Starting phenix.real_space_refine on Sat Jul 4 12:01:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyf_46042/07_2026/9cyf_46042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyf_46042/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cyf_46042/07_2026/9cyf_46042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyf_46042/07_2026/9cyf_46042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cyf_46042/07_2026/9cyf_46042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyf_46042/07_2026/9cyf_46042.map" } 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-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.01, per 1000 atoms: 0.20 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: 1.92 Conformation dependent library (CDL) restraints added in 677.7 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: 0.55 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: 2.45 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: 0.03 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: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.290 Find NCS groups from input model: 0.420 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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/Z covalent geometry : bond 0.00624 / 0.27 (20468) covalent geometry : angle 0.93317 / 0.47 (27780) SS BOND : bond 0.00656 / 0.38 ( 44) SS BOND : angle 2.52446 / 1.71 ( 88) hydrogen bonds : bond 0.23271 / 15.53 ( 568) hydrogen bonds : angle 10.69751 / 7.53 ( 1596) link_ALPHA1-2 : bond 0.00685 / 0.34 ( 4) link_ALPHA1-2 : angle 0.95881 / 0.52 ( 12) link_ALPHA1-3 : bond 0.00363 / 0.22 ( 8) link_ALPHA1-3 : angle 1.63645 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00290 / 0.17 ( 8) link_ALPHA1-6 : angle 2.00570 / 1.09 ( 24) link_BETA1-4 : bond 0.00448 / 0.29 ( 20) link_BETA1-4 : angle 2.29757 / 1.58 ( 60) link_NAG-ASN : bond 0.00619 / 0.32 ( 24) link_NAG-ASN : angle 3.65997 / 2.16 ( 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 : 0.559 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: 0.4363 time to fit residues: 138.7299 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 : 0.691 ------------------------------------------------------------------------------- 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... 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 = 0.3866 r_free = 0.3866 target = 0.167205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116928 restraints weight = 21453.845| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.84 r_work: 0.3134 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0988 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= 0.142 Angle : 0.668 10.040 28060 Z= 0.337 Chirality : 0.048 0.216 3204 Planarity : 0.004 0.047 3468 Dihedral : 9.527 77.847 4006 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.05 % Allowed : 21.01 % Favored : 75.94 % 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: -1.11 (0.16), residues: 2468 helix: -1.14 (0.90), residues: 24 sheet: -0.34 (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 G 66 TYR 0.015 0.002 TYR D 121 PHE 0.014 0.002 PHE A 354 TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS D 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (20468) covalent geometry : angle 0.63552 / 0.33 (27780) SS BOND : bond 0.00409 / 0.26 ( 44) SS BOND : angle 1.87795 / 1.30 ( 88) hydrogen bonds : bond 0.04583 / 3.08 ( 568) hydrogen bonds : angle 7.51547 / 5.29 ( 1596) link_ALPHA1-2 : bond 0.00459 / 0.23 ( 4) link_ALPHA1-2 : angle 1.52555 / 0.81 ( 12) link_ALPHA1-3 : bond 0.00844 / 0.54 ( 8) link_ALPHA1-3 : angle 1.91803 / 1.06 ( 24) link_ALPHA1-6 : bond 0.00438 / 0.26 ( 8) link_ALPHA1-6 : angle 1.38859 / 0.81 ( 24) link_BETA1-4 : bond 0.00688 / 0.44 ( 20) link_BETA1-4 : angle 2.25411 / 1.61 ( 60) link_NAG-ASN : bond 0.00332 / 0.18 ( 24) link_NAG-ASN : angle 2.69570 / 1.66 ( 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 313 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 248 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.9135 (ptm) cc_final: 0.8774 (ptp) REVERT: A 368 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: A 417 CYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7273 (t) REVERT: H 52 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5449 (mp) REVERT: B 362 MET cc_start: 0.9131 (ptm) cc_final: 0.8774 (ptp) REVERT: B 368 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: B 417 CYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7278 (t) REVERT: E 52 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5450 (mp) REVERT: C 362 MET cc_start: 0.9144 (ptm) cc_final: 0.8772 (ptp) REVERT: C 368 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: C 417 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7263 (t) REVERT: F 52 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5442 (mp) REVERT: D 362 MET cc_start: 0.9136 (ptm) cc_final: 0.8763 (ptp) REVERT: D 368 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: D 417 CYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7266 (t) REVERT: G 52 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5445 (mp) outliers start: 65 outliers final: 20 residues processed: 288 average time/residue: 0.4236 time to fit residues: 142.8993 Evaluate side-chains 256 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 441 ASN B 294 ASN B 441 ASN C 294 ASN C 441 ASN D 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.166072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116665 restraints weight = 21463.905| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.15 r_work: 0.3116 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1315 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= 0.148 Angle : 0.624 9.762 28060 Z= 0.312 Chirality : 0.048 0.227 3204 Planarity : 0.004 0.046 3468 Dihedral : 8.562 63.842 4000 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.96 % Allowed : 23.07 % Favored : 73.97 % 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: -0.84 (0.17), residues: 2468 helix: -0.83 (0.96), residues: 24 sheet: -0.11 (0.18), residues: 884 loop : -0.81 (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 B 121 PHE 0.013 0.002 PHE B 410 TRP 0.013 0.001 TRP C 178 HIS 0.005 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (20468) covalent geometry : angle 0.59862 / 0.31 (27780) SS BOND : bond 0.00261 / 0.17 ( 44) SS BOND : angle 1.33121 / 0.92 ( 88) hydrogen bonds : bond 0.04017 / 2.68 ( 568) hydrogen bonds : angle 6.63915 / 4.70 ( 1596) link_ALPHA1-2 : bond 0.00397 / 0.20 ( 4) link_ALPHA1-2 : angle 1.53563 / 0.83 ( 12) link_ALPHA1-3 : bond 0.00806 / 0.51 ( 8) link_ALPHA1-3 : angle 1.71546 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00496 / 0.30 ( 8) link_ALPHA1-6 : angle 1.48473 / 0.87 ( 24) link_BETA1-4 : bond 0.00509 / 0.32 ( 20) link_BETA1-4 : angle 2.01757 / 1.39 ( 60) link_NAG-ASN : bond 0.00352 / 0.20 ( 24) link_NAG-ASN : angle 2.45381 / 1.52 ( 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 311 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.9160 (ptm) cc_final: 0.8791 (ptp) REVERT: A 368 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: H 52 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5451 (mp) REVERT: H 83 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6077 (p) REVERT: B 362 MET cc_start: 0.9163 (ptm) cc_final: 0.8794 (ptp) REVERT: B 368 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: E 52 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5441 (mp) REVERT: E 83 THR cc_start: 0.6410 (OUTLIER) cc_final: 0.6073 (p) REVERT: C 368 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: F 52 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5437 (mp) REVERT: F 83 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.6084 (p) REVERT: D 368 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: G 52 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5444 (mp) REVERT: G 83 THR cc_start: 0.6422 (OUTLIER) cc_final: 0.6086 (p) outliers start: 63 outliers final: 20 residues processed: 303 average time/residue: 0.4066 time to fit residues: 146.8735 Evaluate side-chains 269 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 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 368 GLU 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 368 GLU 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: 0.0670 chunk 143 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 168 HIS A 173 GLN A 294 ASN H 39 GLN B 104 ASN B 147 ASN B 168 HIS B 173 GLN B 294 ASN E 39 GLN C 104 ASN C 147 ASN C 168 HIS 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.161851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111735 restraints weight = 21726.669| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.98 r_work: 0.2981 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 20576 Z= 0.279 Angle : 0.731 10.014 28060 Z= 0.364 Chirality : 0.052 0.239 3204 Planarity : 0.005 0.044 3468 Dihedral : 8.705 61.472 4000 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.03 % Allowed : 20.16 % Favored : 74.81 % 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: -0.84 (0.17), residues: 2468 helix: -1.10 (0.92), residues: 24 sheet: -0.09 (0.18), residues: 960 loop : -0.85 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 100C TYR 0.014 0.002 TYR A 374 PHE 0.017 0.003 PHE C 410 TRP 0.015 0.002 TRP C 178 HIS 0.006 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 (20468) covalent geometry : angle 0.69986 / 0.36 (27780) SS BOND : bond 0.00495 / 0.31 ( 44) SS BOND : angle 1.72814 / 1.19 ( 88) hydrogen bonds : bond 0.04296 / 2.86 ( 568) hydrogen bonds : angle 6.70784 / 4.77 ( 1596) link_ALPHA1-2 : bond 0.00378 / 0.19 ( 4) link_ALPHA1-2 : angle 1.68604 / 0.89 ( 12) link_ALPHA1-3 : bond 0.00607 / 0.38 ( 8) link_ALPHA1-3 : angle 2.01125 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00374 / 0.22 ( 8) link_ALPHA1-6 : angle 1.61336 / 0.93 ( 24) link_BETA1-4 : bond 0.00472 / 0.31 ( 20) link_BETA1-4 : angle 2.38987 / 1.62 ( 60) link_NAG-ASN : bond 0.00609 / 0.32 ( 24) link_NAG-ASN : angle 2.81796 / 1.72 ( 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 339 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 232 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8470 (m-30) cc_final: 0.8180 (m-30) REVERT: A 308 LYS cc_start: 0.8432 (mttt) cc_final: 0.7982 (mmmt) REVERT: A 362 MET cc_start: 0.9184 (ptm) cc_final: 0.8849 (ptp) REVERT: A 368 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: A 415 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8208 (ttpt) REVERT: A 417 CYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7368 (t) REVERT: A 431 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5068 (pttm) REVERT: H 50 TYR cc_start: 0.8154 (p90) cc_final: 0.7953 (p90) REVERT: H 96 ASP cc_start: 0.7555 (t0) cc_final: 0.7222 (t0) REVERT: B 127 ASP cc_start: 0.8464 (m-30) cc_final: 0.8178 (m-30) REVERT: B 308 LYS cc_start: 0.8432 (mttt) cc_final: 0.7980 (mmmt) REVERT: B 362 MET cc_start: 0.9191 (ptm) cc_final: 0.8851 (ptp) REVERT: B 368 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: B 415 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8213 (ttpt) REVERT: B 417 CYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7359 (t) REVERT: B 431 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5072 (pttm) REVERT: E 96 ASP cc_start: 0.7557 (t0) cc_final: 0.7234 (t0) REVERT: C 127 ASP cc_start: 0.8490 (m-30) cc_final: 0.8206 (m-30) REVERT: C 308 LYS cc_start: 0.8434 (mttt) cc_final: 0.7980 (mmmt) REVERT: C 362 MET cc_start: 0.9190 (ptm) cc_final: 0.8845 (ptp) REVERT: C 368 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: C 415 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8235 (ttpt) REVERT: C 417 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7365 (t) REVERT: C 431 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5062 (pttm) REVERT: F 50 TYR cc_start: 0.8159 (p90) cc_final: 0.7958 (p90) REVERT: F 96 ASP cc_start: 0.7562 (t0) cc_final: 0.7231 (t0) REVERT: D 308 LYS cc_start: 0.8431 (mttt) cc_final: 0.7984 (mmmt) REVERT: D 362 MET cc_start: 0.9187 (ptm) cc_final: 0.8838 (ptp) REVERT: D 368 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: D 415 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8223 (ttpt) REVERT: D 417 CYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7365 (t) REVERT: D 431 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5066 (pttm) REVERT: G 96 ASP cc_start: 0.7552 (t0) cc_final: 0.7218 (t0) outliers start: 107 outliers final: 44 residues processed: 305 average time/residue: 0.4086 time to fit residues: 146.9117 Evaluate side-chains 290 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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: 0.5980 chunk 65 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 209 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.165567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114290 restraints weight = 21437.397| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.89 r_work: 0.3097 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1651 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= 0.142 Angle : 0.631 9.813 28060 Z= 0.312 Chirality : 0.048 0.221 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.946 55.914 4000 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.90 % Allowed : 22.32 % Favored : 73.78 % 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: -0.72 (0.17), residues: 2468 helix: -1.10 (0.91), residues: 24 sheet: 0.19 (0.18), residues: 884 loop : -0.87 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.011 0.001 TYR F 50 PHE 0.015 0.002 PHE D 410 TRP 0.017 0.001 TRP C 178 HIS 0.004 0.001 HIS D 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (20468) covalent geometry : angle 0.60566 / 0.31 (27780) SS BOND : bond 0.00391 / 0.27 ( 44) SS BOND : angle 1.53548 / 1.07 ( 88) hydrogen bonds : bond 0.03472 / 2.32 ( 568) hydrogen bonds : angle 6.30850 / 4.48 ( 1596) link_ALPHA1-2 : bond 0.00268 / 0.13 ( 4) link_ALPHA1-2 : angle 1.74412 / 0.94 ( 12) link_ALPHA1-3 : bond 0.00927 / 0.59 ( 8) link_ALPHA1-3 : angle 1.70746 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00477 / 0.29 ( 8) link_ALPHA1-6 : angle 1.48417 / 0.87 ( 24) link_BETA1-4 : bond 0.00488 / 0.31 ( 20) link_BETA1-4 : angle 1.94394 / 1.34 ( 60) link_NAG-ASN : bond 0.00334 / 0.20 ( 24) link_NAG-ASN : angle 2.33210 / 1.46 ( 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 333 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 250 time to evaluate : 0.581 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: 0.8430 (mttt) cc_final: 0.8075 (mmpt) REVERT: A 362 MET cc_start: 0.9180 (ptm) cc_final: 0.8825 (ptp) REVERT: A 368 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: A 431 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.4873 (pttm) REVERT: H 50 TYR cc_start: 0.8210 (p90) cc_final: 0.7951 (p90) REVERT: H 96 ASP cc_start: 0.7481 (t0) cc_final: 0.7264 (t0) REVERT: B 308 LYS cc_start: 0.8423 (mttt) cc_final: 0.8070 (mmpt) REVERT: B 362 MET cc_start: 0.9178 (ptm) cc_final: 0.8823 (ptp) REVERT: B 368 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: B 431 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.4873 (pttm) REVERT: E 96 ASP cc_start: 0.7496 (t0) cc_final: 0.7275 (t0) REVERT: C 308 LYS cc_start: 0.8428 (mttt) cc_final: 0.8073 (mmpt) REVERT: C 362 MET cc_start: 0.9179 (ptm) cc_final: 0.8819 (ptp) REVERT: C 368 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: C 431 LYS cc_start: 0.5688 (OUTLIER) cc_final: 0.4872 (pttm) REVERT: F 50 TYR cc_start: 0.8208 (p90) cc_final: 0.7947 (p90) REVERT: F 96 ASP cc_start: 0.7495 (t0) cc_final: 0.7286 (t0) REVERT: D 308 LYS cc_start: 0.8425 (mttt) cc_final: 0.8073 (mmpt) REVERT: D 362 MET cc_start: 0.9176 (ptm) cc_final: 0.8813 (ptp) REVERT: D 368 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: D 431 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.4872 (pttm) REVERT: G 96 ASP cc_start: 0.7487 (t0) cc_final: 0.7277 (t0) outliers start: 83 outliers final: 36 residues processed: 318 average time/residue: 0.4469 time to fit residues: 167.6008 Evaluate side-chains 292 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 20 THR 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 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 F residue 89 MET Chi-restraints excluded: chain J residue 20 THR 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 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 187 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 173 GLN A 294 ASN H 39 GLN 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 D 441 ASN G 39 GLN G 76 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.165254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115859 restraints weight = 21437.045| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.92 r_work: 0.3098 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1784 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= 0.151 Angle : 0.628 9.815 28060 Z= 0.311 Chirality : 0.048 0.223 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.747 56.271 4000 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.57 % Allowed : 23.12 % 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: -0.63 (0.17), residues: 2468 helix: -1.06 (0.91), residues: 24 sheet: 0.25 (0.18), residues: 884 loop : -0.81 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 100C TYR 0.011 0.001 TYR B 374 PHE 0.014 0.002 PHE C 410 TRP 0.014 0.001 TRP C 178 HIS 0.003 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (20468) covalent geometry : angle 0.60311 / 0.30 (27780) SS BOND : bond 0.00290 / 0.19 ( 44) SS BOND : angle 1.43670 / 0.98 ( 88) hydrogen bonds : bond 0.03450 / 2.30 ( 568) hydrogen bonds : angle 6.20303 / 4.41 ( 1596) link_ALPHA1-2 : bond 0.00368 / 0.18 ( 4) link_ALPHA1-2 : angle 1.66066 / 0.90 ( 12) link_ALPHA1-3 : bond 0.00842 / 0.54 ( 8) link_ALPHA1-3 : angle 1.67526 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00470 / 0.29 ( 8) link_ALPHA1-6 : angle 1.52103 / 0.90 ( 24) link_BETA1-4 : bond 0.00468 / 0.30 ( 20) link_BETA1-4 : angle 1.92099 / 1.31 ( 60) link_NAG-ASN : bond 0.00339 / 0.19 ( 24) link_NAG-ASN : angle 2.40661 / 1.51 ( 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 324 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 248 time to evaluate : 0.634 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: 0.8415 (mttt) cc_final: 0.8012 (mmpt) REVERT: A 362 MET cc_start: 0.9180 (ptm) cc_final: 0.8828 (ptp) REVERT: A 368 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: A 431 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.4830 (pttm) REVERT: H 50 TYR cc_start: 0.8182 (p90) cc_final: 0.7938 (p90) REVERT: B 308 LYS cc_start: 0.8417 (mttt) cc_final: 0.8011 (mmpt) REVERT: B 362 MET cc_start: 0.9181 (ptm) cc_final: 0.8829 (ptp) REVERT: B 368 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: B 431 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.4827 (pttm) REVERT: C 308 LYS cc_start: 0.8410 (mttt) cc_final: 0.8003 (mmpt) REVERT: C 362 MET cc_start: 0.9178 (ptm) cc_final: 0.8825 (ptp) REVERT: C 368 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: C 431 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.4824 (pttm) REVERT: F 50 TYR cc_start: 0.8181 (p90) cc_final: 0.7936 (p90) REVERT: D 308 LYS cc_start: 0.8403 (mttt) cc_final: 0.8011 (mmpt) REVERT: D 362 MET cc_start: 0.9178 (ptm) cc_final: 0.8821 (ptp) REVERT: D 368 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: D 431 LYS cc_start: 0.5599 (OUTLIER) cc_final: 0.4824 (pttm) outliers start: 76 outliers final: 48 residues processed: 304 average time/residue: 0.3847 time to fit residues: 138.8351 Evaluate side-chains 309 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 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 105 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 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 105 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 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 105 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 F 76 ASN D 104 ASN D 173 GLN D 294 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114708 restraints weight = 21548.712| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.96 r_work: 0.3091 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20576 Z= 0.177 Angle : 0.645 9.832 28060 Z= 0.319 Chirality : 0.049 0.229 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.696 56.832 4000 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.43 % Allowed : 23.83 % Favored : 72.74 % 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: -1.17 (0.88), residues: 24 sheet: 0.14 (0.18), residues: 948 loop : -0.78 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100C TYR 0.013 0.002 TYR C 374 PHE 0.014 0.002 PHE A 410 TRP 0.014 0.001 TRP B 178 HIS 0.003 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (20468) covalent geometry : angle 0.61833 / 0.31 (27780) SS BOND : bond 0.00338 / 0.22 ( 44) SS BOND : angle 1.50258 / 1.03 ( 88) hydrogen bonds : bond 0.03557 / 2.37 ( 568) hydrogen bonds : angle 6.16957 / 4.39 ( 1596) link_ALPHA1-2 : bond 0.00291 / 0.15 ( 4) link_ALPHA1-2 : angle 1.66403 / 0.90 ( 12) link_ALPHA1-3 : bond 0.00812 / 0.52 ( 8) link_ALPHA1-3 : angle 1.72413 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00413 / 0.25 ( 8) link_ALPHA1-6 : angle 1.56406 / 0.92 ( 24) link_BETA1-4 : bond 0.00445 / 0.28 ( 20) link_BETA1-4 : angle 1.94489 / 1.31 ( 60) link_NAG-ASN : bond 0.00390 / 0.22 ( 24) link_NAG-ASN : angle 2.51645 / 1.58 ( 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 325 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 252 time to evaluate : 0.502 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: 0.8417 (mttt) cc_final: 0.8015 (mmpt) REVERT: A 362 MET cc_start: 0.9172 (ptm) cc_final: 0.8808 (ptp) REVERT: A 368 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: A 431 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.4904 (pttm) REVERT: H 50 TYR cc_start: 0.8200 (p90) cc_final: 0.7928 (p90) REVERT: B 308 LYS cc_start: 0.8420 (mttt) cc_final: 0.8014 (mmpt) REVERT: B 362 MET cc_start: 0.9173 (ptm) cc_final: 0.8810 (ptp) REVERT: B 368 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: B 431 LYS cc_start: 0.5721 (OUTLIER) cc_final: 0.4896 (pttm) REVERT: C 308 LYS cc_start: 0.8409 (mttt) cc_final: 0.8008 (mmpt) REVERT: C 362 MET cc_start: 0.9178 (ptm) cc_final: 0.8813 (ptp) REVERT: C 431 LYS cc_start: 0.5727 (OUTLIER) cc_final: 0.4898 (pttm) REVERT: F 50 TYR cc_start: 0.8196 (p90) cc_final: 0.7921 (p90) REVERT: D 308 LYS cc_start: 0.8400 (mttt) cc_final: 0.8011 (mmpt) REVERT: D 362 MET cc_start: 0.9179 (ptm) cc_final: 0.8811 (ptp) REVERT: D 368 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: D 431 LYS cc_start: 0.5721 (OUTLIER) cc_final: 0.4895 (pttm) outliers start: 73 outliers final: 48 residues processed: 312 average time/residue: 0.3956 time to fit residues: 146.5154 Evaluate side-chains 305 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 F residue 52 LEU 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3826 r_free = 0.3826 target = 0.163184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112919 restraints weight = 21586.802| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.96 r_work: 0.3059 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20576 Z= 0.216 Angle : 0.670 9.871 28060 Z= 0.332 Chirality : 0.050 0.231 3204 Planarity : 0.004 0.045 3468 Dihedral : 7.814 57.659 4000 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.62 % Allowed : 24.01 % Favored : 72.37 % 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: -1.27 (0.87), residues: 24 sheet: 0.06 (0.18), residues: 956 loop : -0.78 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 100C TYR 0.013 0.002 TYR B 374 PHE 0.015 0.002 PHE C 410 TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (20468) covalent geometry : angle 0.64177 / 0.32 (27780) SS BOND : bond 0.00392 / 0.25 ( 44) SS BOND : angle 1.54006 / 1.05 ( 88) hydrogen bonds : bond 0.03661 / 2.45 ( 568) hydrogen bonds : angle 6.22198 / 4.43 ( 1596) link_ALPHA1-2 : bond 0.00262 / 0.13 ( 4) link_ALPHA1-2 : angle 1.68225 / 0.90 ( 12) link_ALPHA1-3 : bond 0.00727 / 0.46 ( 8) link_ALPHA1-3 : angle 1.81875 / 1.01 ( 24) link_ALPHA1-6 : bond 0.00378 / 0.23 ( 8) link_ALPHA1-6 : angle 1.59656 / 0.93 ( 24) link_BETA1-4 : bond 0.00413 / 0.26 ( 20) link_BETA1-4 : angle 2.06977 / 1.39 ( 60) link_NAG-ASN : bond 0.00483 / 0.26 ( 24) link_NAG-ASN : angle 2.66372 / 1.66 ( 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 315 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 238 time to evaluate : 0.723 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: A 308 LYS cc_start: 0.8407 (mttt) cc_final: 0.7934 (mmmt) REVERT: A 362 MET cc_start: 0.9164 (ptm) cc_final: 0.8812 (ptp) REVERT: A 431 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5029 (pttm) REVERT: H 50 TYR cc_start: 0.8250 (p90) cc_final: 0.7915 (p90) REVERT: B 308 LYS cc_start: 0.8407 (mttt) cc_final: 0.7932 (mmmt) REVERT: B 362 MET cc_start: 0.9165 (ptm) cc_final: 0.8816 (ptp) REVERT: B 431 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5027 (pttm) REVERT: C 308 LYS cc_start: 0.8404 (mttt) cc_final: 0.7926 (mmmt) REVERT: C 362 MET cc_start: 0.9155 (ptm) cc_final: 0.8809 (ptp) REVERT: C 431 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5022 (pttm) REVERT: F 50 TYR cc_start: 0.8255 (p90) cc_final: 0.7918 (p90) REVERT: D 199 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8407 (mptm) REVERT: D 308 LYS cc_start: 0.8401 (mttt) cc_final: 0.7930 (mmmt) REVERT: D 362 MET cc_start: 0.9162 (ptm) cc_final: 0.8817 (ptp) REVERT: D 431 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5024 (pttm) outliers start: 77 outliers final: 47 residues processed: 297 average time/residue: 0.3915 time to fit residues: 138.4487 Evaluate side-chains 297 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 162 GLU 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 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 105 SER Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 162 GLU 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 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 105 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 162 GLU 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 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 162 GLU Chi-restraints excluded: chain D residue 199 LYS 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 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: 0.7980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 173 GLN A 294 ASN H 76 ASN B 104 ASN B 173 GLN B 294 ASN E 76 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.165004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111740 restraints weight = 21364.481| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.85 r_work: 0.3088 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20576 Z= 0.153 Angle : 0.629 9.811 28060 Z= 0.311 Chirality : 0.048 0.223 3204 Planarity : 0.004 0.046 3468 Dihedral : 7.564 56.495 4000 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.82 % Allowed : 24.91 % Favored : 72.27 % 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: -0.68 (0.17), residues: 2468 helix: -1.12 (0.90), residues: 24 sheet: 0.04 (0.18), residues: 920 loop : -0.73 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 100C TYR 0.011 0.001 TYR B 374 PHE 0.013 0.002 PHE A 410 TRP 0.017 0.001 TRP D 178 HIS 0.002 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (20468) covalent geometry : angle 0.60425 / 0.31 (27780) SS BOND : bond 0.00310 / 0.20 ( 44) SS BOND : angle 1.37673 / 0.93 ( 88) hydrogen bonds : bond 0.03282 / 2.22 ( 568) hydrogen bonds : angle 6.05834 / 4.31 ( 1596) link_ALPHA1-2 : bond 0.00262 / 0.13 ( 4) link_ALPHA1-2 : angle 1.72586 / 0.93 ( 12) link_ALPHA1-3 : bond 0.00867 / 0.55 ( 8) link_ALPHA1-3 : angle 1.67094 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00454 / 0.28 ( 8) link_ALPHA1-6 : angle 1.53312 / 0.90 ( 24) link_BETA1-4 : bond 0.00469 / 0.30 ( 20) link_BETA1-4 : angle 1.86215 / 1.27 ( 60) link_NAG-ASN : bond 0.00348 / 0.20 ( 24) link_NAG-ASN : angle 2.44139 / 1.53 ( 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 304 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8431 (mttt) cc_final: 0.7938 (mmmt) REVERT: A 362 MET cc_start: 0.9142 (ptm) cc_final: 0.8789 (ptp) REVERT: A 431 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.4929 (pttm) REVERT: H 50 TYR cc_start: 0.8309 (p90) cc_final: 0.7956 (p90) REVERT: H 52 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.5932 (pp) REVERT: B 308 LYS cc_start: 0.8439 (mttt) cc_final: 0.7942 (mmmt) REVERT: B 362 MET cc_start: 0.9142 (ptm) cc_final: 0.8790 (ptp) REVERT: B 431 LYS cc_start: 0.5810 (OUTLIER) cc_final: 0.4930 (pttm) REVERT: C 308 LYS cc_start: 0.8432 (mttt) cc_final: 0.7940 (mmmt) REVERT: C 362 MET cc_start: 0.9138 (ptm) cc_final: 0.8781 (ptp) REVERT: C 431 LYS cc_start: 0.5808 (OUTLIER) cc_final: 0.4930 (pttm) REVERT: F 50 TYR cc_start: 0.8305 (p90) cc_final: 0.7941 (p90) REVERT: F 52 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.5928 (pp) REVERT: D 199 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8415 (mptm) REVERT: D 308 LYS cc_start: 0.8414 (mttt) cc_final: 0.7938 (mmmt) REVERT: D 362 MET cc_start: 0.9142 (ptm) cc_final: 0.8784 (ptp) REVERT: D 431 LYS cc_start: 0.5812 (OUTLIER) cc_final: 0.4933 (pttm) outliers start: 60 outliers final: 39 residues processed: 292 average time/residue: 0.3985 time to fit residues: 138.0309 Evaluate side-chains 287 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 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 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 F residue 52 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 199 LYS 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 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: 0.8980 chunk 3 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3845 r_free = 0.3845 target = 0.164967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115548 restraints weight = 21508.758| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.88 r_work: 0.3101 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20576 Z= 0.162 Angle : 0.635 9.808 28060 Z= 0.314 Chirality : 0.048 0.225 3204 Planarity : 0.004 0.046 3468 Dihedral : 7.477 56.429 4000 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.30 % Allowed : 25.33 % Favored : 72.37 % 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: -0.70 (0.17), residues: 2468 helix: -1.13 (0.89), residues: 24 sheet: 0.02 (0.18), residues: 916 loop : -0.74 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100C TYR 0.012 0.002 TYR D 374 PHE 0.013 0.002 PHE D 410 TRP 0.015 0.001 TRP B 178 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (20468) covalent geometry : angle 0.61036 / 0.31 (27780) SS BOND : bond 0.00307 / 0.20 ( 44) SS BOND : angle 1.35336 / 0.92 ( 88) hydrogen bonds : bond 0.03295 / 2.21 ( 568) hydrogen bonds : angle 6.01059 / 4.28 ( 1596) link_ALPHA1-2 : bond 0.00260 / 0.13 ( 4) link_ALPHA1-2 : angle 1.66926 / 0.90 ( 12) link_ALPHA1-3 : bond 0.00842 / 0.54 ( 8) link_ALPHA1-3 : angle 1.65712 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00429 / 0.26 ( 8) link_ALPHA1-6 : angle 1.54675 / 0.91 ( 24) link_BETA1-4 : bond 0.00459 / 0.29 ( 20) link_BETA1-4 : angle 1.86705 / 1.26 ( 60) link_NAG-ASN : bond 0.00401 / 0.23 ( 24) link_NAG-ASN : angle 2.51127 / 1.59 ( 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 285 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8442 (mttt) cc_final: 0.7907 (mmmt) REVERT: A 362 MET cc_start: 0.9135 (ptm) cc_final: 0.8767 (ptp) REVERT: A 431 LYS cc_start: 0.5796 (OUTLIER) cc_final: 0.4916 (pttm) REVERT: H 50 TYR cc_start: 0.8281 (p90) cc_final: 0.7877 (p90) REVERT: H 52 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5889 (pp) REVERT: B 308 LYS cc_start: 0.8432 (mttt) cc_final: 0.7903 (mmmt) REVERT: B 362 MET cc_start: 0.9140 (ptm) cc_final: 0.8774 (ptp) REVERT: B 431 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.4909 (pttm) REVERT: E 52 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5778 (pp) REVERT: C 308 LYS cc_start: 0.8431 (mttt) cc_final: 0.7901 (mmmt) REVERT: C 362 MET cc_start: 0.9126 (ptm) cc_final: 0.8754 (ptp) REVERT: C 431 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.4908 (pttm) REVERT: F 50 TYR cc_start: 0.8281 (p90) cc_final: 0.7871 (p90) REVERT: F 52 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5886 (pp) REVERT: D 199 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8305 (mptm) REVERT: D 308 LYS cc_start: 0.8421 (mttt) cc_final: 0.7901 (mmmt) REVERT: D 362 MET cc_start: 0.9129 (ptm) cc_final: 0.8754 (ptp) REVERT: D 431 LYS cc_start: 0.5789 (OUTLIER) cc_final: 0.4913 (pttm) REVERT: G 52 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5791 (pp) outliers start: 49 outliers final: 36 residues processed: 280 average time/residue: 0.3997 time to fit residues: 132.5017 Evaluate side-chains 286 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 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 F residue 52 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 199 LYS 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 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: 0.9990 chunk 189 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 175 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3854 r_free = 0.3854 target = 0.165694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116233 restraints weight = 21537.005| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.88 r_work: 0.3114 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20576 Z= 0.151 Angle : 0.624 9.798 28060 Z= 0.308 Chirality : 0.048 0.223 3204 Planarity : 0.004 0.046 3468 Dihedral : 7.342 56.017 4000 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.54 % Allowed : 25.09 % Favored : 72.37 % 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: -0.68 (0.17), residues: 2468 helix: -1.08 (0.90), residues: 24 sheet: 0.02 (0.18), residues: 916 loop : -0.72 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 100C TYR 0.011 0.001 TYR B 374 PHE 0.013 0.002 PHE C 410 TRP 0.015 0.001 TRP B 178 HIS 0.002 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (20468) covalent geometry : angle 0.60010 / 0.30 (27780) SS BOND : bond 0.00275 / 0.17 ( 44) SS BOND : angle 1.28317 / 0.87 ( 88) hydrogen bonds : bond 0.03169 / 2.13 ( 568) hydrogen bonds : angle 5.93823 / 4.22 ( 1596) link_ALPHA1-2 : bond 0.00246 / 0.12 ( 4) link_ALPHA1-2 : angle 1.67355 / 0.91 ( 12) link_ALPHA1-3 : bond 0.00875 / 0.56 ( 8) link_ALPHA1-3 : angle 1.60356 / 0.91 ( 24) link_ALPHA1-6 : bond 0.00455 / 0.28 ( 8) link_ALPHA1-6 : angle 1.52228 / 0.90 ( 24) link_BETA1-4 : bond 0.00465 / 0.30 ( 20) link_BETA1-4 : angle 1.78423 / 1.20 ( 60) link_NAG-ASN : bond 0.00349 / 0.20 ( 24) link_NAG-ASN : angle 2.43860 / 1.55 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.20 seconds wall clock time: 96 minutes 43.76 seconds (5803.76 seconds total)