Starting phenix.real_space_refine on Thu Jun 19 19:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozh_17309/06_2025/8ozh_17309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozh_17309/06_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_17309/06_2025/8ozh_17309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozh_17309/06_2025/8ozh_17309.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozh_17309/06_2025/8ozh_17309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozh_17309/06_2025/8ozh_17309.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.77, per 1000 atoms: 0.73 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: 7.46 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.63 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: 8.12 Time building geometry restraints manager: 8.59 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: 0.15 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: 8.680 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: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.420 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.003 TRP H 721 HIS 0.009 0.002 HIS C 154 PHE 0.024 0.003 PHE E 87 TYR 0.031 0.004 TYR H 688 ARG 0.006 0.001 ARG A 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00854 ( 33) link_NAG-ASN : angle 3.07905 ( 99) 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_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) hydrogen bonds : bond 0.25717 ( 871) hydrogen bonds : angle 7.78422 ( 2316) SS BOND : bond 0.02672 ( 21) SS BOND : angle 2.97726 ( 42) covalent geometry : bond 0.01400 (23355) covalent geometry : angle 1.72120 (31740) *********************** 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 : 2.616 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: 1.6820 time to fit residues: 584.1727 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 : 2.579 ------------------------------------------------------------------------------- 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 217 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 596 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.086605 restraints weight = 25559.263| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.92 r_work: 0.2598 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23484 Z= 0.173 Angle : 0.713 7.732 32106 Z= 0.346 Chirality : 0.048 0.319 3906 Planarity : 0.004 0.030 3792 Dihedral : 12.879 84.233 5355 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.92 % Allowed : 8.91 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2601 helix: 0.54 (0.17), residues: 876 sheet: -0.45 (0.26), residues: 351 loop : -1.03 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 980 HIS 0.006 0.001 HIS L 868 PHE 0.017 0.002 PHE K 317 TYR 0.019 0.002 TYR C 470 ARG 0.005 0.001 ARG H 613 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 33) link_NAG-ASN : angle 2.45905 ( 99) link_ALPHA1-6 : bond 0.00530 ( 15) link_ALPHA1-6 : angle 1.71293 ( 45) link_BETA1-2 : bond 0.00832 ( 3) link_BETA1-2 : angle 4.47378 ( 9) link_BETA1-4 : bond 0.00691 ( 39) link_BETA1-4 : angle 2.53831 ( 117) link_ALPHA1-2 : bond 0.01200 ( 3) link_ALPHA1-2 : angle 2.36492 ( 9) link_ALPHA1-3 : bond 0.00906 ( 15) link_ALPHA1-3 : angle 1.54416 ( 45) hydrogen bonds : bond 0.06395 ( 871) hydrogen bonds : angle 4.92797 ( 2316) SS BOND : bond 0.00826 ( 21) SS BOND : angle 1.41582 ( 42) covalent geometry : bond 0.00378 (23355) covalent geometry : angle 0.67417 (31740) *********************** 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 276 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.7478 (tttt) cc_final: 0.7134 (tttp) REVERT: C 207 MET cc_start: 0.9014 (mmt) cc_final: 0.8392 (mmt) REVERT: C 283 ARG cc_start: 0.7214 (mmt180) cc_final: 0.6292 (mmt90) REVERT: C 439 ARG cc_start: 0.8419 (mtm180) cc_final: 0.8015 (mtt90) REVERT: C 511 LYS cc_start: 0.8673 (tttt) cc_final: 0.8338 (mptt) REVERT: D 621 GLU cc_start: 0.7990 (pt0) cc_final: 0.7746 (mp0) REVERT: D 631 GLU cc_start: 0.8213 (tt0) cc_final: 0.7976 (mt-10) REVERT: D 637 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: D 797 LYS cc_start: 0.8564 (mttt) cc_final: 0.8143 (mttp) REVERT: D 807 LYS cc_start: 0.9075 (mttt) cc_final: 0.8858 (mttm) REVERT: D 851 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: G 295 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7404 (mm-40) REVERT: G 338 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7292 (mtm-85) REVERT: G 464 ASP cc_start: 0.7534 (m-30) cc_final: 0.7161 (m-30) REVERT: G 511 LYS cc_start: 0.8599 (tttt) cc_final: 0.8231 (mptp) REVERT: H 637 GLN cc_start: 0.8405 (tp40) cc_final: 0.8202 (mm-40) REVERT: H 644 ASN cc_start: 0.9189 (t0) cc_final: 0.8969 (t0) REVERT: H 797 LYS cc_start: 0.8615 (mttt) cc_final: 0.8298 (mtpp) REVERT: H 862 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8927 (tp) REVERT: I 97 LYS cc_start: 0.8176 (mttp) cc_final: 0.7758 (mtpt) REVERT: K 187 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8330 (mp0) REVERT: K 194 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8019 (tt0) REVERT: K 295 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7291 (mm-40) REVERT: K 408 LYS cc_start: 0.7199 (ttmm) cc_final: 0.6492 (tptp) REVERT: K 511 LYS cc_start: 0.8635 (tttt) cc_final: 0.8271 (mptt) REVERT: L 631 GLU cc_start: 0.8096 (tt0) cc_final: 0.7847 (tt0) outliers start: 46 outliers final: 16 residues processed: 262 average time/residue: 1.7281 time to fit residues: 510.5439 Evaluate side-chains 225 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 4.748 ------------------------------------------------------------------------------- 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 851 GLU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 295 GLN 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 740 THR 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 740 THR 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 156 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 863 GLN K 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.126876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.086709 restraints weight = 25683.453| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.91 r_work: 0.2600 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 23484 Z= 0.189 Angle : 0.720 13.547 32106 Z= 0.344 Chirality : 0.050 0.620 3906 Planarity : 0.005 0.035 3792 Dihedral : 11.696 84.725 5353 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.76 % Allowed : 10.08 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2601 helix: 1.18 (0.18), residues: 879 sheet: -0.08 (0.28), residues: 336 loop : -0.92 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 702 HIS 0.006 0.001 HIS C 154 PHE 0.016 0.002 PHE L 800 TYR 0.020 0.002 TYR H 688 ARG 0.005 0.001 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 33) link_NAG-ASN : angle 2.31782 ( 99) link_ALPHA1-6 : bond 0.00589 ( 15) link_ALPHA1-6 : angle 1.76666 ( 45) link_BETA1-2 : bond 0.00896 ( 3) link_BETA1-2 : angle 3.89947 ( 9) link_BETA1-4 : bond 0.00707 ( 39) link_BETA1-4 : angle 2.34724 ( 117) link_ALPHA1-2 : bond 0.01185 ( 3) link_ALPHA1-2 : angle 2.89113 ( 9) link_ALPHA1-3 : bond 0.01044 ( 15) link_ALPHA1-3 : angle 1.50567 ( 45) hydrogen bonds : bond 0.06499 ( 871) hydrogen bonds : angle 4.73452 ( 2316) SS BOND : bond 0.00802 ( 21) SS BOND : angle 2.72816 ( 42) covalent geometry : bond 0.00458 (23355) covalent geometry : angle 0.68064 (31740) *********************** 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 280 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8556 (ttp80) cc_final: 0.8138 (ttm170) REVERT: B 131 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: C 207 MET cc_start: 0.8943 (mmt) cc_final: 0.8388 (mmt) REVERT: C 283 ARG cc_start: 0.7084 (mmt180) cc_final: 0.6064 (mmt90) REVERT: C 408 LYS cc_start: 0.6692 (tptp) cc_final: 0.6036 (tppt) REVERT: C 511 LYS cc_start: 0.8656 (tttt) cc_final: 0.8348 (mptt) REVERT: D 621 GLU cc_start: 0.8118 (pt0) cc_final: 0.7802 (mp0) REVERT: D 631 GLU cc_start: 0.8264 (tt0) cc_final: 0.8037 (mt-10) REVERT: D 637 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: D 797 LYS cc_start: 0.8604 (mttt) cc_final: 0.8108 (mtmt) REVERT: D 851 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: G 211 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: G 295 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7398 (mm-40) REVERT: G 338 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7349 (mtm-85) REVERT: G 401 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: G 464 ASP cc_start: 0.7591 (m-30) cc_final: 0.7201 (m-30) REVERT: G 511 LYS cc_start: 0.8627 (tttt) cc_final: 0.8256 (mptp) REVERT: H 631 GLU cc_start: 0.8125 (tt0) cc_final: 0.7836 (tt0) REVERT: H 797 LYS cc_start: 0.8617 (mttt) cc_final: 0.8296 (mtpp) REVERT: H 862 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8993 (tp) REVERT: I 97 LYS cc_start: 0.8125 (mttp) cc_final: 0.7705 (mtpt) REVERT: I 100 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: K 187 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8349 (mp0) REVERT: K 295 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7261 (mm-40) REVERT: K 401 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: K 408 LYS cc_start: 0.7144 (ttmm) cc_final: 0.6382 (tptp) REVERT: K 436 ARG cc_start: 0.7155 (ttt180) cc_final: 0.6580 (tmt170) REVERT: K 511 LYS cc_start: 0.8682 (tttt) cc_final: 0.8270 (mptp) REVERT: L 797 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8167 (mmtm) outliers start: 66 outliers final: 30 residues processed: 259 average time/residue: 1.5644 time to fit residues: 455.9951 Evaluate side-chains 241 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 483 SER 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 851 GLU 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 152 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 295 GLN Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 401 GLU 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 841 LEU Chi-restraints excluded: chain H residue 862 LEU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain J residue 131 GLN 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 401 GLU Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain K residue 547 ASP 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 Chi-restraints excluded: chain L residue 969 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 102 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 214 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 76 optimal weight: 0.0070 chunk 47 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 131 GLN H 722 ASN H 863 GLN J 131 GLN L 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.130226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090308 restraints weight = 25998.244| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.88 r_work: 0.2651 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 23484 Z= 0.116 Angle : 0.597 11.497 32106 Z= 0.282 Chirality : 0.045 0.439 3906 Planarity : 0.004 0.043 3792 Dihedral : 10.270 81.532 5353 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.43 % Allowed : 10.96 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2601 helix: 1.67 (0.18), residues: 879 sheet: 0.26 (0.27), residues: 351 loop : -0.77 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 926 HIS 0.003 0.001 HIS L 743 PHE 0.009 0.001 PHE C 317 TYR 0.019 0.001 TYR G 470 ARG 0.007 0.000 ARG G 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 33) link_NAG-ASN : angle 2.03844 ( 99) link_ALPHA1-6 : bond 0.00631 ( 15) link_ALPHA1-6 : angle 1.80789 ( 45) link_BETA1-2 : bond 0.00888 ( 3) link_BETA1-2 : angle 3.86720 ( 9) link_BETA1-4 : bond 0.00562 ( 39) link_BETA1-4 : angle 2.04740 ( 117) link_ALPHA1-2 : bond 0.01112 ( 3) link_ALPHA1-2 : angle 2.64405 ( 9) link_ALPHA1-3 : bond 0.01051 ( 15) link_ALPHA1-3 : angle 1.57240 ( 45) hydrogen bonds : bond 0.04635 ( 871) hydrogen bonds : angle 4.43364 ( 2316) SS BOND : bond 0.00887 ( 21) SS BOND : angle 2.09771 ( 42) covalent geometry : bond 0.00255 (23355) covalent geometry : angle 0.55878 (31740) *********************** 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 281 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8078 (ttm170) REVERT: C 207 MET cc_start: 0.8942 (mmt) cc_final: 0.8408 (mmt) REVERT: C 283 ARG cc_start: 0.6992 (mmt180) cc_final: 0.6590 (mmt90) REVERT: C 408 LYS cc_start: 0.6658 (tptp) cc_final: 0.6057 (tppt) REVERT: C 511 LYS cc_start: 0.8596 (tttt) cc_final: 0.8260 (mptm) REVERT: D 621 GLU cc_start: 0.7983 (pt0) cc_final: 0.7781 (mp0) REVERT: D 637 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: D 797 LYS cc_start: 0.8502 (mttt) cc_final: 0.8276 (ttpm) REVERT: D 851 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: G 408 LYS cc_start: 0.6825 (tptp) cc_final: 0.6288 (ttmm) REVERT: G 464 ASP cc_start: 0.7555 (m-30) cc_final: 0.7211 (m-30) REVERT: G 511 LYS cc_start: 0.8557 (tttt) cc_final: 0.8299 (mptt) REVERT: H 631 GLU cc_start: 0.7995 (tt0) cc_final: 0.7696 (tt0) REVERT: H 797 LYS cc_start: 0.8572 (mttt) cc_final: 0.8295 (mtpp) REVERT: I 97 LYS cc_start: 0.7976 (mttp) cc_final: 0.7566 (mtpt) REVERT: K 187 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8383 (mp0) REVERT: K 295 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7226 (mm-40) REVERT: K 338 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7101 (mtm-85) REVERT: K 408 LYS cc_start: 0.7174 (ttmm) cc_final: 0.6482 (tptp) REVERT: K 436 ARG cc_start: 0.7267 (ttt180) cc_final: 0.6721 (tmt170) REVERT: K 511 LYS cc_start: 0.8574 (tttt) cc_final: 0.8222 (mptp) REVERT: L 761 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8287 (mt-10) outliers start: 58 outliers final: 20 residues processed: 260 average time/residue: 1.5355 time to fit residues: 449.7978 Evaluate side-chains 228 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 851 GLU Chi-restraints excluded: chain D residue 875 LYS Chi-restraints excluded: chain G residue 198 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 K residue 295 GLN Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 547 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 168 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.129433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.089457 restraints weight = 25978.584| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.89 r_work: 0.2635 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 23484 Z= 0.129 Angle : 0.617 13.813 32106 Z= 0.292 Chirality : 0.045 0.384 3906 Planarity : 0.004 0.035 3792 Dihedral : 10.028 81.307 5353 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 11.33 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2601 helix: 1.74 (0.18), residues: 879 sheet: 0.41 (0.30), residues: 306 loop : -0.72 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 702 HIS 0.005 0.001 HIS C 154 PHE 0.011 0.001 PHE L 800 TYR 0.018 0.001 TYR G 470 ARG 0.006 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 33) link_NAG-ASN : angle 2.03079 ( 99) link_ALPHA1-6 : bond 0.00586 ( 15) link_ALPHA1-6 : angle 1.84868 ( 45) link_BETA1-2 : bond 0.00874 ( 3) link_BETA1-2 : angle 3.78305 ( 9) link_BETA1-4 : bond 0.00586 ( 39) link_BETA1-4 : angle 1.93281 ( 117) link_ALPHA1-2 : bond 0.01150 ( 3) link_ALPHA1-2 : angle 2.67379 ( 9) link_ALPHA1-3 : bond 0.01029 ( 15) link_ALPHA1-3 : angle 1.54253 ( 45) hydrogen bonds : bond 0.04989 ( 871) hydrogen bonds : angle 4.39285 ( 2316) SS BOND : bond 0.00847 ( 21) SS BOND : angle 2.11445 ( 42) covalent geometry : bond 0.00298 (23355) covalent geometry : angle 0.58204 (31740) *********************** 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 271 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8566 (ttp80) cc_final: 0.7954 (ttm170) REVERT: C 207 MET cc_start: 0.8955 (mmt) cc_final: 0.8377 (mmt) REVERT: C 283 ARG cc_start: 0.6920 (mmt180) cc_final: 0.6518 (mmt90) REVERT: C 408 LYS cc_start: 0.6677 (tptp) cc_final: 0.6029 (tppt) REVERT: C 511 LYS cc_start: 0.8561 (tttt) cc_final: 0.8220 (mptm) REVERT: D 621 GLU cc_start: 0.7985 (pt0) cc_final: 0.7758 (mp0) REVERT: D 637 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: D 797 LYS cc_start: 0.8557 (mttt) cc_final: 0.8314 (ttpm) REVERT: D 851 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: G 401 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: G 408 LYS cc_start: 0.6819 (tptp) cc_final: 0.6204 (ttmm) REVERT: G 464 ASP cc_start: 0.7624 (m-30) cc_final: 0.7393 (m-30) REVERT: G 511 LYS cc_start: 0.8507 (tttt) cc_final: 0.8189 (mptp) REVERT: H 797 LYS cc_start: 0.8533 (mttt) cc_final: 0.8245 (mtpp) REVERT: H 862 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8721 (tp) REVERT: I 97 LYS cc_start: 0.7863 (mttp) cc_final: 0.7479 (mtpt) REVERT: K 187 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8317 (mp0) REVERT: K 295 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7212 (mm-40) REVERT: K 338 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7050 (mtm-85) REVERT: K 408 LYS cc_start: 0.7188 (ttmm) cc_final: 0.6519 (tptp) REVERT: K 436 ARG cc_start: 0.7250 (ttt180) cc_final: 0.7036 (ttt180) REVERT: K 511 LYS cc_start: 0.8531 (tttt) cc_final: 0.8179 (mptp) REVERT: L 631 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: L 761 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8325 (mt-10) outliers start: 59 outliers final: 33 residues processed: 251 average time/residue: 1.5734 time to fit residues: 444.7000 Evaluate side-chains 247 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 626 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 851 GLU 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 D residue 973 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 401 GLU 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 295 GLN Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain K residue 547 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 218 optimal weight: 0.0980 chunk 203 optimal weight: 4.9990 chunk 100 optimal weight: 0.0470 chunk 235 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.0284 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.087731 restraints weight = 25869.154| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.93 r_work: 0.2636 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 23484 Z= 0.151 Angle : 0.648 18.379 32106 Z= 0.307 Chirality : 0.046 0.401 3906 Planarity : 0.004 0.035 3792 Dihedral : 9.987 81.068 5353 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.89 % Allowed : 11.13 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2601 helix: 1.62 (0.18), residues: 879 sheet: 0.45 (0.30), residues: 306 loop : -0.72 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 400 HIS 0.006 0.001 HIS C 154 PHE 0.014 0.001 PHE L 800 TYR 0.018 0.002 TYR G 470 ARG 0.004 0.000 ARG K 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 33) link_NAG-ASN : angle 2.08851 ( 99) link_ALPHA1-6 : bond 0.00542 ( 15) link_ALPHA1-6 : angle 1.85385 ( 45) link_BETA1-2 : bond 0.00881 ( 3) link_BETA1-2 : angle 3.71571 ( 9) link_BETA1-4 : bond 0.00595 ( 39) link_BETA1-4 : angle 1.94668 ( 117) link_ALPHA1-2 : bond 0.01123 ( 3) link_ALPHA1-2 : angle 2.61639 ( 9) link_ALPHA1-3 : bond 0.01002 ( 15) link_ALPHA1-3 : angle 1.53002 ( 45) hydrogen bonds : bond 0.05482 ( 871) hydrogen bonds : angle 4.44709 ( 2316) SS BOND : bond 0.01020 ( 21) SS BOND : angle 2.41991 ( 42) covalent geometry : bond 0.00364 (23355) covalent geometry : angle 0.61292 (31740) *********************** 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 276 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8595 (ttp80) cc_final: 0.7923 (ttm170) REVERT: C 211 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: C 276 TYR cc_start: 0.8964 (t80) cc_final: 0.8755 (t80) REVERT: C 283 ARG cc_start: 0.6884 (mmt180) cc_final: 0.6638 (mmt90) REVERT: C 401 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: C 408 LYS cc_start: 0.6659 (tptp) cc_final: 0.5957 (tppt) REVERT: C 511 LYS cc_start: 0.8564 (tttt) cc_final: 0.8229 (mptt) REVERT: D 621 GLU cc_start: 0.8025 (pt0) cc_final: 0.7765 (mp0) REVERT: D 637 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: D 797 LYS cc_start: 0.8541 (mttt) cc_final: 0.8316 (ttpm) REVERT: D 851 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: E 112 GLN cc_start: 0.8763 (tt0) cc_final: 0.8528 (tt0) REVERT: G 211 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: G 401 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: G 408 LYS cc_start: 0.6789 (tptp) cc_final: 0.6231 (ttmm) REVERT: G 464 ASP cc_start: 0.7580 (m-30) cc_final: 0.7366 (m-30) REVERT: G 511 LYS cc_start: 0.8573 (tttt) cc_final: 0.8217 (mptp) REVERT: H 631 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: H 797 LYS cc_start: 0.8544 (mttt) cc_final: 0.8255 (mtpp) REVERT: H 834 GLU cc_start: 0.8548 (tt0) cc_final: 0.8339 (tt0) REVERT: H 885 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8899 (t) REVERT: I 97 LYS cc_start: 0.7899 (mttp) cc_final: 0.7495 (mtpt) REVERT: K 187 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8268 (mp0) REVERT: K 221 GLU cc_start: 0.8410 (tt0) cc_final: 0.7891 (tp30) REVERT: K 295 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7220 (mm-40) REVERT: K 338 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7070 (mtm-85) REVERT: K 408 LYS cc_start: 0.7119 (ttmm) cc_final: 0.6474 (tptp) REVERT: K 498 GLU cc_start: 0.8240 (tt0) cc_final: 0.7923 (tt0) REVERT: K 511 LYS cc_start: 0.8538 (tttt) cc_final: 0.8234 (mptt) REVERT: L 583 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8174 (mmm) REVERT: L 631 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7592 (mt-10) outliers start: 69 outliers final: 37 residues processed: 253 average time/residue: 1.5166 time to fit residues: 433.0058 Evaluate side-chains 251 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 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 401 GLU Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 752 CYS 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 851 GLU 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 D residue 973 LEU Chi-restraints excluded: chain G residue 152 GLU 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 401 GLU Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 598 SER Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 631 GLU 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 885 SER Chi-restraints excluded: chain H residue 969 LEU Chi-restraints excluded: chain H residue 973 LEU Chi-restraints excluded: chain K residue 295 GLN Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET 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 754 GLU 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 176 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 248 optimal weight: 0.0980 chunk 181 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 863 GLN I 112 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 = 0.3353 r_free = 0.3353 target = 0.129351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.089410 restraints weight = 26003.538| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.89 r_work: 0.2643 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2485 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= 0.125 Angle : 0.611 18.095 32106 Z= 0.288 Chirality : 0.045 0.403 3906 Planarity : 0.004 0.035 3792 Dihedral : 9.612 79.916 5353 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.55 % Allowed : 11.63 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2601 helix: 1.76 (0.18), residues: 873 sheet: 0.55 (0.30), residues: 306 loop : -0.65 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 721 HIS 0.004 0.001 HIS C 154 PHE 0.009 0.001 PHE L 800 TYR 0.017 0.001 TYR H 688 ARG 0.004 0.000 ARG K 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 33) link_NAG-ASN : angle 1.97193 ( 99) link_ALPHA1-6 : bond 0.00571 ( 15) link_ALPHA1-6 : angle 1.80825 ( 45) link_BETA1-2 : bond 0.00900 ( 3) link_BETA1-2 : angle 3.74392 ( 9) link_BETA1-4 : bond 0.00567 ( 39) link_BETA1-4 : angle 1.84710 ( 117) link_ALPHA1-2 : bond 0.01100 ( 3) link_ALPHA1-2 : angle 2.55606 ( 9) link_ALPHA1-3 : bond 0.01020 ( 15) link_ALPHA1-3 : angle 1.55296 ( 45) hydrogen bonds : bond 0.04840 ( 871) hydrogen bonds : angle 4.38618 ( 2316) SS BOND : bond 0.01009 ( 21) SS BOND : angle 2.27427 ( 42) covalent geometry : bond 0.00287 (23355) covalent geometry : angle 0.57589 (31740) *********************** 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 266 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8569 (ttp80) cc_final: 0.7930 (ttm170) REVERT: C 211 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8329 (tp30) REVERT: C 283 ARG cc_start: 0.6913 (mmt180) cc_final: 0.6675 (mmt90) REVERT: C 408 LYS cc_start: 0.6464 (tptp) cc_final: 0.5967 (tppt) REVERT: C 436 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6835 (tmt170) REVERT: C 511 LYS cc_start: 0.8523 (tttt) cc_final: 0.8176 (mptm) REVERT: D 621 GLU cc_start: 0.8007 (pt0) cc_final: 0.7747 (mp0) REVERT: D 637 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: D 752 CYS cc_start: 0.8544 (t) cc_final: 0.7958 (p) REVERT: D 797 LYS cc_start: 0.8464 (mttt) cc_final: 0.8224 (ttpm) REVERT: D 851 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: G 408 LYS cc_start: 0.6805 (tptp) cc_final: 0.6291 (ttmm) REVERT: G 511 LYS cc_start: 0.8562 (tttt) cc_final: 0.8199 (mptm) REVERT: H 631 GLU cc_start: 0.8057 (tt0) cc_final: 0.7796 (tt0) REVERT: H 797 LYS cc_start: 0.8523 (mttt) cc_final: 0.8249 (mtpp) REVERT: I 97 LYS cc_start: 0.7870 (mttp) cc_final: 0.7492 (mtpt) REVERT: K 187 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8250 (mp0) REVERT: K 211 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8196 (tp30) REVERT: K 221 GLU cc_start: 0.8392 (tt0) cc_final: 0.7853 (tp30) REVERT: K 295 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7177 (mm-40) REVERT: K 338 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7030 (mtm-85) REVERT: K 408 LYS cc_start: 0.7182 (ttmm) cc_final: 0.6555 (tptp) REVERT: K 511 LYS cc_start: 0.8619 (tttt) cc_final: 0.8250 (mptt) REVERT: L 583 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8215 (mmm) REVERT: L 631 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7472 (mt-10) outliers start: 61 outliers final: 33 residues processed: 247 average time/residue: 1.7673 time to fit residues: 493.9333 Evaluate side-chains 244 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 737 THR 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 851 GLU 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 D residue 973 LEU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 470 TYR Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain G residue 547 ASP Chi-restraints excluded: chain H residue 598 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 753 VAL Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain K residue 295 GLN Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 165 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 863 GLN I 112 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 = 0.3348 r_free = 0.3348 target = 0.128928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.088274 restraints weight = 25866.421| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.93 r_work: 0.2615 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 23484 Z= 0.137 Angle : 0.632 18.228 32106 Z= 0.297 Chirality : 0.046 0.420 3906 Planarity : 0.004 0.034 3792 Dihedral : 9.561 79.580 5353 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 11.96 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2601 helix: 1.69 (0.18), residues: 879 sheet: 0.66 (0.29), residues: 336 loop : -0.69 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 702 HIS 0.005 0.001 HIS C 154 PHE 0.011 0.001 PHE L 800 TYR 0.018 0.001 TYR H 688 ARG 0.004 0.000 ARG K 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 33) link_NAG-ASN : angle 2.10855 ( 99) link_ALPHA1-6 : bond 0.00556 ( 15) link_ALPHA1-6 : angle 1.82289 ( 45) link_BETA1-2 : bond 0.00890 ( 3) link_BETA1-2 : angle 3.72845 ( 9) link_BETA1-4 : bond 0.00567 ( 39) link_BETA1-4 : angle 1.84487 ( 117) link_ALPHA1-2 : bond 0.01097 ( 3) link_ALPHA1-2 : angle 2.55973 ( 9) link_ALPHA1-3 : bond 0.01014 ( 15) link_ALPHA1-3 : angle 1.54773 ( 45) hydrogen bonds : bond 0.05042 ( 871) hydrogen bonds : angle 4.39547 ( 2316) SS BOND : bond 0.01052 ( 21) SS BOND : angle 2.37479 ( 42) covalent geometry : bond 0.00324 (23355) covalent geometry : angle 0.59646 (31740) *********************** 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 260 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8325 (tp30) REVERT: C 283 ARG cc_start: 0.6920 (mmt180) cc_final: 0.6686 (mmt90) REVERT: C 408 LYS cc_start: 0.6485 (tptp) cc_final: 0.5988 (tppt) REVERT: C 436 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6847 (tmt170) REVERT: C 464 ASP cc_start: 0.7366 (m-30) cc_final: 0.6939 (m-30) REVERT: C 511 LYS cc_start: 0.8538 (tttt) cc_final: 0.8213 (mptm) REVERT: D 621 GLU cc_start: 0.8034 (pt0) cc_final: 0.7761 (mp0) REVERT: D 637 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: D 752 CYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7993 (p) REVERT: D 797 LYS cc_start: 0.8475 (mttt) cc_final: 0.8255 (ttpm) REVERT: D 851 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: E 112 GLN cc_start: 0.8779 (tt0) cc_final: 0.8539 (tt0) REVERT: G 295 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7440 (mm-40) REVERT: G 408 LYS cc_start: 0.6837 (tptp) cc_final: 0.6289 (ttmm) REVERT: G 511 LYS cc_start: 0.8587 (tttt) cc_final: 0.8235 (mptm) REVERT: H 631 GLU cc_start: 0.8058 (tt0) cc_final: 0.7779 (mt-10) REVERT: H 797 LYS cc_start: 0.8523 (mttt) cc_final: 0.8252 (mtpp) REVERT: I 97 LYS cc_start: 0.7922 (mttp) cc_final: 0.7549 (mtpt) REVERT: K 187 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8271 (mp0) REVERT: K 211 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: K 221 GLU cc_start: 0.8420 (tt0) cc_final: 0.7907 (tp30) REVERT: K 338 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7059 (mtm-85) REVERT: K 408 LYS cc_start: 0.7215 (ttmm) cc_final: 0.6574 (tptp) REVERT: K 511 LYS cc_start: 0.8631 (tttt) cc_final: 0.8247 (mptm) REVERT: L 583 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: L 620 MET cc_start: 0.8117 (mtm) cc_final: 0.7835 (mtm) REVERT: L 631 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7528 (mt-10) outliers start: 60 outliers final: 38 residues processed: 238 average time/residue: 1.5763 time to fit residues: 422.6606 Evaluate side-chains 246 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 851 GLU 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 D residue 973 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 295 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 598 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 753 VAL Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET Chi-restraints excluded: chain L residue 598 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 230 optimal weight: 0.0970 chunk 33 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 722 ASN G 489 GLN H 863 GLN I 112 GLN L 637 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.130972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090227 restraints weight = 25944.478| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.93 r_work: 0.2690 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 23484 Z= 0.109 Angle : 0.594 17.201 32106 Z= 0.278 Chirality : 0.045 0.410 3906 Planarity : 0.004 0.034 3792 Dihedral : 9.144 77.948 5353 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.38 % Allowed : 12.17 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2601 helix: 1.88 (0.18), residues: 876 sheet: 0.68 (0.30), residues: 306 loop : -0.56 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 721 HIS 0.003 0.001 HIS C 154 PHE 0.008 0.001 PHE E 73 TYR 0.025 0.001 TYR G 470 ARG 0.008 0.000 ARG K 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 33) link_NAG-ASN : angle 2.12835 ( 99) link_ALPHA1-6 : bond 0.00613 ( 15) link_ALPHA1-6 : angle 1.79522 ( 45) link_BETA1-2 : bond 0.00900 ( 3) link_BETA1-2 : angle 3.78474 ( 9) link_BETA1-4 : bond 0.00558 ( 39) link_BETA1-4 : angle 1.74164 ( 117) link_ALPHA1-2 : bond 0.01102 ( 3) link_ALPHA1-2 : angle 2.47052 ( 9) link_ALPHA1-3 : bond 0.01055 ( 15) link_ALPHA1-3 : angle 1.58151 ( 45) hydrogen bonds : bond 0.04346 ( 871) hydrogen bonds : angle 4.32491 ( 2316) SS BOND : bond 0.01006 ( 21) SS BOND : angle 2.17170 ( 42) covalent geometry : bond 0.00239 (23355) covalent geometry : angle 0.55840 (31740) *********************** 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 264 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: C 283 ARG cc_start: 0.6826 (mmt180) cc_final: 0.6432 (mmt90) REVERT: C 408 LYS cc_start: 0.6446 (tptp) cc_final: 0.5973 (tppt) REVERT: C 436 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6831 (tmt170) REVERT: C 464 ASP cc_start: 0.7354 (m-30) cc_final: 0.6923 (m-30) REVERT: C 511 LYS cc_start: 0.8433 (tttt) cc_final: 0.8125 (mptm) REVERT: D 621 GLU cc_start: 0.8009 (pt0) cc_final: 0.7761 (mp0) REVERT: D 637 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: D 752 CYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7963 (p) REVERT: D 797 LYS cc_start: 0.8490 (mttt) cc_final: 0.8242 (ttpm) REVERT: D 851 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: G 295 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7367 (mm-40) REVERT: G 408 LYS cc_start: 0.6808 (tptp) cc_final: 0.6279 (ttmm) REVERT: G 511 LYS cc_start: 0.8501 (tttt) cc_final: 0.8150 (mptm) REVERT: H 631 GLU cc_start: 0.7964 (tt0) cc_final: 0.7707 (tt0) REVERT: H 797 LYS cc_start: 0.8502 (mttt) cc_final: 0.8234 (mtpp) REVERT: I 97 LYS cc_start: 0.7807 (mttp) cc_final: 0.7454 (mtpt) REVERT: K 187 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8265 (mp0) REVERT: K 211 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: K 221 GLU cc_start: 0.8388 (tt0) cc_final: 0.7859 (tp30) REVERT: K 338 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7004 (mtm-85) REVERT: K 408 LYS cc_start: 0.7184 (ttmm) cc_final: 0.6559 (tptp) REVERT: K 511 LYS cc_start: 0.8600 (tttt) cc_final: 0.8243 (mptm) REVERT: L 583 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: L 604 ASN cc_start: 0.8829 (p0) cc_final: 0.8494 (p0) REVERT: L 631 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: L 761 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8343 (mt-10) outliers start: 57 outliers final: 31 residues processed: 243 average time/residue: 1.5936 time to fit residues: 437.5646 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 851 GLU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 295 GLN 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 H residue 841 LEU Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 631 GLU 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 152 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 143 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 863 GLN I 112 GLN K 321 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 = 0.3361 r_free = 0.3361 target = 0.129986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.089477 restraints weight = 26084.705| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.94 r_work: 0.2660 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2625 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= 0.124 Angle : 0.614 17.936 32106 Z= 0.288 Chirality : 0.045 0.414 3906 Planarity : 0.004 0.034 3792 Dihedral : 9.065 77.213 5351 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.84 % Allowed : 12.88 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2601 helix: 1.83 (0.18), residues: 876 sheet: 0.70 (0.29), residues: 348 loop : -0.55 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 95 HIS 0.004 0.001 HIS C 154 PHE 0.011 0.001 PHE L 800 TYR 0.021 0.001 TYR G 470 ARG 0.007 0.000 ARG K 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 33) link_NAG-ASN : angle 2.14856 ( 99) link_ALPHA1-6 : bond 0.00588 ( 15) link_ALPHA1-6 : angle 1.80509 ( 45) link_BETA1-2 : bond 0.00880 ( 3) link_BETA1-2 : angle 3.77596 ( 9) link_BETA1-4 : bond 0.00566 ( 39) link_BETA1-4 : angle 1.74206 ( 117) link_ALPHA1-2 : bond 0.01098 ( 3) link_ALPHA1-2 : angle 2.47152 ( 9) link_ALPHA1-3 : bond 0.01022 ( 15) link_ALPHA1-3 : angle 1.57163 ( 45) hydrogen bonds : bond 0.04696 ( 871) hydrogen bonds : angle 4.32459 ( 2316) SS BOND : bond 0.01086 ( 21) SS BOND : angle 2.26616 ( 42) covalent geometry : bond 0.00284 (23355) covalent geometry : angle 0.57918 (31740) ********************** 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 245 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: C 283 ARG cc_start: 0.6819 (mmt180) cc_final: 0.6426 (mmt90) REVERT: C 408 LYS cc_start: 0.6445 (tptp) cc_final: 0.5966 (tppt) REVERT: C 436 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6832 (tmt170) REVERT: C 464 ASP cc_start: 0.7356 (m-30) cc_final: 0.6925 (m-30) REVERT: C 511 LYS cc_start: 0.8434 (tttt) cc_final: 0.8127 (mptm) REVERT: D 621 GLU cc_start: 0.7993 (pt0) cc_final: 0.7735 (mp0) REVERT: D 637 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: D 752 CYS cc_start: 0.8530 (t) cc_final: 0.7961 (p) REVERT: D 797 LYS cc_start: 0.8511 (mttt) cc_final: 0.8263 (ttpm) REVERT: D 851 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: G 295 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7354 (mm-40) REVERT: G 408 LYS cc_start: 0.6799 (tptp) cc_final: 0.6273 (ttmm) REVERT: G 511 LYS cc_start: 0.8486 (tttt) cc_final: 0.8164 (mptm) REVERT: H 631 GLU cc_start: 0.8027 (tt0) cc_final: 0.7761 (mt-10) REVERT: H 797 LYS cc_start: 0.8509 (mttt) cc_final: 0.8229 (mtpp) REVERT: I 97 LYS cc_start: 0.7825 (mttp) cc_final: 0.7476 (mtpt) REVERT: K 187 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8231 (mp0) REVERT: K 211 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8242 (tp30) REVERT: K 221 GLU cc_start: 0.8403 (tt0) cc_final: 0.7871 (tp30) REVERT: K 338 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6963 (mtm-85) REVERT: K 408 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6556 (tptp) REVERT: K 511 LYS cc_start: 0.8608 (tttt) cc_final: 0.8245 (mptm) REVERT: L 583 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8250 (mmm) REVERT: L 604 ASN cc_start: 0.8858 (p0) cc_final: 0.8498 (p0) REVERT: L 631 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7495 (mt-10) outliers start: 44 outliers final: 32 residues processed: 230 average time/residue: 1.6560 time to fit residues: 428.1656 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 851 GLU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 295 GLN 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 H residue 841 LEU Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET 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 101 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 241 optimal weight: 0.0980 chunk 213 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 863 GLN I 112 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 = 0.3362 r_free = 0.3362 target = 0.130036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.089459 restraints weight = 25957.434| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.92 r_work: 0.2671 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2639 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= 0.123 Angle : 0.609 17.754 32106 Z= 0.286 Chirality : 0.045 0.415 3906 Planarity : 0.004 0.034 3792 Dihedral : 8.925 75.712 5351 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.92 % Allowed : 12.84 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2601 helix: 1.82 (0.18), residues: 876 sheet: 0.78 (0.29), residues: 336 loop : -0.55 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 400 HIS 0.004 0.001 HIS C 154 PHE 0.010 0.001 PHE H 800 TYR 0.023 0.001 TYR G 470 ARG 0.006 0.000 ARG K 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 33) link_NAG-ASN : angle 2.13057 ( 99) link_ALPHA1-6 : bond 0.00587 ( 15) link_ALPHA1-6 : angle 1.78622 ( 45) link_BETA1-2 : bond 0.00887 ( 3) link_BETA1-2 : angle 3.77418 ( 9) link_BETA1-4 : bond 0.00551 ( 39) link_BETA1-4 : angle 1.74075 ( 117) link_ALPHA1-2 : bond 0.01080 ( 3) link_ALPHA1-2 : angle 2.41482 ( 9) link_ALPHA1-3 : bond 0.01021 ( 15) link_ALPHA1-3 : angle 1.57134 ( 45) hydrogen bonds : bond 0.04671 ( 871) hydrogen bonds : angle 4.31442 ( 2316) SS BOND : bond 0.01079 ( 21) SS BOND : angle 2.24772 ( 42) covalent geometry : bond 0.00283 (23355) covalent geometry : angle 0.57428 (31740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18604.74 seconds wall clock time: 322 minutes 30.59 seconds (19350.59 seconds total)