151 (ptm) cc_final: 0.8790 (ptp) REVERT: A 368 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: H 52 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5556 (mp) REVERT: H 83 THR cc_start: 0.6623 (OUTLIER) cc_final: 0.6285 (p) REVERT: B 308 LYS cc_start: 0.8410 (mttt) cc_final: 0.8047 (mmpt) REVERT: B 362 MET cc_start: 0.9157 (ptm) cc_final: 0.8794 (ptp) REVERT: B 368 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: E 52 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5550 (mp) REVERT: E 83 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6282 (p) REVERT: C 368 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: C 392 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8837 (tp) REVERT: F 52 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5543 (mp) REVERT: F 83 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.6305 (p) REVERT: D 368 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: D 392 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8843 (tp) REVERT: G 52 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5554 (mp) REVERT: G 83 THR cc_start: 0.6627 (OUTLIER) cc_final: 0.6288 (p) outliers start: 61 outliers final: 24 residues processed: 302 average time/residue: 0.4301 time to fit residues: 152.4773 Evaluate side-chains 270 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 24 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN H 39 GLN B 168 HIS B 294 ASN E 39 GLN C 168 HIS C 294 ASN F 39 GLN D 294 ASN G 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114710 restraints weight = 21578.611| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.98 r_work: 0.3098 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20576 Z= 0.164 Angle : 0.631 9.834 28060 Z= 0.313 Chirality : 0.048 0.225 3204 Planarity : 0.004 0.045 3468 Dihedral : 8.157 57.110 4000 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.37 % Allowed : 21.52 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.17), residues: 2468 helix: -0.75 (0.96), residues: 24 sheet: 0.10 (0.18), residues: 884 loop : -0.86 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100C TYR 0.011 0.001 TYR B 121 PHE 0.014 0.002 PHE B 410 TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00378 (20468) covalent geometry : angle 0.60429 (27780) SS BOND : bond 0.00298 ( 44) SS BOND : angle 1.46556 ( 88) hydrogen bonds : bond 0.03650 ( 568) hydrogen bonds : angle 6.35348 ( 1596) link_ALPHA1-2 : bond 0.00397 ( 4) link_ALPHA1-2 : angle 1.58405 ( 12) link_ALPHA1-3 : bond 0.00824 ( 8) link_ALPHA1-3 : angle 1.75146 ( 24) link_ALPHA1-6 : bond 0.00477 ( 8) link_ALPHA1-6 : angle 1.49922 ( 24) link_BETA1-4 : bond 0.00490 ( 20) link_BETA1-4 : angle 1.94935 ( 60) link_NAG-ASN : bond 0.00409 ( 24) link_NAG-ASN : angle 2.46255 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 235 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: A 431 LYS cc_start: 0.5665 (OUTLIER) cc_final: 0.5021 (pttm) REVERT: B 368 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: B 431 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5023 (pttm) REVERT: C 368 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: C 431 LYS cc_start: 0.5672 (OUTLIER) cc_final: 0.5018 (pttm) REVERT: D 368 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: D 431 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5020 (pttm) outliers start: 93 outliers final: 38 residues processed: 306 average time/residue: 0.4691 time to fit residues: 167.8855 Evaluate side-chains 286 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 168 HIS A 173 GLN A 294 ASN B 104 ASN B 173 GLN B 294 ASN E 39 GLN C 104 ASN C 173 GLN C 294 ASN F 39 GLN D 104 ASN D 168 HIS D 173 GLN D 294 ASN G 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.163390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113906 restraints weight = 21490.828| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.95 r_work: 0.3093 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20576 Z= 0.184 Angle : 0.649 9.837 28060 Z= 0.321 Chirality : 0.049 0.229 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.893 56.866 4000 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.09 % Allowed : 22.60 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2468 helix: -0.84 (0.96), residues: 24 sheet: 0.24 (0.18), residues: 924 loop : -0.86 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 100C TYR 0.012 0.002 TYR A 374 PHE 0.014 0.002 PHE A 410 TRP 0.014 0.001 TRP C 178 HIS 0.003 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00425 (20468) covalent geometry : angle 0.62092 (27780) SS BOND : bond 0.00382 ( 44) SS BOND : angle 1.67901 ( 88) hydrogen bonds : bond 0.03690 ( 568) hydrogen bonds : angle 6.27964 ( 1596) link_ALPHA1-2 : bond 0.00331 ( 4) link_ALPHA1-2 : angle 1.65132 ( 12) link_ALPHA1-3 : bond 0.00776 ( 8) link_ALPHA1-3 : angle 1.76411 ( 24) link_ALPHA1-6 : bond 0.00418 ( 8) link_ALPHA1-6 : angle 1.55720 ( 24) link_BETA1-4 : bond 0.00435 ( 20) link_BETA1-4 : angle 1.98813 ( 60) link_NAG-ASN : bond 0.00428 ( 24) link_NAG-ASN : angle 2.48462 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 240 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8413 (mttt) cc_final: 0.8010 (mmpt) REVERT: A 362 MET cc_start: 0.9173 (ptm) cc_final: 0.8828 (ptp) REVERT: A 368 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 431 LYS cc_start: 0.5633 (OUTLIER) cc_final: 0.4881 (pttm) REVERT: B 308 LYS cc_start: 0.8414 (mttt) cc_final: 0.8013 (mmpt) REVERT: B 362 MET cc_start: 0.9180 (ptm) cc_final: 0.8833 (ptp) REVERT: B 368 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: B 431 LYS cc_start: 0.5628 (OUTLIER) cc_final: 0.4878 (pttm) REVERT: C 308 LYS cc_start: 0.8415 (mttt) cc_final: 0.8013 (mmpt) REVERT: C 362 MET cc_start: 0.9171 (ptm) cc_final: 0.8822 (ptp) REVERT: C 368 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: C 431 LYS cc_start: 0.5626 (OUTLIER) cc_final: 0.4870 (pttm) REVERT: D 128 LYS cc_start: 0.8340 (ptpp) cc_final: 0.8075 (pttm) REVERT: D 308 LYS cc_start: 0.8405 (mttt) cc_final: 0.8009 (mmpt) REVERT: D 362 MET cc_start: 0.9174 (ptm) cc_final: 0.8823 (ptp) REVERT: D 368 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: D 431 LYS cc_start: 0.5627 (OUTLIER) cc_final: 0.4878 (pttm) outliers start: 87 outliers final: 40 residues processed: 304 average time/residue: 0.4231 time to fit residues: 152.0315 Evaluate side-chains 292 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 173 GLN A 294 ASN B 104 ASN B 173 GLN B 294 ASN C 104 ASN C 173 GLN C 294 ASN D 104 ASN D 173 GLN D 294 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115022 restraints weight = 21464.237| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.90 r_work: 0.3077 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20576 Z= 0.197 Angle : 0.655 9.848 28060 Z= 0.324 Chirality : 0.049 0.230 3204 Planarity : 0.004 0.044 3468 Dihedral : 7.842 57.120 4000 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.42 % Allowed : 22.74 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2468 helix: -0.99 (0.93), residues: 24 sheet: 0.27 (0.18), residues: 924 loop : -0.83 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100C TYR 0.012 0.002 TYR B 374 PHE 0.015 0.002 PHE D 410 TRP 0.015 0.001 TRP C 178 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00458 (20468) covalent geometry : angle 0.62749 (27780) SS BOND : bond 0.00348 ( 44) SS BOND : angle 1.63507 ( 88) hydrogen bonds : bond 0.03683 ( 568) hydrogen bonds : angle 6.26414 ( 1596) link_ALPHA1-2 : bond 0.00292 ( 4) link_ALPHA1-2 : angle 1.67313 ( 12) link_ALPHA1-3 : bond 0.00771 ( 8) link_ALPHA1-3 : angle 1.79880 ( 24) link_ALPHA1-6 : bond 0.00411 ( 8) link_ALPHA1-6 : angle 1.56323 ( 24) link_BETA1-4 : bond 0.00440 ( 20) link_BETA1-4 : angle 2.03092 ( 60) link_NAG-ASN : bond 0.00422 ( 24) link_NAG-ASN : angle 2.53845 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 248 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8407 (mttt) cc_final: 0.8036 (mmpt) REVERT: A 362 MET cc_start: 0.9178 (ptm) cc_final: 0.8837 (ptp) REVERT: A 368 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: A 431 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.4885 (pttm) REVERT: H 96 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: B 308 LYS cc_start: 0.8407 (mttt) cc_final: 0.8038 (mmpt) REVERT: B 362 MET cc_start: 0.9181 (ptm) cc_final: 0.8835 (ptp) REVERT: B 368 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: B 431 LYS cc_start: 0.5672 (OUTLIER) cc_final: 0.4874 (pttm) REVERT: E 96 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6696 (m-30) REVERT: C 308 LYS cc_start: 0.8409 (mttt) cc_final: 0.8037 (mmpt) REVERT: C 362 MET cc_start: 0.9179 (ptm) cc_final: 0.8829 (ptp) REVERT: C 368 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: C 431 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.4868 (pttm) REVERT: F 96 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: D 308 LYS cc_start: 0.8408 (mttt) cc_final: 0.7918 (mmmt) REVERT: D 362 MET cc_start: 0.9184 (ptm) cc_final: 0.8836 (ptp) REVERT: D 368 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: D 431 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.4858 (pttm) REVERT: G 96 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6696 (m-30) outliers start: 94 outliers final: 46 residues processed: 317 average time/residue: 0.4256 time to fit residues: 159.5586 Evaluate side-chains 302 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN H 76 ASN B 294 ASN E 76 ASN C 294 ASN F 76 ASN D 294 ASN G 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.166426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113612 restraints weight = 21473.968| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.83 r_work: 0.3113 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20576 Z= 0.130 Angle : 0.608 9.787 28060 Z= 0.300 Chirality : 0.047 0.223 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.453 55.719 4000 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.29 % Allowed : 24.30 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2468 helix: -0.85 (0.94), residues: 24 sheet: 0.21 (0.18), residues: 908 loop : -0.75 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.010 0.001 TYR A 121 PHE 0.013 0.002 PHE C 410 TRP 0.016 0.001 TRP C 178 HIS 0.002 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00294 (20468) covalent geometry : angle 0.58314 (27780) SS BOND : bond 0.00267 ( 44) SS BOND : angle 1.43691 ( 88) hydrogen bonds : bond 0.03204 ( 568) hydrogen bonds : angle 6.00229 ( 1596) link_ALPHA1-2 : bond 0.00281 ( 4) link_ALPHA1-2 : angle 1.71253 ( 12) link_ALPHA1-3 : bond 0.00896 ( 8) link_ALPHA1-3 : angle 1.57313 ( 24) link_ALPHA1-6 : bond 0.00502 ( 8) link_ALPHA1-6 : angle 1.48363 ( 24) link_BETA1-4 : bond 0.00501 ( 20) link_BETA1-4 : angle 1.77465 ( 60) link_NAG-ASN : bond 0.00305 ( 24) link_NAG-ASN : angle 2.34450 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 243 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8419 (mttt) cc_final: 0.8068 (mmpt) REVERT: A 362 MET cc_start: 0.9180 (ptm) cc_final: 0.8835 (ptp) REVERT: A 368 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: A 431 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.4909 (pttm) REVERT: H 96 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: B 308 LYS cc_start: 0.8423 (mttt) cc_final: 0.8066 (mmpt) REVERT: B 362 MET cc_start: 0.9177 (ptm) cc_final: 0.8830 (ptp) REVERT: B 368 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: B 431 LYS cc_start: 0.5640 (OUTLIER) cc_final: 0.4910 (pttm) REVERT: E 96 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: C 308 LYS cc_start: 0.8421 (mttt) cc_final: 0.8064 (mmpt) REVERT: C 362 MET cc_start: 0.9173 (ptm) cc_final: 0.8821 (ptp) REVERT: C 368 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: C 431 LYS cc_start: 0.5650 (OUTLIER) cc_final: 0.4908 (pttm) REVERT: F 96 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: D 308 LYS cc_start: 0.8412 (mttt) cc_final: 0.8064 (mmpt) REVERT: D 362 MET cc_start: 0.9174 (ptm) cc_final: 0.8824 (ptp) REVERT: D 368 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: D 431 LYS cc_start: 0.5652 (OUTLIER) cc_final: 0.4910 (pttm) REVERT: G 96 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6758 (m-30) outliers start: 70 outliers final: 41 residues processed: 303 average time/residue: 0.4207 time to fit residues: 149.9623 Evaluate side-chains 294 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 213 optimal weight: 0.0030 chunk 101 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 173 GLN A 294 ASN B 104 ASN B 173 GLN B 294 ASN E 39 GLN C 104 ASN C 173 GLN C 294 ASN F 39 GLN D 104 ASN D 173 GLN D 294 ASN G 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112747 restraints weight = 21628.627| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.97 r_work: 0.3020 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20576 Z= 0.251 Angle : 0.687 9.924 28060 Z= 0.340 Chirality : 0.051 0.235 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.854 58.036 4000 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.71 % Allowed : 24.15 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2468 helix: -1.15 (0.90), residues: 24 sheet: 0.04 (0.18), residues: 960 loop : -0.77 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 100C TYR 0.013 0.002 TYR D 374 PHE 0.016 0.002 PHE C 410 TRP 0.013 0.002 TRP A 178 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00590 (20468) covalent geometry : angle 0.65816 (27780) SS BOND : bond 0.00453 ( 44) SS BOND : angle 1.65555 ( 88) hydrogen bonds : bond 0.03772 ( 568) hydrogen bonds : angle 6.23835 ( 1596) link_ALPHA1-2 : bond 0.00254 ( 4) link_ALPHA1-2 : angle 1.66253 ( 12) link_ALPHA1-3 : bond 0.00667 ( 8) link_ALPHA1-3 : angle 1.84890 ( 24) link_ALPHA1-6 : bond 0.00338 ( 8) link_ALPHA1-6 : angle 1.65021 ( 24) link_BETA1-4 : bond 0.00393 ( 20) link_BETA1-4 : angle 2.13741 ( 60) link_NAG-ASN : bond 0.00526 ( 24) link_NAG-ASN : angle 2.67990 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 237 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8402 (mttt) cc_final: 0.7859 (mmmt) REVERT: A 362 MET cc_start: 0.9175 (ptm) cc_final: 0.8821 (ptp) REVERT: A 431 LYS cc_start: 0.5815 (OUTLIER) cc_final: 0.4945 (pttm) REVERT: H 96 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6665 (m-30) REVERT: B 308 LYS cc_start: 0.8404 (mttt) cc_final: 0.7858 (mmmt) REVERT: B 362 MET cc_start: 0.9175 (ptm) cc_final: 0.8821 (ptp) REVERT: B 431 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4941 (pttm) REVERT: E 96 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: C 308 LYS cc_start: 0.8402 (mttt) cc_final: 0.7856 (mmmt) REVERT: C 362 MET cc_start: 0.9196 (ptm) cc_final: 0.8839 (ptp) REVERT: C 431 LYS cc_start: 0.5807 (OUTLIER) cc_final: 0.4934 (pttm) REVERT: F 96 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: D 308 LYS cc_start: 0.8399 (mttt) cc_final: 0.7858 (mmmt) REVERT: D 362 MET cc_start: 0.9198 (ptm) cc_final: 0.8845 (ptp) REVERT: D 431 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.4946 (pttm) REVERT: G 96 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6664 (m-30) outliers start: 79 outliers final: 44 residues processed: 299 average time/residue: 0.4469 time to fit residues: 156.9720 Evaluate side-chains 289 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 173 GLN A 294 ASN B 104 ASN B 173 GLN B 294 ASN C 104 ASN C 173 GLN C 294 ASN D 104 ASN D 173 GLN D 294 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109486 restraints weight = 21447.633| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.86 r_work: 0.3068 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20576 Z= 0.189 Angle : 0.649 9.816 28060 Z= 0.321 Chirality : 0.049 0.224 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.694 57.115 4000 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.01 % Allowed : 25.19 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2468 helix: -1.17 (0.89), residues: 24 sheet: 0.07 (0.18), residues: 956 loop : -0.79 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 100C TYR 0.012 0.002 TYR A 374 PHE 0.015 0.002 PHE A 410 TRP 0.016 0.001 TRP C 178 HIS 0.003 0.001 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00440 (20468) covalent geometry : angle 0.62311 (27780) SS BOND : bond 0.00372 ( 44) SS BOND : angle 1.51225 ( 88) hydrogen bonds : bond 0.03457 ( 568) hydrogen bonds : angle 6.13788 ( 1596) link_ALPHA1-2 : bond 0.00203 ( 4) link_ALPHA1-2 : angle 1.72132 ( 12) link_ALPHA1-3 : bond 0.00772 ( 8) link_ALPHA1-3 : angle 1.75619 ( 24) link_ALPHA1-6 : bond 0.00405 ( 8) link_ALPHA1-6 : angle 1.55238 ( 24) link_BETA1-4 : bond 0.00443 ( 20) link_BETA1-4 : angle 1.97612 ( 60) link_NAG-ASN : bond 0.00407 ( 24) link_NAG-ASN : angle 2.48927 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8415 (mttt) cc_final: 0.7946 (mmmt) REVERT: A 362 MET cc_start: 0.9158 (ptm) cc_final: 0.8801 (ptp) REVERT: A 431 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.4959 (pttm) REVERT: H 52 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.5991 (pp) REVERT: H 96 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: B 308 LYS cc_start: 0.8413 (mttt) cc_final: 0.7944 (mmmt) REVERT: B 362 MET cc_start: 0.9161 (ptm) cc_final: 0.8808 (ptp) REVERT: B 431 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.4952 (pttm) REVERT: E 52 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.5981 (pp) REVERT: E 96 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6724 (m-30) REVERT: C 308 LYS cc_start: 0.8409 (mttt) cc_final: 0.7939 (mmmt) REVERT: C 362 MET cc_start: 0.9153 (ptm) cc_final: 0.8798 (ptp) REVERT: C 431 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.4950 (pttm) REVERT: F 52 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.5979 (pp) REVERT: F 96 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6745 (m-30) REVERT: D 308 LYS cc_start: 0.8406 (mttt) cc_final: 0.7940 (mmmt) REVERT: D 362 MET cc_start: 0.9158 (ptm) cc_final: 0.8801 (ptp) REVERT: D 431 LYS cc_start: 0.5841 (OUTLIER) cc_final: 0.4946 (pttm) REVERT: G 52 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5982 (pp) REVERT: G 96 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6711 (m-30) outliers start: 64 outliers final: 40 residues processed: 302 average time/residue: 0.4262 time to fit residues: 151.4381 Evaluate side-chains 295 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 173 GLN A 294 ASN B 104 ASN B 173 GLN B 294 ASN C 104 ASN C 173 GLN C 294 ASN D 104 ASN D 173 GLN D 294 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112497 restraints weight = 21501.319| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.83 r_work: 0.3098 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20576 Z= 0.144 Angle : 0.620 9.795 28060 Z= 0.306 Chirality : 0.048 0.223 3204 Planarity : 0.004 0.047 3468 Dihedral : 7.428 56.268 4000 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.40 % Allowed : 25.61 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2468 helix: -1.00 (0.92), residues: 24 sheet: 0.06 (0.18), residues: 916 loop : -0.76 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.011 0.001 TYR A 374 PHE 0.013 0.002 PHE D 410 TRP 0.016 0.001 TRP D 178 HIS 0.002 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00330 (20468) covalent geometry : angle 0.59614 (27780) SS BOND : bond 0.00286 ( 44) SS BOND : angle 1.33112 ( 88) hydrogen bonds : bond 0.03227 ( 568) hydrogen bonds : angle 5.99621 ( 1596) link_ALPHA1-2 : bond 0.00246 ( 4) link_ALPHA1-2 : angle 1.69697 ( 12) link_ALPHA1-3 : bond 0.00888 ( 8) link_ALPHA1-3 : angle 1.61400 ( 24) link_ALPHA1-6 : bond 0.00464 ( 8) link_ALPHA1-6 : angle 1.51740 ( 24) link_BETA1-4 : bond 0.00481 ( 20) link_BETA1-4 : angle 1.81284 ( 60) link_NAG-ASN : bond 0.00345 ( 24) link_NAG-ASN : angle 2.42607 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8427 (mttt) cc_final: 0.7931 (mmmt) REVERT: A 362 MET cc_start: 0.9134 (ptm) cc_final: 0.8782 (ptp) REVERT: A 431 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.4905 (pttm) REVERT: H 52 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6025 (pp) REVERT: H 96 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: B 308 LYS cc_start: 0.8428 (mttt) cc_final: 0.7932 (mmmt) REVERT: B 362 MET cc_start: 0.9141 (ptm) cc_final: 0.8787 (ptp) REVERT: B 431 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.4925 (pttm) REVERT: E 52 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6014 (pp) REVERT: E 96 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: C 308 LYS cc_start: 0.8420 (mttt) cc_final: 0.7924 (mmmt) REVERT: C 362 MET cc_start: 0.9131 (ptm) cc_final: 0.8779 (ptp) REVERT: C 431 LYS cc_start: 0.5781 (OUTLIER) cc_final: 0.4929 (pttm) REVERT: F 52 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6018 (pp) REVERT: F 96 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6816 (m-30) REVERT: D 308 LYS cc_start: 0.8412 (mttt) cc_final: 0.7920 (mmmt) REVERT: D 362 MET cc_start: 0.9135 (ptm) cc_final: 0.8781 (ptp) REVERT: D 431 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.4914 (pttm) REVERT: G 52 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6019 (pp) REVERT: G 96 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6800 (m-30) outliers start: 51 outliers final: 35 residues processed: 294 average time/residue: 0.4302 time to fit residues: 148.9122 Evaluate side-chains 295 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 190 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 132 optimal weight: 0.0870 chunk 175 optimal weight: 0.0040 chunk 91 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 overall best weight: 0.6772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 294 ASN C 294 ASN D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113211 restraints weight = 21569.314| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.83 r_work: 0.3109 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20576 Z= 0.138 Angle : 0.613 9.784 28060 Z= 0.301 Chirality : 0.048 0.224 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.274 55.778 4000 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.40 % Allowed : 25.56 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2468 helix: -0.88 (0.94), residues: 24 sheet: 0.09 (0.18), residues: 916 loop : -0.73 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 400 TYR 0.011 0.001 TYR D 374 PHE 0.013 0.002 PHE B 354 TRP 0.015 0.001 TRP B 178 HIS 0.003 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00315 (20468) covalent geometry : angle 0.58860 (27780) SS BOND : bond 0.00267 ( 44) SS BOND : angle 1.27957 ( 88) hydrogen bonds : bond 0.03094 ( 568) hydrogen bonds : angle 5.87810 ( 1596) link_ALPHA1-2 : bond 0.00264 ( 4) link_ALPHA1-2 : angle 1.66519 ( 12) link_ALPHA1-3 : bond 0.00887 ( 8) link_ALPHA1-3 : angle 1.56789 ( 24) link_ALPHA1-6 : bond 0.00474 ( 8) link_ALPHA1-6 : angle 1.50938 ( 24) link_BETA1-4 : bond 0.00468 ( 20) link_BETA1-4 : angle 1.77552 ( 60) link_NAG-ASN : bond 0.00335 ( 24) link_NAG-ASN : angle 2.50080 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5966.56 seconds wall clock time: 102 minutes 54.45 seconds (6174.45 seconds total)