Starting phenix.real_space_refine on Sun Oct 12 08:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozh_17309/10_2025/8ozh_17309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozh_17309/10_2025/8ozh_17309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozh_17309/10_2025/8ozh_17309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozh_17309/10_2025/8ozh_17309.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozh_17309/10_2025/8ozh_17309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozh_17309/10_2025/8ozh_17309.cif" } resolution = 2.91 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= 0.003 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 P 3 5.49 5 S 111 5.16 5 C 14640 2.51 5 N 3600 2.21 5 O 4482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22836 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "C" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3328 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 377} Chain breaks: 2 Chain: "D" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "E" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "G" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3328 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 377} Chain breaks: 2 Chain: "H" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "I" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "K" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3328 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 377} Chain breaks: 2 Chain: "L" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "e" 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: "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: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "g" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.04, per 1000 atoms: 0.26 Number of scatterers: 22836 At special positions: 0 Unit cell: (119.88, 113.4, 212.76, 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) S 111 16.00 P 3 15.00 O 4482 8.00 N 3600 7.00 C 14640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 506 " distance=2.06 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 318 " distance=2.07 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 381 " distance=2.05 Simple disulfide: pdb=" SG CYS C 449 " - pdb=" SG CYS C 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 763 " - pdb=" SG CYS D 771 " distance=2.07 Simple disulfide: pdb=" SG CYS D 780 " - pdb=" SG CYS D 789 " distance=2.05 Simple disulfide: pdb=" SG CYS D 820 " - pdb=" SG CYS D 838 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 506 " distance=2.06 Simple disulfide: pdb=" SG CYS G 235 " - pdb=" SG CYS G 318 " distance=2.07 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS G 381 " distance=2.05 Simple disulfide: pdb=" SG CYS G 449 " - pdb=" SG CYS G 457 " distance=2.03 Simple disulfide: pdb=" SG CYS H 763 " - pdb=" SG CYS H 771 " distance=2.07 Simple disulfide: pdb=" SG CYS H 780 " - pdb=" SG CYS H 789 " distance=2.05 Simple disulfide: pdb=" SG CYS H 820 " - pdb=" SG CYS H 838 " distance=2.05 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 506 " distance=2.06 Simple disulfide: pdb=" SG CYS K 235 " - pdb=" SG CYS K 318 " distance=2.07 Simple disulfide: pdb=" SG CYS K 256 " - pdb=" SG CYS K 381 " distance=2.05 Simple disulfide: pdb=" SG CYS K 449 " - pdb=" SG CYS K 457 " distance=2.03 Simple disulfide: pdb=" SG CYS L 763 " - pdb=" SG CYS L 771 " distance=2.07 Simple disulfide: pdb=" SG CYS L 780 " - pdb=" SG CYS L 789 " distance=2.05 Simple disulfide: pdb=" SG CYS L 820 " - pdb=" SG CYS L 838 " distance=2.05 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 e 5 " - " MAN e 6 " " MAN f 5 " - " MAN f 6 " " MAN g 5 " - " MAN g 6 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA e 3 " - " MAN e 8 " " MAN e 4 " - " MAN e 5 " " BMA f 3 " - " MAN f 8 " " MAN f 4 " - " MAN f 5 " " BMA g 3 " - " MAN g 8 " " MAN g 4 " - " MAN g 5 " " BMA h 3 " - " MAN h 6 " " MAN h 4 " - " MAN h 5 " " BMA i 3 " - " MAN i 6 " " MAN i 4 " - " MAN i 5 " " BMA j 3 " - " MAN j 6 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 6 " " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " " MAN f 4 " - " MAN f 7 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 7 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " BETA1-2 " MAN V 4 " - " NAG V 5 " " MAN W 4 " - " NAG W 5 " " MAN X 4 " - " NAG X 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG C1001 " - " ASN C 405 " " NAG C1002 " - " ASN C 311 " " NAG C1003 " - " ASN C 556 " " NAG G1001 " - " ASN G 405 " " NAG G1002 " - " ASN G 311 " " NAG G1003 " - " ASN G 556 " " NAG K1001 " - " ASN K 405 " " NAG K1002 " - " ASN K 311 " " NAG K1003 " - " ASN K 556 " " NAG M 1 " - " ASN A 109 " " NAG N 1 " - " ASN E 109 " " NAG O 1 " - " ASN I 109 " " NAG P 1 " - " ASN C 141 " " NAG Q 1 " - " ASN G 141 " " NAG R 1 " - " ASN K 141 " " NAG S 1 " - " ASN C 183 " " NAG T 1 " - " ASN G 183 " " NAG U 1 " - " ASN K 183 " " NAG V 1 " - " ASN C 391 " " NAG W 1 " - " ASN G 391 " " NAG X 1 " - " ASN K 391 " " NAG Y 1 " - " ASN C 527 " " NAG Z 1 " - " ASN G 527 " " NAG a 1 " - " ASN K 527 " " NAG b 1 " - " ASN D 833 " " NAG c 1 " - " ASN H 833 " " NAG d 1 " - " ASN L 833 " " NAG e 1 " - " ASN D 808 " " NAG f 1 " - " ASN H 808 " " NAG g 1 " - " ASN L 808 " " NAG h 1 " - " ASN D 782 " " NAG i 1 " - " ASN H 782 " " NAG j 1 " - " ASN L 782 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5046 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 33 sheets defined 40.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 59 through 101 removed outlier: 3.507A pdb=" N ILE A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.564A pdb=" N ALA A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 175 through 182 removed outlier: 3.669A pdb=" N ASN C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 205 removed outlier: 3.634A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 219 Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.559A pdb=" N TRP C 273 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.925A pdb=" N LYS C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 332 through 347 removed outlier: 3.523A pdb=" N ARG C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.937A pdb=" N SER C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 3.650A pdb=" N VAL C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 471 through 478 Processing helix chain 'C' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS C 511 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA C 512 " --> pdb=" O ILE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 526 removed outlier: 3.553A pdb=" N PHE C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 537 through 540 Processing helix chain 'D' and resid 596 through 602 Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 624 through 629 removed outlier: 4.208A pdb=" N SER D 628 " --> pdb=" O LEU D 624 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 629 " --> pdb=" O HIS D 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 624 through 629' Processing helix chain 'D' and resid 631 through 652 removed outlier: 3.518A pdb=" N ALA D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 652 " --> pdb=" O THR D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.902A pdb=" N TYR D 659 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET D 660 " --> pdb=" O TRP D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 660' Processing helix chain 'D' and resid 661 through 670 Processing helix chain 'D' and resid 672 through 683 removed outlier: 3.506A pdb=" N LYS D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 876 Processing helix chain 'D' and resid 889 through 895 Processing helix chain 'D' and resid 897 through 903 Processing helix chain 'D' and resid 910 through 923 removed outlier: 3.564A pdb=" N GLN D 917 " --> pdb=" O ALA D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 979 removed outlier: 3.583A pdb=" N LYS D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) Proline residue: D 960 - end of helix removed outlier: 3.643A pdb=" N PHE D 975 " --> pdb=" O VAL D 971 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 101 removed outlier: 3.508A pdb=" N ILE E 77 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.563A pdb=" N ALA E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 175 through 182 removed outlier: 3.669A pdb=" N ASN G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 205 removed outlier: 3.634A pdb=" N LYS G 190 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 203 " --> pdb=" O GLU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 219 Processing helix chain 'G' and resid 220 through 233 Processing helix chain 'G' and resid 270 through 276 removed outlier: 3.558A pdb=" N TRP G 273 " --> pdb=" O GLN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 removed outlier: 3.925A pdb=" N LYS G 292 " --> pdb=" O THR G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 332 through 347 removed outlier: 3.523A pdb=" N ARG G 338 " --> pdb=" O GLU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 359 Processing helix chain 'G' and resid 378 through 383 removed outlier: 3.936A pdb=" N SER G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 391 removed outlier: 3.649A pdb=" N VAL G 387 " --> pdb=" O LYS G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 406 Processing helix chain 'G' and resid 471 through 478 Processing helix chain 'G' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS G 511 " --> pdb=" O LYS G 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA G 512 " --> pdb=" O ILE G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 526 removed outlier: 3.553A pdb=" N PHE G 520 " --> pdb=" O ASP G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 536 Processing helix chain 'G' and resid 537 through 540 Processing helix chain 'H' and resid 596 through 602 Processing helix chain 'H' and resid 620 through 624 Processing helix chain 'H' and resid 624 through 629 removed outlier: 4.208A pdb=" N SER H 628 " --> pdb=" O LEU H 624 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 629 " --> pdb=" O HIS H 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 624 through 629' Processing helix chain 'H' and resid 631 through 652 removed outlier: 3.518A pdb=" N ALA H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU H 652 " --> pdb=" O THR H 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 656 through 660 removed outlier: 3.902A pdb=" N TYR H 659 " --> pdb=" O ASP H 656 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET H 660 " --> pdb=" O TRP H 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 656 through 660' Processing helix chain 'H' and resid 661 through 670 Processing helix chain 'H' and resid 672 through 683 removed outlier: 3.506A pdb=" N LYS H 677 " --> pdb=" O ASP H 673 " (cutoff:3.500A) Processing helix chain 'H' and resid 869 through 876 Processing helix chain 'H' and resid 889 through 895 Processing helix chain 'H' and resid 897 through 903 Processing helix chain 'H' and resid 910 through 923 removed outlier: 3.564A pdb=" N GLN H 917 " --> pdb=" O ALA H 913 " (cutoff:3.500A) Processing helix chain 'H' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU H 940 " --> pdb=" O ILE H 936 " (cutoff:3.500A) Processing helix chain 'H' and resid 946 through 979 removed outlier: 3.583A pdb=" N LYS H 959 " --> pdb=" O LEU H 955 " (cutoff:3.500A) Proline residue: H 960 - end of helix removed outlier: 3.643A pdb=" N PHE H 975 " --> pdb=" O VAL H 971 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 101 removed outlier: 3.507A pdb=" N ILE I 77 " --> pdb=" O PHE I 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN I 100 " --> pdb=" O ASN I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 114 removed outlier: 3.564A pdb=" N ALA I 114 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 147 No H-bonds generated for 'chain 'K' and resid 145 through 147' Processing helix chain 'K' and resid 175 through 182 removed outlier: 3.670A pdb=" N ASN K 181 " --> pdb=" O ASN K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 205 removed outlier: 3.634A pdb=" N LYS K 190 " --> pdb=" O GLN K 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 203 " --> pdb=" O GLU K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 219 Processing helix chain 'K' and resid 220 through 233 Processing helix chain 'K' and resid 270 through 276 removed outlier: 3.559A pdb=" N TRP K 273 " --> pdb=" O GLN K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 293 removed outlier: 3.925A pdb=" N LYS K 292 " --> pdb=" O THR K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 Processing helix chain 'K' and resid 332 through 347 removed outlier: 3.523A pdb=" N ARG K 338 " --> pdb=" O GLU K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 359 Processing helix chain 'K' and resid 378 through 383 removed outlier: 3.936A pdb=" N SER K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 391 removed outlier: 3.649A pdb=" N VAL K 387 " --> pdb=" O LYS K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 406 Processing helix chain 'K' and resid 471 through 478 Processing helix chain 'K' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS K 511 " --> pdb=" O LYS K 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA K 512 " --> pdb=" O ILE K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 526 removed outlier: 3.553A pdb=" N PHE K 520 " --> pdb=" O ASP K 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 536 Processing helix chain 'K' and resid 537 through 540 Processing helix chain 'L' and resid 596 through 602 Processing helix chain 'L' and resid 620 through 624 Processing helix chain 'L' and resid 624 through 629 removed outlier: 4.208A pdb=" N SER L 628 " --> pdb=" O LEU L 624 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL L 629 " --> pdb=" O HIS L 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 624 through 629' Processing helix chain 'L' and resid 631 through 652 removed outlier: 3.518A pdb=" N ALA L 635 " --> pdb=" O GLU L 631 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU L 652 " --> pdb=" O THR L 648 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 660 removed outlier: 3.902A pdb=" N TYR L 659 " --> pdb=" O ASP L 656 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET L 660 " --> pdb=" O TRP L 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 656 through 660' Processing helix chain 'L' and resid 661 through 670 Processing helix chain 'L' and resid 672 through 683 removed outlier: 3.506A pdb=" N LYS L 677 " --> pdb=" O ASP L 673 " (cutoff:3.500A) Processing helix chain 'L' and resid 869 through 876 Processing helix chain 'L' and resid 889 through 895 Processing helix chain 'L' and resid 897 through 903 Processing helix chain 'L' and resid 910 through 923 removed outlier: 3.565A pdb=" N GLN L 917 " --> pdb=" O ALA L 913 " (cutoff:3.500A) Processing helix chain 'L' and resid 926 through 942 removed outlier: 3.619A pdb=" N LEU L 940 " --> pdb=" O ILE L 936 " (cutoff:3.500A) Processing helix chain 'L' and resid 946 through 979 removed outlier: 3.583A pdb=" N LYS L 959 " --> pdb=" O LEU L 955 " (cutoff:3.500A) Proline residue: L 960 - end of helix removed outlier: 3.643A pdb=" N PHE L 975 " --> pdb=" O VAL L 971 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 134 removed outlier: 4.156A pdb=" N LYS C 136 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.421A pdb=" N ASN D 720 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR D 757 " --> pdb=" O VAL D 777 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS D 763 " --> pdb=" O CYS D 771 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS D 771 " --> pdb=" O CYS D 763 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG D 765 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL D 773 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N ARG C 163 " --> pdb=" O VAL D 773 " (cutoff:3.500A) removed outlier: 16.251A pdb=" N LYS D 775 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 23.496A pdb=" N LEU C 165 " --> pdb=" O LYS D 775 " (cutoff:3.500A) removed outlier: 29.023A pdb=" N VAL D 777 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 35.808A pdb=" N LEU C 167 " --> pdb=" O VAL D 777 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL D 616 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER C 168 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR D 618 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 170 " --> pdb=" O THR D 618 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 593 through 594 removed outlier: 9.274A pdb=" N TYR D 610 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 164 " --> pdb=" O TYR D 610 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 612 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY C 166 " --> pdb=" O LEU D 612 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 158 " --> pdb=" O ILE D 716 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE D 716 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 160 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE D 712 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL C 164 " --> pdb=" O LEU D 710 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 710 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY C 166 " --> pdb=" O TYR D 708 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR D 708 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C 168 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU D 706 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE C 170 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 704 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET C 172 " --> pdb=" O TRP D 702 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP D 702 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN C 174 " --> pdb=" O THR D 700 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR D 700 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA D 701 " --> pdb=" O GLN D 692 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN D 692 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU D 703 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL D 690 " --> pdb=" O GLU D 703 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY D 705 " --> pdb=" O TYR D 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG D 684 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 498 through 501 Processing sheet with id=AA6, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.674A pdb=" N PHE C 301 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AA8, first strand: chain 'C' and resid 393 through 395 Processing sheet with id=AA9, first strand: chain 'D' and resid 590 through 591 Processing sheet with id=AB1, first strand: chain 'D' and resid 728 through 732 removed outlier: 6.902A pdb=" N VAL D 791 " --> pdb=" O VAL D 883 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 836 through 838 Processing sheet with id=AB3, first strand: chain 'D' and resid 850 through 851 Processing sheet with id=AB4, first strand: chain 'D' and resid 864 through 865 Processing sheet with id=AB5, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AB6, first strand: chain 'F' and resid 128 through 134 removed outlier: 4.157A pdb=" N LYS G 136 " --> pdb=" O VAL F 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 149 through 154 removed outlier: 4.422A pdb=" N ASN H 720 " --> pdb=" O HIS G 154 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR H 757 " --> pdb=" O VAL H 777 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS H 763 " --> pdb=" O CYS H 771 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS H 771 " --> pdb=" O CYS H 763 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG H 765 " --> pdb=" O VAL H 769 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL H 769 " --> pdb=" O ARG H 765 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL H 773 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N ARG G 163 " --> pdb=" O VAL H 773 " (cutoff:3.500A) removed outlier: 16.252A pdb=" N LYS H 775 " --> pdb=" O ARG G 163 " (cutoff:3.500A) removed outlier: 23.495A pdb=" N LEU G 165 " --> pdb=" O LYS H 775 " (cutoff:3.500A) removed outlier: 29.023A pdb=" N VAL H 777 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 35.808A pdb=" N LEU G 167 " --> pdb=" O VAL H 777 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL H 616 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER G 168 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR H 618 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 170 " --> pdb=" O THR H 618 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 593 through 594 removed outlier: 9.273A pdb=" N TYR H 610 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL G 164 " --> pdb=" O TYR H 610 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU H 612 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY G 166 " --> pdb=" O LEU H 612 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE G 158 " --> pdb=" O ILE H 716 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE H 716 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL G 160 " --> pdb=" O LYS H 714 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE H 712 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL G 164 " --> pdb=" O LEU H 710 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU H 710 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY G 166 " --> pdb=" O TYR H 708 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR H 708 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER G 168 " --> pdb=" O LEU H 706 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU H 706 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE G 170 " --> pdb=" O ILE H 704 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE H 704 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET G 172 " --> pdb=" O TRP H 702 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP H 702 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN G 174 " --> pdb=" O THR H 700 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR H 700 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA H 701 " --> pdb=" O GLN H 692 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN H 692 " --> pdb=" O ALA H 701 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU H 703 " --> pdb=" O VAL H 690 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL H 690 " --> pdb=" O GLU H 703 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY H 705 " --> pdb=" O TYR H 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG H 684 " --> pdb=" O GLU H 709 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 498 through 501 Processing sheet with id=AC1, first strand: chain 'G' and resid 250 through 251 removed outlier: 3.675A pdb=" N PHE G 301 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=AC3, first strand: chain 'G' and resid 393 through 395 Processing sheet with id=AC4, first strand: chain 'H' and resid 728 through 732 removed outlier: 6.902A pdb=" N VAL H 791 " --> pdb=" O VAL H 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 836 through 838 Processing sheet with id=AC6, first strand: chain 'H' and resid 850 through 851 Processing sheet with id=AC7, first strand: chain 'J' and resid 128 through 134 removed outlier: 4.157A pdb=" N LYS K 136 " --> pdb=" O VAL J 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 149 through 154 removed outlier: 4.422A pdb=" N ASN L 720 " --> pdb=" O HIS K 154 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR L 757 " --> pdb=" O VAL L 777 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS L 763 " --> pdb=" O CYS L 771 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS L 771 " --> pdb=" O CYS L 763 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG L 765 " --> pdb=" O VAL L 769 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL L 769 " --> pdb=" O ARG L 765 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL L 773 " --> pdb=" O LYS K 161 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N ARG K 163 " --> pdb=" O VAL L 773 " (cutoff:3.500A) removed outlier: 16.252A pdb=" N LYS L 775 " --> pdb=" O ARG K 163 " (cutoff:3.500A) removed outlier: 23.495A pdb=" N LEU K 165 " --> pdb=" O LYS L 775 " (cutoff:3.500A) removed outlier: 29.023A pdb=" N VAL L 777 " --> pdb=" O LEU K 165 " (cutoff:3.500A) removed outlier: 35.808A pdb=" N LEU K 167 " --> pdb=" O VAL L 777 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL L 616 " --> pdb=" O GLY K 166 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER K 168 " --> pdb=" O VAL L 616 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR L 618 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE K 170 " --> pdb=" O THR L 618 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 593 through 594 removed outlier: 9.274A pdb=" N TYR L 610 " --> pdb=" O GLU K 162 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL K 164 " --> pdb=" O TYR L 610 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU L 612 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY K 166 " --> pdb=" O LEU L 612 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE K 158 " --> pdb=" O ILE L 716 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE L 716 " --> pdb=" O ILE K 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL K 160 " --> pdb=" O LYS L 714 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE L 712 " --> pdb=" O GLU K 162 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL K 164 " --> pdb=" O LEU L 710 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU L 710 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY K 166 " --> pdb=" O TYR L 708 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR L 708 " --> pdb=" O GLY K 166 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER K 168 " --> pdb=" O LEU L 706 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU L 706 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE K 170 " --> pdb=" O ILE L 704 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE L 704 " --> pdb=" O ILE K 170 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET K 172 " --> pdb=" O TRP L 702 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP L 702 " --> pdb=" O MET K 172 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN K 174 " --> pdb=" O THR L 700 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR L 700 " --> pdb=" O ASN K 174 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA L 701 " --> pdb=" O GLN L 692 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN L 692 " --> pdb=" O ALA L 701 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU L 703 " --> pdb=" O VAL L 690 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL L 690 " --> pdb=" O GLU L 703 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY L 705 " --> pdb=" O TYR L 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG L 684 " --> pdb=" O GLU L 709 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 498 through 501 Processing sheet with id=AD2, first strand: chain 'K' and resid 250 through 251 removed outlier: 3.674A pdb=" N PHE K 301 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 282 through 283 Processing sheet with id=AD4, first strand: chain 'K' and resid 393 through 395 Processing sheet with id=AD5, first strand: chain 'L' and resid 728 through 732 removed outlier: 6.902A pdb=" N VAL L 791 " --> pdb=" O VAL L 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 836 through 838 871 hydrogen bonds defined for protein. 2316 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: 4.35 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4047 1.33 - 1.45: 5937 1.45 - 1.58: 13209 1.58 - 1.70: 6 1.70 - 1.83: 156 Bond restraints: 23355 Sorted by residual: bond pdb=" N ILE K 303 " pdb=" CA ILE K 303 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.38e+01 bond pdb=" N ILE G 303 " pdb=" CA ILE G 303 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.37e+01 bond pdb=" N ILE C 303 " pdb=" CA ILE C 303 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.35e+01 bond pdb=" N ILE D 712 " pdb=" CA ILE D 712 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.96e+01 bond pdb=" N ILE L 712 " pdb=" CA ILE L 712 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.95e+01 ... (remaining 23350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 25062 2.18 - 4.35: 6237 4.35 - 6.53: 432 6.53 - 8.70: 3 8.70 - 10.88: 6 Bond angle restraints: 31740 Sorted by residual: angle pdb=" C MET D 583 " pdb=" N GLY D 584 " pdb=" CA GLY D 584 " ideal model delta sigma weight residual 120.13 126.25 -6.12 1.26e+00 6.30e-01 2.36e+01 angle pdb=" C MET L 583 " pdb=" N GLY L 584 " pdb=" CA GLY L 584 " ideal model delta sigma weight residual 120.13 126.25 -6.12 1.26e+00 6.30e-01 2.36e+01 angle pdb=" C MET H 583 " pdb=" N GLY H 584 " pdb=" CA GLY H 584 " ideal model delta sigma weight residual 120.13 126.23 -6.10 1.26e+00 6.30e-01 2.34e+01 angle pdb=" C GLY C 215 " pdb=" N ASP C 216 " pdb=" CA ASP C 216 " ideal model delta sigma weight residual 120.67 126.84 -6.17 1.34e+00 5.57e-01 2.12e+01 angle pdb=" C GLY K 215 " pdb=" N ASP K 216 " pdb=" CA ASP K 216 " ideal model delta sigma weight residual 120.67 126.82 -6.15 1.34e+00 5.57e-01 2.11e+01 ... (remaining 31735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 14588 23.81 - 47.62: 736 47.62 - 71.43: 183 71.43 - 95.24: 93 95.24 - 119.04: 54 Dihedral angle restraints: 15654 sinusoidal: 7854 harmonic: 7800 Sorted by residual: dihedral pdb=" CA TRP C 246 " pdb=" C TRP C 246 " pdb=" N PRO C 247 " pdb=" CA PRO C 247 " ideal model delta harmonic sigma weight residual -180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP K 246 " pdb=" C TRP K 246 " pdb=" N PRO K 247 " pdb=" CA PRO K 247 " ideal model delta harmonic sigma weight residual -180.00 -157.87 -22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP G 246 " pdb=" C TRP G 246 " pdb=" N PRO G 247 " pdb=" CA PRO G 247 " ideal model delta harmonic sigma weight residual -180.00 -157.87 -22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 15651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2712 0.097 - 0.195: 1084 0.195 - 0.292: 107 0.292 - 0.390: 0 0.390 - 0.487: 3 Chirality restraints: 3906 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.78e+01 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.73e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.72e+01 ... (remaining 3903 not shown) Planarity restraints: 3825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.067 2.00e-02 2.50e+03 5.59e-02 3.90e+01 pdb=" C7 NAG R 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.067 2.00e-02 2.50e+03 5.58e-02 3.90e+01 pdb=" C7 NAG Q 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " -0.067 2.00e-02 2.50e+03 5.58e-02 3.89e+01 pdb=" C7 NAG P 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.006 2.00e-02 2.50e+03 ... (remaining 3822 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 8299 2.92 - 3.42: 19597 3.42 - 3.91: 36665 3.91 - 4.41: 38754 4.41 - 4.90: 67020 Nonbonded interactions: 170335 Sorted by model distance: nonbonded pdb=" OH TYR C 151 " pdb=" OE2 GLU D 856 " model vdw 2.430 3.040 nonbonded pdb=" OH TYR K 151 " pdb=" OE2 GLU L 856 " model vdw 2.430 3.040 nonbonded pdb=" OH TYR G 151 " pdb=" OE2 GLU H 856 " model vdw 2.430 3.040 nonbonded pdb=" NH1 ARG D 654 " pdb=" OE2 GLU H 652 " model vdw 2.468 3.120 nonbonded pdb=" NH1 ARG H 654 " pdb=" OE2 GLU L 652 " model vdw 2.468 3.120 ... (remaining 170330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'V' and (resid 1 through 4 or resid 6)) selection = (chain 'W' and (resid 1 through 4 or resid 6)) selection = (chain 'X' and (resid 1 through 4 or resid 6)) selection = (chain 'h' and (resid 1 through 4 or resid 6)) selection = (chain 'i' and (resid 1 through 4 or resid 6)) selection = (chain 'j' and (resid 1 through 4 or resid 6)) } ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' } 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: 7.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.010 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.014 0.053 23484 Z= 1.044 Angle : 1.745 10.876 32106 Z= 1.236 Chirality : 0.092 0.487 3906 Planarity : 0.005 0.056 3792 Dihedral : 17.490 119.045 10545 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.75 % Allowed : 5.40 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: -2.87 (0.14), residues: 2601 helix: -2.52 (0.13), residues: 852 sheet: -1.02 (0.29), residues: 273 loop : -1.67 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 92 TYR 0.031 0.004 TYR H 688 PHE 0.024 0.003 PHE E 87 TRP 0.014 0.003 TRP H 721 HIS 0.009 0.002 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.01400 (23355) covalent geometry : angle 1.72120 (31740) SS BOND : bond 0.02672 ( 21) SS BOND : angle 2.97726 ( 42) hydrogen bonds : bond 0.25717 ( 871) hydrogen bonds : angle 7.78422 ( 2316) link_ALPHA1-2 : bond 0.00941 ( 3) link_ALPHA1-2 : angle 5.20060 ( 9) link_ALPHA1-3 : bond 0.00663 ( 15) link_ALPHA1-3 : angle 2.95231 ( 45) link_ALPHA1-6 : bond 0.00610 ( 15) link_ALPHA1-6 : angle 2.25803 ( 45) link_BETA1-2 : bond 0.00793 ( 3) link_BETA1-2 : angle 6.20300 ( 9) link_BETA1-4 : bond 0.00736 ( 39) link_BETA1-4 : angle 3.21014 ( 117) link_NAG-ASN : bond 0.00854 ( 33) link_NAG-ASN : angle 3.07905 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.6428 (tttt) cc_final: 0.6163 (tttm) REVERT: C 151 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.8155 (p90) REVERT: C 187 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7361 (mp0) REVERT: C 325 LYS cc_start: 0.7668 (tttt) cc_final: 0.7337 (ptpp) REVERT: C 341 LEU cc_start: 0.7513 (mt) cc_final: 0.7278 (mt) REVERT: C 395 TYR cc_start: 0.7597 (m-80) cc_final: 0.7261 (m-80) REVERT: C 408 LYS cc_start: 0.6673 (ttpp) cc_final: 0.6408 (tptp) REVERT: C 439 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7713 (mtt90) REVERT: C 464 ASP cc_start: 0.7364 (m-30) cc_final: 0.7094 (m-30) REVERT: C 511 LYS cc_start: 0.7607 (tttt) cc_final: 0.7011 (mptt) REVERT: C 560 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6749 (mm-30) REVERT: D 603 GLU cc_start: 0.8592 (tt0) cc_final: 0.8236 (tp30) REVERT: D 621 GLU cc_start: 0.7428 (pt0) cc_final: 0.6870 (mp0) REVERT: D 631 GLU cc_start: 0.8114 (tt0) cc_final: 0.7867 (tt0) REVERT: D 797 LYS cc_start: 0.8115 (mttt) cc_final: 0.7678 (mtmt) REVERT: D 807 LYS cc_start: 0.8536 (mttt) cc_final: 0.8173 (mttm) REVERT: D 850 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7113 (mp0) REVERT: G 187 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7095 (mp0) REVERT: G 207 MET cc_start: 0.8185 (mmt) cc_final: 0.7825 (mmt) REVERT: G 374 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7670 (mt-10) REVERT: G 408 LYS cc_start: 0.6502 (ttpp) cc_final: 0.6232 (tptp) REVERT: G 439 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7716 (mtt90) REVERT: G 464 ASP cc_start: 0.7517 (m-30) cc_final: 0.7241 (m-30) REVERT: G 491 LYS cc_start: 0.8053 (mttt) cc_final: 0.7811 (mttm) REVERT: G 511 LYS cc_start: 0.7583 (tttt) cc_final: 0.6941 (mptt) REVERT: H 596 GLN cc_start: 0.7227 (mt0) cc_final: 0.6987 (mt0) REVERT: H 603 GLU cc_start: 0.8437 (tt0) cc_final: 0.8043 (tp30) REVERT: H 631 GLU cc_start: 0.8014 (tt0) cc_final: 0.7695 (tt0) REVERT: H 644 ASN cc_start: 0.8342 (t0) cc_final: 0.8123 (t0) REVERT: H 797 LYS cc_start: 0.8235 (mttt) cc_final: 0.7922 (mtmt) REVERT: H 850 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7122 (mp0) REVERT: I 97 LYS cc_start: 0.6386 (mttp) cc_final: 0.6021 (mtpt) REVERT: I 100 GLN cc_start: 0.8599 (mt0) cc_final: 0.8314 (mt0) REVERT: K 187 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7182 (mp0) REVERT: K 194 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7004 (tt0) REVERT: K 325 LYS cc_start: 0.7823 (tttt) cc_final: 0.7423 (ptpp) REVERT: K 374 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7432 (mm-30) REVERT: K 395 TYR cc_start: 0.7646 (m-80) cc_final: 0.7347 (m-80) REVERT: K 439 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7787 (mtt180) REVERT: K 464 ASP cc_start: 0.7139 (m-30) cc_final: 0.6882 (m-30) REVERT: K 511 LYS cc_start: 0.7587 (tttt) cc_final: 0.7020 (mptt) REVERT: L 603 GLU cc_start: 0.8443 (tt0) cc_final: 0.8036 (tp30) REVERT: L 621 GLU cc_start: 0.7519 (pt0) cc_final: 0.7020 (mp0) REVERT: L 631 GLU cc_start: 0.7774 (tt0) cc_final: 0.7467 (tt0) REVERT: L 765 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7516 (mtt-85) REVERT: L 851 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7317 (tm-30) outliers start: 18 outliers final: 2 residues processed: 310 average time/residue: 0.8401 time to fit residues: 292.2419 Evaluate side-chains 221 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 667 GLN D 907 HIS F 131 GLN H 863 GLN H 907 HIS J 131 GLN L 638 HIS L 907 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.129042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.088182 restraints weight = 25669.593| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.95 r_work: 0.2620 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23484 Z= 0.142 Angle : 0.679 7.988 32106 Z= 0.329 Chirality : 0.046 0.306 3906 Planarity : 0.004 0.027 3792 Dihedral : 12.837 82.823 5355 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.84 % Allowed : 8.74 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: -0.56 (0.16), residues: 2601 helix: 0.64 (0.17), residues: 876 sheet: -0.47 (0.26), residues: 351 loop : -0.99 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 269 TYR 0.020 0.001 TYR K 470 PHE 0.013 0.002 PHE K 317 TRP 0.012 0.001 TRP L 980 HIS 0.005 0.001 HIS L 868 Details of bonding type rmsd covalent geometry : bond 0.00283 (23355) covalent geometry : angle 0.63896 (31740) SS BOND : bond 0.00457 ( 21) SS BOND : angle 1.24611 ( 42) hydrogen bonds : bond 0.06050 ( 871) hydrogen bonds : angle 4.90384 ( 2316) link_ALPHA1-2 : bond 0.01361 ( 3) link_ALPHA1-2 : angle 2.19994 ( 9) link_ALPHA1-3 : bond 0.01056 ( 15) link_ALPHA1-3 : angle 1.57373 ( 45) link_ALPHA1-6 : bond 0.00682 ( 15) link_ALPHA1-6 : angle 1.71000 ( 45) link_BETA1-2 : bond 0.00810 ( 3) link_BETA1-2 : angle 4.61796 ( 9) link_BETA1-4 : bond 0.00823 ( 39) link_BETA1-4 : angle 2.46099 ( 117) link_NAG-ASN : bond 0.00599 ( 33) link_NAG-ASN : angle 2.40046 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.7464 (tttt) cc_final: 0.7231 (tttm) REVERT: C 187 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8295 (mp0) REVERT: C 207 MET cc_start: 0.9001 (mmt) cc_final: 0.8371 (mmt) REVERT: C 283 ARG cc_start: 0.7204 (mmt180) cc_final: 0.6276 (mmt90) REVERT: C 439 ARG cc_start: 0.8420 (mtm180) cc_final: 0.7967 (mtt90) REVERT: C 511 LYS cc_start: 0.8624 (tttt) cc_final: 0.8296 (mptt) REVERT: D 631 GLU cc_start: 0.8101 (tt0) cc_final: 0.7854 (tt0) REVERT: D 637 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: D 797 LYS cc_start: 0.8588 (mttt) cc_final: 0.8166 (mttp) REVERT: D 807 LYS cc_start: 0.9055 (mttt) cc_final: 0.8841 (mttm) REVERT: G 338 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7239 (mtm-85) REVERT: G 439 ARG cc_start: 0.8613 (mtm180) cc_final: 0.8409 (mtt90) REVERT: G 464 ASP cc_start: 0.7497 (m-30) cc_final: 0.7083 (m-30) REVERT: G 511 LYS cc_start: 0.8614 (tttt) cc_final: 0.8221 (mptp) REVERT: H 631 GLU cc_start: 0.7899 (tt0) cc_final: 0.7621 (tt0) REVERT: H 637 GLN cc_start: 0.8355 (tp40) cc_final: 0.8128 (mm-40) REVERT: H 644 ASN cc_start: 0.9137 (t0) cc_final: 0.8905 (t0) REVERT: H 797 LYS cc_start: 0.8603 (mttt) cc_final: 0.8289 (mtpp) REVERT: H 862 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9145 (tp) REVERT: I 97 LYS cc_start: 0.8178 (mttp) cc_final: 0.7755 (mtpt) REVERT: K 187 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8323 (mp0) REVERT: K 194 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7983 (tt0) REVERT: K 295 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7271 (mm-40) REVERT: K 408 LYS cc_start: 0.7267 (ttmm) cc_final: 0.6553 (tptp) REVERT: K 439 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8189 (mtt90) REVERT: K 511 LYS cc_start: 0.8626 (tttt) cc_final: 0.8259 (mptt) REVERT: L 631 GLU cc_start: 0.8014 (tt0) cc_final: 0.7772 (tt0) outliers start: 44 outliers final: 14 residues processed: 265 average time/residue: 0.8186 time to fit residues: 241.7799 Evaluate side-chains 220 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 862 LEU Chi-restraints excluded: chain K residue 295 GLN Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 110 optimal weight: 1.9990 chunk 218 optimal weight: 0.0980 chunk 114 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 240 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 246 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 722 ASN H 722 ASN H 863 GLN J 131 GLN K 346 ASN L 637 GLN L 722 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.090420 restraints weight = 25973.339| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.92 r_work: 0.2658 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 23484 Z= 0.120 Angle : 0.617 10.779 32106 Z= 0.293 Chirality : 0.046 0.538 3906 Planarity : 0.004 0.031 3792 Dihedral : 10.938 79.414 5353 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 10.04 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.26 (0.16), residues: 2601 helix: 1.69 (0.18), residues: 879 sheet: -0.01 (0.28), residues: 321 loop : -0.77 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 269 TYR 0.020 0.001 TYR K 470 PHE 0.011 0.001 PHE E 73 TRP 0.008 0.001 TRP H 926 HIS 0.002 0.001 HIS K 314 Details of bonding type rmsd covalent geometry : bond 0.00257 (23355) covalent geometry : angle 0.57769 (31740) SS BOND : bond 0.00618 ( 21) SS BOND : angle 2.29062 ( 42) hydrogen bonds : bond 0.04848 ( 871) hydrogen bonds : angle 4.52288 ( 2316) link_ALPHA1-2 : bond 0.01207 ( 3) link_ALPHA1-2 : angle 2.80266 ( 9) link_ALPHA1-3 : bond 0.01070 ( 15) link_ALPHA1-3 : angle 1.50733 ( 45) link_ALPHA1-6 : bond 0.00674 ( 15) link_ALPHA1-6 : angle 1.75667 ( 45) link_BETA1-2 : bond 0.00853 ( 3) link_BETA1-2 : angle 4.00592 ( 9) link_BETA1-4 : bond 0.00647 ( 39) link_BETA1-4 : angle 2.15459 ( 117) link_NAG-ASN : bond 0.00424 ( 33) link_NAG-ASN : angle 2.07188 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8074 (ttm170) REVERT: B 131 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8574 (mt0) REVERT: C 187 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8319 (mp0) REVERT: C 207 MET cc_start: 0.8984 (mmt) cc_final: 0.8328 (mmt) REVERT: C 283 ARG cc_start: 0.7114 (mmt180) cc_final: 0.6136 (mmt90) REVERT: C 439 ARG cc_start: 0.8360 (mtm180) cc_final: 0.8062 (mtt90) REVERT: C 511 LYS cc_start: 0.8540 (tttt) cc_final: 0.8189 (mptt) REVERT: D 637 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: D 797 LYS cc_start: 0.8501 (mttt) cc_final: 0.8225 (ttpm) REVERT: D 862 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8752 (tp) REVERT: G 338 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7202 (mtm-85) REVERT: G 464 ASP cc_start: 0.7480 (m-30) cc_final: 0.7124 (m-30) REVERT: G 511 LYS cc_start: 0.8511 (tttt) cc_final: 0.8173 (mptm) REVERT: H 644 ASN cc_start: 0.9151 (t0) cc_final: 0.8923 (t0) REVERT: H 797 LYS cc_start: 0.8536 (mttt) cc_final: 0.8225 (mtpp) REVERT: H 862 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8749 (tp) REVERT: I 97 LYS cc_start: 0.7950 (mttp) cc_final: 0.7487 (mtpt) REVERT: I 100 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: K 187 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8241 (mp0) REVERT: K 194 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7821 (tt0) REVERT: K 221 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7806 (tp30) REVERT: K 295 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7206 (mm-40) REVERT: K 408 LYS cc_start: 0.7190 (ttmm) cc_final: 0.6516 (tptp) REVERT: K 436 ARG cc_start: 0.7236 (ttt180) cc_final: 0.6978 (ttt180) REVERT: K 511 LYS cc_start: 0.8568 (tttt) cc_final: 0.8174 (mptt) REVERT: L 631 GLU cc_start: 0.7918 (tt0) cc_final: 0.7660 (tt0) outliers start: 55 outliers final: 19 residues processed: 263 average time/residue: 0.7830 time to fit residues: 231.1957 Evaluate side-chains 227 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 862 LEU Chi-restraints excluded: chain D residue 875 LYS Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 660 MET Chi-restraints excluded: chain H residue 740 THR Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 862 LEU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 295 GLN Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 660 MET Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 253 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 139 optimal weight: 0.0050 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 161 optimal weight: 0.4980 chunk 144 optimal weight: 0.0970 chunk 177 optimal weight: 0.0670 chunk 240 optimal weight: 0.6980 overall best weight: 0.1930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 645 HIS D 694 HIS F 131 GLN H 694 HIS H 863 GLN K 321 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093789 restraints weight = 26071.462| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.98 r_work: 0.2713 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 23484 Z= 0.101 Angle : 0.559 12.201 32106 Z= 0.262 Chirality : 0.044 0.381 3906 Planarity : 0.003 0.031 3792 Dihedral : 9.397 76.796 5353 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.17 % Allowed : 10.71 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.69 (0.17), residues: 2601 helix: 2.11 (0.18), residues: 882 sheet: 0.59 (0.29), residues: 336 loop : -0.70 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 269 TYR 0.019 0.001 TYR G 470 PHE 0.010 0.001 PHE E 73 TRP 0.007 0.001 TRP L 926 HIS 0.002 0.000 HIS L 743 Details of bonding type rmsd covalent geometry : bond 0.00206 (23355) covalent geometry : angle 0.52284 (31740) SS BOND : bond 0.00619 ( 21) SS BOND : angle 1.95990 ( 42) hydrogen bonds : bond 0.03732 ( 871) hydrogen bonds : angle 4.23745 ( 2316) link_ALPHA1-2 : bond 0.01127 ( 3) link_ALPHA1-2 : angle 2.48767 ( 9) link_ALPHA1-3 : bond 0.01101 ( 15) link_ALPHA1-3 : angle 1.65907 ( 45) link_ALPHA1-6 : bond 0.00701 ( 15) link_ALPHA1-6 : angle 1.86612 ( 45) link_BETA1-2 : bond 0.00880 ( 3) link_BETA1-2 : angle 3.88100 ( 9) link_BETA1-4 : bond 0.00549 ( 39) link_BETA1-4 : angle 1.82206 ( 117) link_NAG-ASN : bond 0.00412 ( 33) link_NAG-ASN : angle 1.85344 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8550 (ttp80) cc_final: 0.7952 (ttm170) REVERT: C 187 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8267 (mp0) REVERT: C 207 MET cc_start: 0.8980 (mmt) cc_final: 0.8190 (mmt) REVERT: C 283 ARG cc_start: 0.6978 (mmt180) cc_final: 0.6213 (mmt90) REVERT: C 408 LYS cc_start: 0.6650 (tptp) cc_final: 0.6018 (tppt) REVERT: C 462 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6446 (tp) REVERT: C 464 ASP cc_start: 0.7363 (m-30) cc_final: 0.6985 (m-30) REVERT: C 511 LYS cc_start: 0.8508 (tttt) cc_final: 0.8150 (mptm) REVERT: D 752 CYS cc_start: 0.8536 (t) cc_final: 0.7949 (p) REVERT: D 761 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7855 (mt-10) REVERT: D 797 LYS cc_start: 0.8452 (mttt) cc_final: 0.8174 (ttpm) REVERT: G 338 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7303 (mtm-85) REVERT: G 408 LYS cc_start: 0.6803 (tptp) cc_final: 0.6235 (ttmm) REVERT: G 511 LYS cc_start: 0.8504 (tttt) cc_final: 0.8196 (mptm) REVERT: H 631 GLU cc_start: 0.7787 (tt0) cc_final: 0.7545 (tt0) REVERT: H 644 ASN cc_start: 0.9138 (t0) cc_final: 0.8936 (t0) REVERT: H 797 LYS cc_start: 0.8466 (mttt) cc_final: 0.8205 (mtpp) REVERT: H 862 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8618 (tp) REVERT: K 187 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8267 (mp0) REVERT: K 194 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7816 (tt0) REVERT: K 221 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: K 408 LYS cc_start: 0.7164 (ttmm) cc_final: 0.6499 (tptp) REVERT: K 436 ARG cc_start: 0.7253 (ttt180) cc_final: 0.7037 (ttt180) REVERT: K 511 LYS cc_start: 0.8566 (tttt) cc_final: 0.8089 (mptt) REVERT: L 631 GLU cc_start: 0.7695 (tt0) cc_final: 0.7451 (tt0) REVERT: L 761 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8199 (mt-10) outliers start: 52 outliers final: 16 residues processed: 267 average time/residue: 0.7615 time to fit residues: 228.1673 Evaluate side-chains 232 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 862 LEU Chi-restraints excluded: chain K residue 202 SER Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 58 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 243 optimal weight: 0.0970 chunk 138 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 934 GLN H 863 GLN K 346 ASN L 644 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.091840 restraints weight = 25845.097| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.94 r_work: 0.2666 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 23484 Z= 0.109 Angle : 0.577 14.931 32106 Z= 0.271 Chirality : 0.044 0.382 3906 Planarity : 0.004 0.033 3792 Dihedral : 9.198 76.090 5353 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.09 % Allowed : 11.63 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.75 (0.17), residues: 2601 helix: 2.15 (0.18), residues: 882 sheet: 0.59 (0.30), residues: 306 loop : -0.61 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 269 TYR 0.019 0.001 TYR G 470 PHE 0.010 0.001 PHE E 73 TRP 0.005 0.001 TRP K 400 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00236 (23355) covalent geometry : angle 0.54290 (31740) SS BOND : bond 0.00763 ( 21) SS BOND : angle 2.06660 ( 42) hydrogen bonds : bond 0.04144 ( 871) hydrogen bonds : angle 4.20465 ( 2316) link_ALPHA1-2 : bond 0.01141 ( 3) link_ALPHA1-2 : angle 2.51410 ( 9) link_ALPHA1-3 : bond 0.01056 ( 15) link_ALPHA1-3 : angle 1.59858 ( 45) link_ALPHA1-6 : bond 0.00648 ( 15) link_ALPHA1-6 : angle 1.83856 ( 45) link_BETA1-2 : bond 0.00863 ( 3) link_BETA1-2 : angle 3.83664 ( 9) link_BETA1-4 : bond 0.00582 ( 39) link_BETA1-4 : angle 1.76459 ( 117) link_NAG-ASN : bond 0.00378 ( 33) link_NAG-ASN : angle 1.85780 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8262 (mp0) REVERT: C 207 MET cc_start: 0.9031 (mmt) cc_final: 0.8346 (mmt) REVERT: C 283 ARG cc_start: 0.6972 (mmt180) cc_final: 0.6189 (mmt90) REVERT: C 408 LYS cc_start: 0.6658 (tptp) cc_final: 0.6017 (tppt) REVERT: C 436 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6829 (tmt170) REVERT: C 462 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6385 (tp) REVERT: C 511 LYS cc_start: 0.8508 (tttt) cc_final: 0.8214 (mptt) REVERT: C 536 MET cc_start: 0.8785 (mtp) cc_final: 0.8581 (mtp) REVERT: D 752 CYS cc_start: 0.8581 (t) cc_final: 0.8031 (p) REVERT: D 761 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7940 (mt-10) REVERT: D 797 LYS cc_start: 0.8462 (mttt) cc_final: 0.8210 (ttpm) REVERT: G 408 LYS cc_start: 0.6833 (tptp) cc_final: 0.6253 (ttmm) REVERT: G 410 MET cc_start: 0.6157 (ttm) cc_final: 0.5939 (ttm) REVERT: G 511 LYS cc_start: 0.8520 (tttt) cc_final: 0.8194 (mptp) REVERT: H 631 GLU cc_start: 0.7904 (tt0) cc_final: 0.7652 (tt0) REVERT: H 797 LYS cc_start: 0.8486 (mttt) cc_final: 0.8236 (mtpp) REVERT: H 862 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8698 (tp) REVERT: K 187 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8274 (mp0) REVERT: K 221 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: K 408 LYS cc_start: 0.7171 (ttmm) cc_final: 0.6487 (tptp) REVERT: K 436 ARG cc_start: 0.7252 (ttt180) cc_final: 0.7047 (ttt180) REVERT: K 511 LYS cc_start: 0.8597 (tttt) cc_final: 0.8253 (mptm) REVERT: L 631 GLU cc_start: 0.7832 (tt0) cc_final: 0.7624 (tt0) REVERT: L 761 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8230 (mt-10) outliers start: 50 outliers final: 26 residues processed: 250 average time/residue: 0.7832 time to fit residues: 219.9752 Evaluate side-chains 235 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 660 MET Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 862 LEU Chi-restraints excluded: chain H residue 969 LEU Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 660 MET Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 163 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 161 optimal weight: 0.0370 chunk 57 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 131 optimal weight: 0.0020 chunk 176 optimal weight: 0.7980 overall best weight: 0.5068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN D 934 GLN H 863 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.091907 restraints weight = 26025.563| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.91 r_work: 0.2672 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 23484 Z= 0.111 Angle : 0.577 16.687 32106 Z= 0.271 Chirality : 0.044 0.390 3906 Planarity : 0.004 0.033 3792 Dihedral : 8.885 75.152 5353 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.13 % Allowed : 11.63 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.79 (0.17), residues: 2601 helix: 2.21 (0.18), residues: 864 sheet: 0.74 (0.29), residues: 336 loop : -0.62 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 269 TYR 0.018 0.001 TYR G 470 PHE 0.010 0.001 PHE E 73 TRP 0.006 0.001 TRP C 400 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00245 (23355) covalent geometry : angle 0.54282 (31740) SS BOND : bond 0.00982 ( 21) SS BOND : angle 2.12647 ( 42) hydrogen bonds : bond 0.04188 ( 871) hydrogen bonds : angle 4.20907 ( 2316) link_ALPHA1-2 : bond 0.01126 ( 3) link_ALPHA1-2 : angle 2.42081 ( 9) link_ALPHA1-3 : bond 0.01047 ( 15) link_ALPHA1-3 : angle 1.61742 ( 45) link_ALPHA1-6 : bond 0.00647 ( 15) link_ALPHA1-6 : angle 1.82069 ( 45) link_BETA1-2 : bond 0.00876 ( 3) link_BETA1-2 : angle 3.82434 ( 9) link_BETA1-4 : bond 0.00570 ( 39) link_BETA1-4 : angle 1.73398 ( 117) link_NAG-ASN : bond 0.00361 ( 33) link_NAG-ASN : angle 1.86682 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8184 (mp0) REVERT: C 207 MET cc_start: 0.8996 (mmt) cc_final: 0.8373 (mmt) REVERT: C 221 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: C 283 ARG cc_start: 0.7006 (mmt180) cc_final: 0.6217 (mmt90) REVERT: C 408 LYS cc_start: 0.6665 (tptp) cc_final: 0.6035 (tppt) REVERT: C 436 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6837 (tmt170) REVERT: C 462 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6390 (tp) REVERT: C 464 ASP cc_start: 0.7591 (m-30) cc_final: 0.7171 (m-30) REVERT: C 511 LYS cc_start: 0.8456 (tttt) cc_final: 0.8125 (mptm) REVERT: C 536 MET cc_start: 0.8710 (mtp) cc_final: 0.8503 (mtp) REVERT: D 752 CYS cc_start: 0.8598 (t) cc_final: 0.8043 (p) REVERT: D 761 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 797 LYS cc_start: 0.8448 (mttt) cc_final: 0.8171 (ttpm) REVERT: G 221 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: G 408 LYS cc_start: 0.6840 (tptp) cc_final: 0.6261 (ttmm) REVERT: G 511 LYS cc_start: 0.8476 (tttt) cc_final: 0.8147 (mptm) REVERT: H 631 GLU cc_start: 0.7971 (tt0) cc_final: 0.7706 (tt0) REVERT: H 797 LYS cc_start: 0.8405 (mttt) cc_final: 0.8158 (mtpp) REVERT: H 862 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8701 (tp) REVERT: K 187 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8253 (mp0) REVERT: K 194 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8196 (mt-10) REVERT: K 221 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: K 408 LYS cc_start: 0.7173 (ttmm) cc_final: 0.6495 (tptp) REVERT: K 511 LYS cc_start: 0.8599 (tttt) cc_final: 0.8231 (mptm) REVERT: L 761 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8238 (mt-10) outliers start: 51 outliers final: 30 residues processed: 248 average time/residue: 0.7374 time to fit residues: 205.7432 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 875 LYS Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 660 MET Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 862 LEU Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 167 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 638 HIS D 934 GLN H 863 GLN L 637 GLN L 893 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.086549 restraints weight = 25979.049| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.91 r_work: 0.2583 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 23484 Z= 0.221 Angle : 0.738 19.921 32106 Z= 0.350 Chirality : 0.050 0.423 3906 Planarity : 0.005 0.039 3792 Dihedral : 9.852 80.372 5353 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.80 % Allowed : 11.17 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.30 (0.17), residues: 2601 helix: 1.54 (0.18), residues: 879 sheet: 0.49 (0.29), residues: 321 loop : -0.75 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 613 TYR 0.024 0.002 TYR D 689 PHE 0.024 0.002 PHE L 800 TRP 0.013 0.002 TRP K 400 HIS 0.009 0.002 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00556 (23355) covalent geometry : angle 0.70375 (31740) SS BOND : bond 0.01274 ( 21) SS BOND : angle 2.78985 ( 42) hydrogen bonds : bond 0.06513 ( 871) hydrogen bonds : angle 4.48467 ( 2316) link_ALPHA1-2 : bond 0.01109 ( 3) link_ALPHA1-2 : angle 2.51922 ( 9) link_ALPHA1-3 : bond 0.00923 ( 15) link_ALPHA1-3 : angle 1.52031 ( 45) link_ALPHA1-6 : bond 0.00478 ( 15) link_ALPHA1-6 : angle 1.89649 ( 45) link_BETA1-2 : bond 0.00838 ( 3) link_BETA1-2 : angle 3.65428 ( 9) link_BETA1-4 : bond 0.00627 ( 39) link_BETA1-4 : angle 2.08865 ( 117) link_NAG-ASN : bond 0.00435 ( 33) link_NAG-ASN : angle 2.20839 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6704 (ttpp) REVERT: C 187 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8198 (mp0) REVERT: C 252 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8360 (mm) REVERT: C 283 ARG cc_start: 0.6891 (mmt180) cc_final: 0.6493 (mmt90) REVERT: C 401 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: C 408 LYS cc_start: 0.6571 (tptp) cc_final: 0.5983 (tppt) REVERT: C 462 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6360 (tp) REVERT: C 464 ASP cc_start: 0.7518 (m-30) cc_final: 0.7141 (m-30) REVERT: C 498 GLU cc_start: 0.8036 (tt0) cc_final: 0.7779 (tt0) REVERT: C 511 LYS cc_start: 0.8518 (tttt) cc_final: 0.8222 (mptt) REVERT: D 637 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: D 752 CYS cc_start: 0.8604 (t) cc_final: 0.8079 (p) REVERT: D 797 LYS cc_start: 0.8550 (mttt) cc_final: 0.8285 (ttpm) REVERT: G 321 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8642 (mm-40) REVERT: G 408 LYS cc_start: 0.6834 (tptp) cc_final: 0.6291 (ttmm) REVERT: G 511 LYS cc_start: 0.8517 (tttt) cc_final: 0.8178 (mptp) REVERT: H 637 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: H 797 LYS cc_start: 0.8538 (mttt) cc_final: 0.8268 (mtpp) REVERT: H 834 GLU cc_start: 0.8563 (tt0) cc_final: 0.8323 (tt0) REVERT: H 862 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9003 (tp) REVERT: K 187 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8266 (mp0) REVERT: K 295 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7171 (mm-40) REVERT: K 408 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6457 (tptp) REVERT: K 498 GLU cc_start: 0.8250 (tt0) cc_final: 0.7918 (tt0) REVERT: K 511 LYS cc_start: 0.8588 (tttt) cc_final: 0.8225 (mptp) REVERT: L 604 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8485 (p0) REVERT: L 631 GLU cc_start: 0.8011 (tt0) cc_final: 0.7775 (mt-10) outliers start: 67 outliers final: 32 residues processed: 255 average time/residue: 0.7679 time to fit residues: 219.7459 Evaluate side-chains 241 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 321 GLN Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 637 GLN Chi-restraints excluded: chain H residue 660 MET Chi-restraints excluded: chain H residue 740 THR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 862 LEU Chi-restraints excluded: chain H residue 969 LEU Chi-restraints excluded: chain H residue 973 LEU Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 295 GLN Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 61 optimal weight: 1.9990 chunk 241 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 190 optimal weight: 0.0980 chunk 129 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 863 GLN L 637 GLN L 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.130215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.090009 restraints weight = 25779.275| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.91 r_work: 0.2667 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 23484 Z= 0.116 Angle : 0.603 17.611 32106 Z= 0.284 Chirality : 0.045 0.414 3906 Planarity : 0.004 0.034 3792 Dihedral : 9.215 76.185 5353 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.97 % Allowed : 12.25 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.57 (0.17), residues: 2601 helix: 1.81 (0.18), residues: 873 sheet: 0.63 (0.30), residues: 306 loop : -0.59 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.017 0.001 TYR G 470 PHE 0.008 0.001 PHE A 73 TRP 0.007 0.001 TRP D 721 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00258 (23355) covalent geometry : angle 0.56866 (31740) SS BOND : bond 0.00997 ( 21) SS BOND : angle 2.25236 ( 42) hydrogen bonds : bond 0.04664 ( 871) hydrogen bonds : angle 4.35869 ( 2316) link_ALPHA1-2 : bond 0.01099 ( 3) link_ALPHA1-2 : angle 2.42373 ( 9) link_ALPHA1-3 : bond 0.00998 ( 15) link_ALPHA1-3 : angle 1.55483 ( 45) link_ALPHA1-6 : bond 0.00590 ( 15) link_ALPHA1-6 : angle 1.78822 ( 45) link_BETA1-2 : bond 0.00894 ( 3) link_BETA1-2 : angle 3.74067 ( 9) link_BETA1-4 : bond 0.00562 ( 39) link_BETA1-4 : angle 1.84683 ( 117) link_NAG-ASN : bond 0.00353 ( 33) link_NAG-ASN : angle 1.94541 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6635 (ttpp) REVERT: C 187 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8181 (mp0) REVERT: C 221 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: C 283 ARG cc_start: 0.6905 (mmt180) cc_final: 0.6532 (mmt90) REVERT: C 408 LYS cc_start: 0.6524 (tptp) cc_final: 0.6023 (tppt) REVERT: C 462 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6214 (tp) REVERT: C 464 ASP cc_start: 0.7561 (m-30) cc_final: 0.7164 (m-30) REVERT: C 511 LYS cc_start: 0.8464 (tttt) cc_final: 0.8141 (mptm) REVERT: D 583 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8471 (mmm) REVERT: D 637 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: D 752 CYS cc_start: 0.8550 (t) cc_final: 0.7954 (p) REVERT: D 761 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 797 LYS cc_start: 0.8448 (mttt) cc_final: 0.8198 (ttpm) REVERT: G 211 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8277 (tp30) REVERT: G 408 LYS cc_start: 0.6845 (tptp) cc_final: 0.6300 (ttmm) REVERT: G 511 LYS cc_start: 0.8477 (tttt) cc_final: 0.8158 (mptm) REVERT: H 631 GLU cc_start: 0.8018 (tt0) cc_final: 0.7749 (tt0) REVERT: H 797 LYS cc_start: 0.8492 (mttt) cc_final: 0.8224 (mtpp) REVERT: K 187 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8237 (mp0) REVERT: K 408 LYS cc_start: 0.7182 (ttmm) cc_final: 0.6499 (tptp) REVERT: K 511 LYS cc_start: 0.8568 (tttt) cc_final: 0.8204 (mptp) REVERT: L 583 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: L 604 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8335 (p0) REVERT: L 631 GLU cc_start: 0.7904 (tt0) cc_final: 0.7669 (mt-10) outliers start: 47 outliers final: 25 residues processed: 240 average time/residue: 0.7700 time to fit residues: 207.2732 Evaluate side-chains 233 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 583 MET Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 660 MET Chi-restraints excluded: chain H residue 740 THR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 660 MET Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 245 optimal weight: 0.4980 chunk 169 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN H 863 GLN L 637 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.088316 restraints weight = 25994.881| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.93 r_work: 0.2632 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 23484 Z= 0.146 Angle : 0.644 18.956 32106 Z= 0.303 Chirality : 0.046 0.430 3906 Planarity : 0.004 0.035 3792 Dihedral : 9.305 77.294 5353 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.88 % Allowed : 12.55 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.50 (0.17), residues: 2601 helix: 1.66 (0.18), residues: 882 sheet: 0.62 (0.29), residues: 321 loop : -0.61 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 269 TYR 0.017 0.001 TYR H 688 PHE 0.014 0.001 PHE L 800 TRP 0.008 0.001 TRP L 702 HIS 0.006 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00350 (23355) covalent geometry : angle 0.61068 (31740) SS BOND : bond 0.01118 ( 21) SS BOND : angle 2.42681 ( 42) hydrogen bonds : bond 0.05231 ( 871) hydrogen bonds : angle 4.37570 ( 2316) link_ALPHA1-2 : bond 0.01087 ( 3) link_ALPHA1-2 : angle 2.48812 ( 9) link_ALPHA1-3 : bond 0.00983 ( 15) link_ALPHA1-3 : angle 1.54021 ( 45) link_ALPHA1-6 : bond 0.00537 ( 15) link_ALPHA1-6 : angle 1.82481 ( 45) link_BETA1-2 : bond 0.00870 ( 3) link_BETA1-2 : angle 3.71356 ( 9) link_BETA1-4 : bond 0.00581 ( 39) link_BETA1-4 : angle 1.87122 ( 117) link_NAG-ASN : bond 0.00372 ( 33) link_NAG-ASN : angle 2.00613 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6649 (ttpp) REVERT: C 187 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8192 (mp0) REVERT: C 283 ARG cc_start: 0.6900 (mmt180) cc_final: 0.6524 (mmt90) REVERT: C 408 LYS cc_start: 0.6465 (tptp) cc_final: 0.5960 (tppt) REVERT: C 462 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6202 (tp) REVERT: C 464 ASP cc_start: 0.7531 (m-30) cc_final: 0.7152 (m-30) REVERT: C 511 LYS cc_start: 0.8478 (tttt) cc_final: 0.8142 (mptm) REVERT: D 637 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: D 752 CYS cc_start: 0.8708 (t) cc_final: 0.8149 (p) REVERT: D 797 LYS cc_start: 0.8470 (mttt) cc_final: 0.8203 (ttpm) REVERT: G 211 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: G 408 LYS cc_start: 0.6840 (tptp) cc_final: 0.6318 (ttmm) REVERT: G 511 LYS cc_start: 0.8491 (tttt) cc_final: 0.8170 (mptm) REVERT: H 631 GLU cc_start: 0.8033 (tt0) cc_final: 0.7795 (mt-10) REVERT: H 797 LYS cc_start: 0.8512 (mttt) cc_final: 0.8241 (mtpp) REVERT: K 187 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8239 (mp0) REVERT: K 408 LYS cc_start: 0.7090 (ttmm) cc_final: 0.6416 (tptp) REVERT: K 498 GLU cc_start: 0.8196 (tt0) cc_final: 0.7867 (tt0) REVERT: K 511 LYS cc_start: 0.8576 (tttt) cc_final: 0.8206 (mptp) REVERT: L 583 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8223 (mmm) REVERT: L 604 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8455 (p0) REVERT: L 631 GLU cc_start: 0.7944 (tt0) cc_final: 0.7630 (mt-10) outliers start: 45 outliers final: 29 residues processed: 233 average time/residue: 0.7584 time to fit residues: 198.1642 Evaluate side-chains 232 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 660 MET Chi-restraints excluded: chain H residue 740 THR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 660 MET Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 841 LEU Chi-restraints excluded: chain L residue 969 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 31 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 227 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 637 GLN H 640 HIS H 863 GLN L 637 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.130185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.090104 restraints weight = 25950.747| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.88 r_work: 0.2671 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 23484 Z= 0.122 Angle : 0.610 18.170 32106 Z= 0.287 Chirality : 0.045 0.423 3906 Planarity : 0.004 0.035 3792 Dihedral : 9.026 75.339 5353 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.71 % Allowed : 12.88 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.64 (0.17), residues: 2601 helix: 1.80 (0.18), residues: 876 sheet: 0.76 (0.29), residues: 336 loop : -0.57 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 269 TYR 0.020 0.001 TYR K 470 PHE 0.009 0.001 PHE H 800 TRP 0.006 0.001 TRP H 721 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00278 (23355) covalent geometry : angle 0.57658 (31740) SS BOND : bond 0.01063 ( 21) SS BOND : angle 2.28657 ( 42) hydrogen bonds : bond 0.04679 ( 871) hydrogen bonds : angle 4.32755 ( 2316) link_ALPHA1-2 : bond 0.01079 ( 3) link_ALPHA1-2 : angle 2.43188 ( 9) link_ALPHA1-3 : bond 0.01016 ( 15) link_ALPHA1-3 : angle 1.56218 ( 45) link_ALPHA1-6 : bond 0.00578 ( 15) link_ALPHA1-6 : angle 1.79182 ( 45) link_BETA1-2 : bond 0.00898 ( 3) link_BETA1-2 : angle 3.74331 ( 9) link_BETA1-4 : bond 0.00560 ( 39) link_BETA1-4 : angle 1.79324 ( 117) link_NAG-ASN : bond 0.00353 ( 33) link_NAG-ASN : angle 1.92050 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7883 (ttm170) REVERT: C 136 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.6573 (ttpp) REVERT: C 187 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8192 (mp0) REVERT: C 221 GLU cc_start: 0.8390 (tt0) cc_final: 0.7833 (tp30) REVERT: C 283 ARG cc_start: 0.6839 (mmt180) cc_final: 0.6385 (tpp-160) REVERT: C 408 LYS cc_start: 0.6513 (tptp) cc_final: 0.6013 (tppt) REVERT: C 462 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6167 (tp) REVERT: C 464 ASP cc_start: 0.7570 (m-30) cc_final: 0.7204 (m-30) REVERT: C 511 LYS cc_start: 0.8401 (tttt) cc_final: 0.8097 (mptm) REVERT: D 637 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7068 (tm130) REVERT: D 752 CYS cc_start: 0.8551 (t) cc_final: 0.7954 (p) REVERT: D 761 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8000 (mt-10) REVERT: D 797 LYS cc_start: 0.8444 (mttt) cc_final: 0.8186 (ttpm) REVERT: G 211 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8329 (tp30) REVERT: G 408 LYS cc_start: 0.6790 (tptp) cc_final: 0.6291 (ttmm) REVERT: G 511 LYS cc_start: 0.8421 (tttt) cc_final: 0.8120 (mptm) REVERT: H 631 GLU cc_start: 0.8024 (tt0) cc_final: 0.7765 (tt0) REVERT: H 797 LYS cc_start: 0.8495 (mttt) cc_final: 0.8229 (mtpp) REVERT: K 187 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8256 (mp0) REVERT: K 408 LYS cc_start: 0.7167 (ttmm) cc_final: 0.6487 (tptp) REVERT: K 511 LYS cc_start: 0.8565 (tttt) cc_final: 0.8235 (mptp) REVERT: L 604 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8432 (p0) REVERT: L 631 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7631 (mt-10) outliers start: 41 outliers final: 28 residues processed: 230 average time/residue: 0.8038 time to fit residues: 206.8124 Evaluate side-chains 233 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 660 MET Chi-restraints excluded: chain H residue 740 THR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 631 GLU Chi-restraints excluded: chain L residue 660 MET Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 841 LEU Chi-restraints excluded: chain L residue 969 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 80 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 chunk 154 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN H 863 GLN L 637 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.130465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090344 restraints weight = 25775.375| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.89 r_work: 0.2646 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 23484 Z= 0.120 Angle : 0.606 17.971 32106 Z= 0.285 Chirality : 0.045 0.422 3906 Planarity : 0.004 0.034 3792 Dihedral : 8.933 74.704 5353 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.84 % Allowed : 12.76 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.66 (0.17), residues: 2601 helix: 1.81 (0.18), residues: 876 sheet: 0.77 (0.29), residues: 336 loop : -0.55 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 269 TYR 0.022 0.001 TYR K 470 PHE 0.009 0.001 PHE H 800 TRP 0.006 0.001 TRP K 400 HIS 0.004 0.001 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00273 (23355) covalent geometry : angle 0.57293 (31740) SS BOND : bond 0.01071 ( 21) SS BOND : angle 2.26367 ( 42) hydrogen bonds : bond 0.04612 ( 871) hydrogen bonds : angle 4.31210 ( 2316) link_ALPHA1-2 : bond 0.01082 ( 3) link_ALPHA1-2 : angle 2.42454 ( 9) link_ALPHA1-3 : bond 0.01017 ( 15) link_ALPHA1-3 : angle 1.56602 ( 45) link_ALPHA1-6 : bond 0.00584 ( 15) link_ALPHA1-6 : angle 1.78517 ( 45) link_BETA1-2 : bond 0.00888 ( 3) link_BETA1-2 : angle 3.75906 ( 9) link_BETA1-4 : bond 0.00565 ( 39) link_BETA1-4 : angle 1.77208 ( 117) link_NAG-ASN : bond 0.00351 ( 33) link_NAG-ASN : angle 1.90370 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8411.26 seconds wall clock time: 143 minutes 58.68 seconds (8638.68 seconds total)