Starting phenix.real_space_refine on Thu May 22 12:45:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozh_17309/05_2025/8ozh_17309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozh_17309/05_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_17309/05_2025/8ozh_17309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozh_17309/05_2025/8ozh_17309.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozh_17309/05_2025/8ozh_17309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozh_17309/05_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-5687/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: 16.18, per 1000 atoms: 0.71 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: 7.48 Conformation dependent library (CDL) restraints added in 2.8 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: 2.70 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: 8.07 Time building geometry restraints manager: 8.48 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'V' and (resid 1 through 4 or resid 6)) selection = (chain 'W' and (resid 1 through 4 or resid 6)) selection = (chain 'X' and (resid 1 through 4 or resid 6)) selection = (chain 'h' and (resid 1 through 4 or resid 6)) selection = (chain 'i' and (resid 1 through 4 or resid 6)) selection = (chain 'j' and (resid 1 through 4 or resid 6)) } ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 55.430 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.190 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.590 ------------------------------------------------------------------------------- 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 : 2.495 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: 1.5966 time to fit residues: 556.8150 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 : 2.686 ------------------------------------------------------------------------------- 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 = 0.127622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.086599 restraints weight = 25561.167| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.92 r_work: 0.2595 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 4.47376 ( 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 : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.7412 (tttt) cc_final: 0.7066 (tttp) REVERT: C 207 MET cc_start: 0.9000 (mmt) cc_final: 0.8374 (mmt) REVERT: C 283 ARG cc_start: 0.7144 (mmt180) cc_final: 0.6221 (mmt90) REVERT: C 439 ARG cc_start: 0.8398 (mtm180) cc_final: 0.7980 (mtt90) REVERT: C 511 LYS cc_start: 0.8646 (tttt) cc_final: 0.8275 (mptt) REVERT: D 621 GLU cc_start: 0.7948 (pt0) cc_final: 0.7696 (mp0) REVERT: D 631 GLU cc_start: 0.8195 (tt0) cc_final: 0.7950 (mt-10) REVERT: D 637 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: D 797 LYS cc_start: 0.8561 (mttt) cc_final: 0.8126 (mttp) REVERT: D 807 LYS cc_start: 0.9066 (mttt) cc_final: 0.8827 (mttm) REVERT: D 851 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: G 295 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7359 (mm-40) REVERT: G 338 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7228 (mtm-85) REVERT: G 439 ARG cc_start: 0.8596 (mtm180) cc_final: 0.8381 (mtt90) REVERT: G 464 ASP cc_start: 0.7508 (m-30) cc_final: 0.7130 (m-30) REVERT: G 511 LYS cc_start: 0.8566 (tttt) cc_final: 0.8164 (mptp) REVERT: H 637 GLN cc_start: 0.8351 (tp40) cc_final: 0.8145 (mm-40) REVERT: H 644 ASN cc_start: 0.9160 (t0) cc_final: 0.8933 (t0) REVERT: H 797 LYS cc_start: 0.8622 (mttt) cc_final: 0.8281 (mtpp) REVERT: H 862 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8917 (tp) REVERT: I 97 LYS cc_start: 0.8082 (mttp) cc_final: 0.7649 (mtpt) REVERT: K 187 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8269 (mp0) REVERT: K 194 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7942 (tt0) REVERT: K 295 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7246 (mm-40) REVERT: K 408 LYS cc_start: 0.7171 (ttmm) cc_final: 0.6463 (tptp) REVERT: K 511 LYS cc_start: 0.8605 (tttt) cc_final: 0.8208 (mptt) REVERT: L 631 GLU cc_start: 0.8071 (tt0) cc_final: 0.7803 (tt0) outliers start: 46 outliers final: 16 residues processed: 262 average time/residue: 1.5732 time to fit residues: 462.7255 Evaluate side-chains 226 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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: 0.9980 chunk 206 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 45 optimal weight: 0.0770 chunk 44 optimal weight: 0.0980 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: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 863 GLN J 131 GLN K 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.087446 restraints weight = 25663.931| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.89 r_work: 0.2638 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 23484 Z= 0.157 Angle : 0.678 12.437 32106 Z= 0.323 Chirality : 0.048 0.552 3906 Planarity : 0.004 0.033 3792 Dihedral : 11.453 82.898 5353 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.59 % Allowed : 10.00 % Favored : 87.41 % 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: 0.00 (0.16), residues: 2601 helix: 1.36 (0.18), residues: 876 sheet: 0.05 (0.27), residues: 351 loop : -0.91 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 95 HIS 0.005 0.001 HIS C 154 PHE 0.014 0.002 PHE K 317 TYR 0.020 0.002 TYR K 470 ARG 0.006 0.001 ARG G 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 33) link_NAG-ASN : angle 2.22348 ( 99) link_ALPHA1-6 : bond 0.00588 ( 15) link_ALPHA1-6 : angle 1.74957 ( 45) link_BETA1-2 : bond 0.00861 ( 3) link_BETA1-2 : angle 3.92812 ( 9) link_BETA1-4 : bond 0.00650 ( 39) link_BETA1-4 : angle 2.27344 ( 117) link_ALPHA1-2 : bond 0.01194 ( 3) link_ALPHA1-2 : angle 2.85450 ( 9) link_ALPHA1-3 : bond 0.00997 ( 15) link_ALPHA1-3 : angle 1.48480 ( 45) hydrogen bonds : bond 0.05925 ( 871) hydrogen bonds : angle 4.66805 ( 2316) SS BOND : bond 0.00819 ( 21) SS BOND : angle 2.49049 ( 42) covalent geometry : bond 0.00365 (23355) covalent geometry : angle 0.63868 (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 277 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8102 (ttm170) REVERT: B 131 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8617 (mt0) REVERT: C 136 LYS cc_start: 0.7429 (tttt) cc_final: 0.7212 (tttm) REVERT: C 207 MET cc_start: 0.8958 (mmt) cc_final: 0.8392 (mmt) REVERT: C 283 ARG cc_start: 0.7107 (mmt180) cc_final: 0.6105 (mmt90) REVERT: C 408 LYS cc_start: 0.6654 (tptp) cc_final: 0.6043 (tppt) REVERT: C 511 LYS cc_start: 0.8604 (tttt) cc_final: 0.8268 (mptt) REVERT: D 621 GLU cc_start: 0.7974 (pt0) cc_final: 0.7702 (mp0) REVERT: D 631 GLU cc_start: 0.8193 (tt0) cc_final: 0.7965 (mt-10) REVERT: D 637 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: D 797 LYS cc_start: 0.8582 (mttt) cc_final: 0.8068 (mtmt) REVERT: D 851 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: E 112 GLN cc_start: 0.8640 (tt0) cc_final: 0.8400 (tt0) REVERT: G 211 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8290 (tp30) REVERT: G 338 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7281 (mtm-85) REVERT: G 401 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: G 464 ASP cc_start: 0.7541 (m-30) cc_final: 0.7180 (m-30) REVERT: G 511 LYS cc_start: 0.8556 (tttt) cc_final: 0.8198 (mptp) REVERT: H 631 GLU cc_start: 0.8028 (tt0) cc_final: 0.7739 (tt0) REVERT: H 797 LYS cc_start: 0.8593 (mttt) cc_final: 0.8264 (mtpp) REVERT: I 97 LYS cc_start: 0.8020 (mttp) cc_final: 0.7562 (mtpt) REVERT: I 100 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: K 187 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8304 (mp0) REVERT: K 194 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7923 (tt0) REVERT: K 295 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7211 (mm-40) REVERT: K 408 LYS cc_start: 0.7130 (ttmm) cc_final: 0.6453 (tptp) REVERT: K 436 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6581 (tmt170) REVERT: K 511 LYS cc_start: 0.8639 (tttt) cc_final: 0.8223 (mptp) REVERT: L 797 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8140 (mmtp) outliers start: 62 outliers final: 26 residues processed: 257 average time/residue: 1.4820 time to fit residues: 430.0713 Evaluate side-chains 233 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 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 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 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 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 I residue 100 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 102 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 214 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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 = 0.3358 r_free = 0.3358 target = 0.129465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.089366 restraints weight = 26010.292| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.89 r_work: 0.2628 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 23484 Z= 0.126 Angle : 0.612 12.337 32106 Z= 0.290 Chirality : 0.046 0.433 3906 Planarity : 0.004 0.035 3792 Dihedral : 10.325 81.302 5353 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.80 % Allowed : 10.37 % Favored : 86.83 % 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: 0.31 (0.17), residues: 2601 helix: 1.66 (0.18), residues: 879 sheet: 0.23 (0.27), residues: 351 loop : -0.78 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 400 HIS 0.003 0.001 HIS C 154 PHE 0.010 0.001 PHE C 317 TYR 0.019 0.001 TYR G 470 ARG 0.008 0.000 ARG G 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 33) link_NAG-ASN : angle 2.07086 ( 99) link_ALPHA1-6 : bond 0.00617 ( 15) link_ALPHA1-6 : angle 1.82306 ( 45) link_BETA1-2 : bond 0.00869 ( 3) link_BETA1-2 : angle 3.83860 ( 9) link_BETA1-4 : bond 0.00589 ( 39) link_BETA1-4 : angle 2.05860 ( 117) link_ALPHA1-2 : bond 0.01149 ( 3) link_ALPHA1-2 : angle 2.64063 ( 9) link_ALPHA1-3 : bond 0.00997 ( 15) link_ALPHA1-3 : angle 1.54343 ( 45) hydrogen bonds : bond 0.04946 ( 871) hydrogen bonds : angle 4.43617 ( 2316) SS BOND : bond 0.00841 ( 21) SS BOND : angle 2.15757 ( 42) covalent geometry : bond 0.00283 (23355) covalent geometry : angle 0.57451 (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 286 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8037 (ttm170) REVERT: B 135 PRO cc_start: 0.8639 (Cg_exo) cc_final: 0.8435 (Cg_endo) REVERT: C 207 MET cc_start: 0.8958 (mmt) cc_final: 0.8396 (mmt) REVERT: C 252 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8346 (mm) REVERT: C 283 ARG cc_start: 0.6970 (mmt180) cc_final: 0.6563 (mmt90) REVERT: C 408 LYS cc_start: 0.6664 (tptp) cc_final: 0.6063 (tppt) REVERT: C 511 LYS cc_start: 0.8541 (tttt) cc_final: 0.8198 (mptm) REVERT: D 621 GLU cc_start: 0.8015 (pt0) cc_final: 0.7797 (mp0) REVERT: D 637 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: D 797 LYS cc_start: 0.8509 (mttt) cc_final: 0.8258 (ttpm) REVERT: D 851 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: D 862 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8882 (tp) REVERT: E 112 GLN cc_start: 0.8602 (tt0) cc_final: 0.8340 (tt0) REVERT: G 408 LYS cc_start: 0.6855 (tptp) cc_final: 0.6298 (ttmm) REVERT: G 464 ASP cc_start: 0.7530 (m-30) cc_final: 0.7181 (m-30) REVERT: G 511 LYS cc_start: 0.8533 (tttt) cc_final: 0.8255 (mptt) REVERT: H 631 GLU cc_start: 0.7965 (tt0) cc_final: 0.7665 (tt0) REVERT: H 797 LYS cc_start: 0.8581 (mttt) cc_final: 0.8290 (mtpp) REVERT: I 97 LYS cc_start: 0.7923 (mttp) cc_final: 0.7545 (mtpt) REVERT: K 187 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8278 (mp0) REVERT: K 194 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7882 (tt0) REVERT: K 295 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7204 (mm-40) REVERT: K 338 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: K 408 LYS cc_start: 0.7218 (ttmm) cc_final: 0.6540 (tptp) REVERT: K 436 ARG cc_start: 0.7247 (ttt180) cc_final: 0.6695 (tmt170) REVERT: K 511 LYS cc_start: 0.8520 (tttt) cc_final: 0.8172 (mptp) REVERT: L 631 GLU cc_start: 0.8104 (tt0) cc_final: 0.7888 (tt0) outliers start: 67 outliers final: 27 residues processed: 267 average time/residue: 1.4508 time to fit residues: 437.6748 Evaluate side-chains 234 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 332 THR 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 740 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 851 GLU Chi-restraints excluded: chain D residue 862 LEU Chi-restraints excluded: chain D residue 875 LYS Chi-restraints excluded: chain D residue 879 ILE 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 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 969 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 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: 4.9990 chunk 65 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 67 optimal weight: 0.0020 chunk 83 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 211 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 131 GLN H 863 GLN L 893 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.090045 restraints weight = 26002.114| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.89 r_work: 0.2664 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 23484 Z= 0.119 Angle : 0.601 13.643 32106 Z= 0.283 Chirality : 0.045 0.414 3906 Planarity : 0.004 0.033 3792 Dihedral : 9.841 80.376 5353 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.59 % Allowed : 11.13 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.17), residues: 2601 helix: 1.80 (0.18), residues: 879 sheet: 0.43 (0.30), residues: 306 loop : -0.71 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 400 HIS 0.004 0.001 HIS C 154 PHE 0.009 0.001 PHE A 73 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 0.00395 ( 33) link_NAG-ASN : angle 1.98902 ( 99) link_ALPHA1-6 : bond 0.00603 ( 15) link_ALPHA1-6 : angle 1.84620 ( 45) link_BETA1-2 : bond 0.00884 ( 3) link_BETA1-2 : angle 3.79752 ( 9) link_BETA1-4 : bond 0.00584 ( 39) link_BETA1-4 : angle 1.88675 ( 117) link_ALPHA1-2 : bond 0.01148 ( 3) link_ALPHA1-2 : angle 2.63536 ( 9) link_ALPHA1-3 : bond 0.01042 ( 15) link_ALPHA1-3 : angle 1.55658 ( 45) hydrogen bonds : bond 0.04731 ( 871) hydrogen bonds : angle 4.35829 ( 2316) SS BOND : bond 0.00914 ( 21) SS BOND : angle 2.01146 ( 42) covalent geometry : bond 0.00266 (23355) covalent geometry : angle 0.56568 (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 276 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8568 (ttp80) cc_final: 0.7957 (ttm170) REVERT: C 207 MET cc_start: 0.8954 (mmt) cc_final: 0.8414 (mmt) REVERT: C 252 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (mm) REVERT: C 283 ARG cc_start: 0.6923 (mmt180) cc_final: 0.6518 (mmt90) REVERT: C 408 LYS cc_start: 0.6640 (tptp) cc_final: 0.6036 (tppt) REVERT: C 511 LYS cc_start: 0.8526 (tttt) cc_final: 0.8179 (mptm) REVERT: D 621 GLU cc_start: 0.7965 (pt0) cc_final: 0.7757 (mp0) REVERT: D 637 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: D 797 LYS cc_start: 0.8531 (mttt) cc_final: 0.8286 (ttpm) REVERT: D 851 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: D 862 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8924 (tp) REVERT: G 401 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: G 408 LYS cc_start: 0.6815 (tptp) cc_final: 0.6196 (ttmm) REVERT: G 464 ASP cc_start: 0.7552 (m-30) cc_final: 0.7208 (m-30) REVERT: G 511 LYS cc_start: 0.8527 (tttt) cc_final: 0.8225 (mptm) REVERT: H 797 LYS cc_start: 0.8524 (mttt) cc_final: 0.8242 (mtpp) REVERT: I 97 LYS cc_start: 0.7914 (mttp) cc_final: 0.7539 (mtpt) REVERT: I 100 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: K 187 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8259 (mp0) REVERT: K 221 GLU cc_start: 0.8364 (tt0) cc_final: 0.7840 (tp30) REVERT: K 295 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7213 (mm-40) REVERT: K 338 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6984 (mtm-85) REVERT: K 408 LYS cc_start: 0.7181 (ttmm) cc_final: 0.6503 (tptp) REVERT: K 436 ARG cc_start: 0.7250 (ttt180) cc_final: 0.7037 (ttt180) REVERT: K 511 LYS cc_start: 0.8523 (tttt) cc_final: 0.8201 (mptt) REVERT: L 631 GLU cc_start: 0.8025 (tt0) cc_final: 0.7776 (tt0) REVERT: L 761 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8254 (mt-10) outliers start: 62 outliers final: 33 residues processed: 254 average time/residue: 1.4438 time to fit residues: 414.9558 Evaluate side-chains 243 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 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 862 LEU Chi-restraints excluded: chain D residue 875 LYS Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain G residue 202 SER 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 740 THR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 973 LEU Chi-restraints excluded: chain I residue 100 GLN 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 626 ASP Chi-restraints excluded: chain L residue 660 MET Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 841 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 218 optimal weight: 0.0370 chunk 203 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN D 722 ASN F 131 GLN H 722 ASN H 863 GLN L 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.091289 restraints weight = 25875.175| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.93 r_work: 0.2704 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 23484 Z= 0.107 Angle : 0.577 17.009 32106 Z= 0.271 Chirality : 0.044 0.372 3906 Planarity : 0.004 0.033 3792 Dihedral : 9.284 78.756 5353 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.34 % Allowed : 11.79 % Favored : 85.86 % 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: 0.64 (0.17), residues: 2601 helix: 2.03 (0.18), residues: 864 sheet: 0.61 (0.30), residues: 306 loop : -0.64 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 721 HIS 0.003 0.001 HIS C 154 PHE 0.009 0.001 PHE E 73 TYR 0.017 0.001 TYR G 470 ARG 0.008 0.000 ARG K 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 33) link_NAG-ASN : angle 1.88016 ( 99) link_ALPHA1-6 : bond 0.00641 ( 15) link_ALPHA1-6 : angle 1.81287 ( 45) link_BETA1-2 : bond 0.00888 ( 3) link_BETA1-2 : angle 3.81896 ( 9) link_BETA1-4 : bond 0.00569 ( 39) link_BETA1-4 : angle 1.75972 ( 117) link_ALPHA1-2 : bond 0.01122 ( 3) link_ALPHA1-2 : angle 2.52816 ( 9) link_ALPHA1-3 : bond 0.01062 ( 15) link_ALPHA1-3 : angle 1.59958 ( 45) hydrogen bonds : bond 0.04158 ( 871) hydrogen bonds : angle 4.28262 ( 2316) SS BOND : bond 0.00832 ( 21) SS BOND : angle 2.08669 ( 42) covalent geometry : bond 0.00230 (23355) covalent geometry : angle 0.54272 (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 271 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 MET cc_start: 0.8964 (mmt) cc_final: 0.8406 (mmt) REVERT: C 283 ARG cc_start: 0.6944 (mmt180) cc_final: 0.6150 (mmt90) REVERT: C 408 LYS cc_start: 0.6622 (tptp) cc_final: 0.6041 (tppt) REVERT: C 436 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6827 (tmt170) REVERT: C 511 LYS cc_start: 0.8479 (tttt) cc_final: 0.8145 (mptm) REVERT: D 752 CYS cc_start: 0.8574 (t) cc_final: 0.8024 (p) REVERT: D 797 LYS cc_start: 0.8495 (mttt) cc_final: 0.8225 (ttpm) REVERT: D 851 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: G 295 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: G 408 LYS cc_start: 0.6801 (tptp) cc_final: 0.6262 (ttmm) REVERT: G 464 ASP cc_start: 0.7621 (m-30) cc_final: 0.7396 (m-30) REVERT: G 511 LYS cc_start: 0.8505 (tttt) cc_final: 0.8178 (mptm) REVERT: H 631 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: H 797 LYS cc_start: 0.8535 (mttt) cc_final: 0.8265 (mtpp) REVERT: I 97 LYS cc_start: 0.7808 (mttp) cc_final: 0.7424 (mtpt) REVERT: K 187 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8273 (mp0) REVERT: K 221 GLU cc_start: 0.8367 (tt0) cc_final: 0.7843 (tp30) REVERT: K 338 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7020 (mtm-85) REVERT: K 408 LYS cc_start: 0.7165 (ttmm) cc_final: 0.6474 (tptp) REVERT: K 436 ARG cc_start: 0.7258 (ttt180) cc_final: 0.7058 (ttt180) REVERT: K 511 LYS cc_start: 0.8613 (tttt) cc_final: 0.8255 (mptm) REVERT: L 583 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8236 (mmm) REVERT: L 604 ASN cc_start: 0.8824 (p0) cc_final: 0.8504 (p0) REVERT: L 631 GLU cc_start: 0.7894 (tt0) cc_final: 0.7626 (tt0) REVERT: L 761 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8343 (mt-10) outliers start: 56 outliers final: 25 residues processed: 249 average time/residue: 1.4769 time to fit residues: 414.7639 Evaluate side-chains 238 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 281 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 851 GLU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 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 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 841 LEU 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 740 THR 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: 3.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 148 optimal weight: 0.0270 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 K 321 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 = 0.130006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.089925 restraints weight = 26049.537| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.89 r_work: 0.2636 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 23484 Z= 0.128 Angle : 0.614 17.994 32106 Z= 0.289 Chirality : 0.045 0.401 3906 Planarity : 0.004 0.034 3792 Dihedral : 9.291 78.270 5353 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 12.34 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.17), residues: 2601 helix: 1.84 (0.18), residues: 882 sheet: 0.69 (0.29), residues: 336 loop : -0.65 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 400 HIS 0.005 0.001 HIS C 154 PHE 0.012 0.001 PHE L 800 TYR 0.017 0.001 TYR G 470 ARG 0.006 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 33) link_NAG-ASN : angle 1.93566 ( 99) link_ALPHA1-6 : bond 0.00586 ( 15) link_ALPHA1-6 : angle 1.83405 ( 45) link_BETA1-2 : bond 0.00876 ( 3) link_BETA1-2 : angle 3.77506 ( 9) link_BETA1-4 : bond 0.00575 ( 39) link_BETA1-4 : angle 1.77620 ( 117) link_ALPHA1-2 : bond 0.01119 ( 3) link_ALPHA1-2 : angle 2.50987 ( 9) link_ALPHA1-3 : bond 0.01016 ( 15) link_ALPHA1-3 : angle 1.57286 ( 45) hydrogen bonds : bond 0.04760 ( 871) hydrogen bonds : angle 4.30296 ( 2316) SS BOND : bond 0.01012 ( 21) SS BOND : angle 2.26303 ( 42) covalent geometry : bond 0.00298 (23355) covalent geometry : angle 0.58031 (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 253 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 MET cc_start: 0.8943 (mmt) cc_final: 0.8419 (mmt) REVERT: C 283 ARG cc_start: 0.6911 (mmt180) cc_final: 0.6088 (mmt90) REVERT: C 408 LYS cc_start: 0.6628 (tptp) cc_final: 0.6027 (tppt) REVERT: C 436 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6832 (tmt170) REVERT: C 511 LYS cc_start: 0.8461 (tttt) cc_final: 0.8131 (mptm) REVERT: D 752 CYS cc_start: 0.8538 (t) cc_final: 0.7975 (p) REVERT: D 797 LYS cc_start: 0.8493 (mttt) cc_final: 0.8252 (ttpm) REVERT: D 851 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: G 295 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7354 (mm-40) REVERT: G 408 LYS cc_start: 0.6823 (tptp) cc_final: 0.6265 (ttmm) REVERT: G 511 LYS cc_start: 0.8509 (tttt) cc_final: 0.8158 (mptm) REVERT: H 631 GLU cc_start: 0.8037 (tt0) cc_final: 0.7782 (tt0) REVERT: H 797 LYS cc_start: 0.8562 (mttt) cc_final: 0.8290 (mtpp) REVERT: K 187 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8230 (mp0) REVERT: K 221 GLU cc_start: 0.8371 (tt0) cc_final: 0.7862 (tp30) REVERT: K 338 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6984 (mtm-85) REVERT: K 408 LYS cc_start: 0.7176 (ttmm) cc_final: 0.6502 (tptp) REVERT: K 511 LYS cc_start: 0.8594 (tttt) cc_final: 0.8242 (mptm) REVERT: L 583 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8207 (mmm) REVERT: L 604 ASN cc_start: 0.8862 (p0) cc_final: 0.8508 (p0) REVERT: L 631 GLU cc_start: 0.8022 (tt0) cc_final: 0.7716 (mt-10) outliers start: 50 outliers final: 31 residues processed: 237 average time/residue: 1.4604 time to fit residues: 391.6666 Evaluate side-chains 235 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 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 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 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 969 LEU 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 440 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 165 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 21 optimal weight: 0.0010 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.090674 restraints weight = 25851.525| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.89 r_work: 0.2662 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 23484 Z= 0.120 Angle : 0.603 17.799 32106 Z= 0.283 Chirality : 0.045 0.409 3906 Planarity : 0.004 0.033 3792 Dihedral : 9.161 77.529 5351 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.17 % Allowed : 12.34 % Favored : 85.49 % 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 (0.17), residues: 2601 helix: 1.86 (0.18), residues: 882 sheet: 0.72 (0.29), residues: 336 loop : -0.62 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 400 HIS 0.004 0.001 HIS C 154 PHE 0.009 0.001 PHE L 800 TYR 0.018 0.001 TYR G 470 ARG 0.005 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 33) link_NAG-ASN : angle 1.91175 ( 99) link_ALPHA1-6 : bond 0.00598 ( 15) link_ALPHA1-6 : angle 1.81488 ( 45) link_BETA1-2 : bond 0.00883 ( 3) link_BETA1-2 : angle 3.78025 ( 9) link_BETA1-4 : bond 0.00569 ( 39) link_BETA1-4 : angle 1.75812 ( 117) link_ALPHA1-2 : bond 0.01112 ( 3) link_ALPHA1-2 : angle 2.46284 ( 9) link_ALPHA1-3 : bond 0.01020 ( 15) link_ALPHA1-3 : angle 1.57513 ( 45) hydrogen bonds : bond 0.04582 ( 871) hydrogen bonds : angle 4.29887 ( 2316) SS BOND : bond 0.01023 ( 21) SS BOND : angle 2.28197 ( 42) covalent geometry : bond 0.00275 (23355) covalent geometry : angle 0.56980 (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 253 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6674 (ttpp) REVERT: C 207 MET cc_start: 0.8942 (mmt) cc_final: 0.8417 (mmt) REVERT: C 211 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: C 283 ARG cc_start: 0.6941 (mmt180) cc_final: 0.6138 (mmt90) REVERT: C 408 LYS cc_start: 0.6622 (tptp) cc_final: 0.6024 (tppt) REVERT: C 436 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6839 (tmt170) REVERT: C 511 LYS cc_start: 0.8456 (tttt) cc_final: 0.8137 (mptm) REVERT: D 752 CYS cc_start: 0.8599 (t) cc_final: 0.8059 (p) REVERT: D 797 LYS cc_start: 0.8492 (mttt) cc_final: 0.8250 (ttpm) REVERT: D 851 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: G 295 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7306 (mm-40) REVERT: G 408 LYS cc_start: 0.6824 (tptp) cc_final: 0.6257 (ttmm) REVERT: G 511 LYS cc_start: 0.8496 (tttt) cc_final: 0.8148 (mptm) REVERT: H 631 GLU cc_start: 0.8004 (tt0) cc_final: 0.7740 (tt0) REVERT: H 797 LYS cc_start: 0.8555 (mttt) cc_final: 0.8283 (mtpp) REVERT: K 187 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8220 (mp0) REVERT: K 221 GLU cc_start: 0.8376 (tt0) cc_final: 0.7862 (tp30) REVERT: K 338 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6978 (mtm-85) REVERT: K 408 LYS cc_start: 0.7167 (ttmm) cc_final: 0.6489 (tptp) REVERT: K 511 LYS cc_start: 0.8588 (tttt) cc_final: 0.8235 (mptm) REVERT: L 583 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: L 604 ASN cc_start: 0.8857 (p0) cc_final: 0.8518 (p0) REVERT: L 631 GLU cc_start: 0.7979 (tt0) cc_final: 0.7682 (mt-10) REVERT: L 761 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8346 (mt-10) outliers start: 52 outliers final: 35 residues processed: 236 average time/residue: 1.5303 time to fit residues: 407.4499 Evaluate side-chains 241 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 152 GLU 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 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 202 SER 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 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 H residue 969 LEU 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 440 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 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: 3.9990 chunk 33 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 0.0070 chunk 212 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 I 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.089647 restraints weight = 26007.021| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.89 r_work: 0.2634 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 23484 Z= 0.128 Angle : 0.617 17.783 32106 Z= 0.289 Chirality : 0.045 0.427 3906 Planarity : 0.004 0.033 3792 Dihedral : 9.122 76.489 5351 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.30 % Allowed : 12.30 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.17), residues: 2601 helix: 1.80 (0.18), residues: 882 sheet: 0.73 (0.29), residues: 336 loop : -0.60 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 400 HIS 0.004 0.001 HIS C 154 PHE 0.011 0.001 PHE L 800 TYR 0.018 0.001 TYR G 470 ARG 0.005 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 33) link_NAG-ASN : angle 2.08571 ( 99) link_ALPHA1-6 : bond 0.00578 ( 15) link_ALPHA1-6 : angle 1.81295 ( 45) link_BETA1-2 : bond 0.00882 ( 3) link_BETA1-2 : angle 3.75995 ( 9) link_BETA1-4 : bond 0.00564 ( 39) link_BETA1-4 : angle 1.77383 ( 117) link_ALPHA1-2 : bond 0.01098 ( 3) link_ALPHA1-2 : angle 2.43818 ( 9) link_ALPHA1-3 : bond 0.01006 ( 15) link_ALPHA1-3 : angle 1.56738 ( 45) hydrogen bonds : bond 0.04786 ( 871) hydrogen bonds : angle 4.31034 ( 2316) SS BOND : bond 0.01045 ( 21) SS BOND : angle 2.33461 ( 42) covalent geometry : bond 0.00298 (23355) covalent geometry : angle 0.58220 (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 257 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.8376 (ttm170) cc_final: 0.7918 (ttm170) REVERT: C 136 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.6675 (ttpp) REVERT: C 207 MET cc_start: 0.8945 (mmt) cc_final: 0.8475 (mmt) REVERT: C 211 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: C 283 ARG cc_start: 0.6869 (mmt180) cc_final: 0.6081 (mmt90) REVERT: C 408 LYS cc_start: 0.6542 (tptp) cc_final: 0.6046 (tppt) REVERT: C 436 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6834 (tmt170) REVERT: C 511 LYS cc_start: 0.8392 (tttt) cc_final: 0.8097 (mptm) REVERT: D 637 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7762 (mm-40) REVERT: D 752 CYS cc_start: 0.8506 (t) cc_final: 0.7938 (p) REVERT: D 797 LYS cc_start: 0.8449 (mttt) cc_final: 0.8218 (ttpm) REVERT: D 851 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: G 295 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7330 (mm-40) REVERT: G 408 LYS cc_start: 0.6786 (tptp) cc_final: 0.6275 (ttmm) REVERT: G 511 LYS cc_start: 0.8492 (tttt) cc_final: 0.8145 (mptm) REVERT: H 631 GLU cc_start: 0.8044 (tt0) cc_final: 0.7817 (mt-10) REVERT: H 797 LYS cc_start: 0.8488 (mttt) cc_final: 0.8234 (mtpp) REVERT: K 187 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8223 (mp0) REVERT: K 211 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: K 221 GLU cc_start: 0.8383 (tt0) cc_final: 0.7866 (tp30) REVERT: K 338 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6980 (mtm-85) REVERT: K 408 LYS cc_start: 0.7186 (ttmm) cc_final: 0.6552 (tptp) REVERT: K 511 LYS cc_start: 0.8577 (tttt) cc_final: 0.8234 (mptm) REVERT: L 583 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8216 (mmm) REVERT: L 631 GLU cc_start: 0.8012 (tt0) cc_final: 0.7714 (mt-10) outliers start: 55 outliers final: 32 residues processed: 238 average time/residue: 1.5221 time to fit residues: 410.0151 Evaluate side-chains 237 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain C residue 136 LYS 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 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 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 332 THR Chi-restraints excluded: chain K residue 338 ARG Chi-restraints excluded: chain K residue 391 ASN Chi-restraints excluded: chain K residue 440 SER Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain L residue 583 MET Chi-restraints excluded: chain L residue 626 ASP Chi-restraints excluded: chain L residue 660 MET Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 841 LEU Chi-restraints excluded: chain L residue 969 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 152 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 234 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 91 optimal weight: 0.0670 chunk 8 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 I 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.131576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.091147 restraints weight = 26022.930| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.95 r_work: 0.2687 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2673 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= 0.108 Angle : 0.591 17.831 32106 Z= 0.276 Chirality : 0.045 0.413 3906 Planarity : 0.004 0.033 3792 Dihedral : 8.839 75.047 5351 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.55 % Allowed : 13.13 % Favored : 85.32 % 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: 0.76 (0.17), residues: 2601 helix: 1.96 (0.18), residues: 876 sheet: 0.80 (0.29), residues: 336 loop : -0.52 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 721 HIS 0.004 0.001 HIS B 132 PHE 0.009 0.001 PHE E 73 TYR 0.022 0.001 TYR K 470 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 33) link_NAG-ASN : angle 2.11187 ( 99) link_ALPHA1-6 : bond 0.00630 ( 15) link_ALPHA1-6 : angle 1.77407 ( 45) link_BETA1-2 : bond 0.00893 ( 3) link_BETA1-2 : angle 3.80657 ( 9) link_BETA1-4 : bond 0.00567 ( 39) link_BETA1-4 : angle 1.70028 ( 117) link_ALPHA1-2 : bond 0.01105 ( 3) link_ALPHA1-2 : angle 2.38649 ( 9) link_ALPHA1-3 : bond 0.01048 ( 15) link_ALPHA1-3 : angle 1.58801 ( 45) hydrogen bonds : bond 0.04224 ( 871) hydrogen bonds : angle 4.28282 ( 2316) SS BOND : bond 0.01050 ( 21) SS BOND : angle 2.13567 ( 42) covalent geometry : bond 0.00235 (23355) covalent geometry : angle 0.55587 (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 237 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 MET cc_start: 0.8927 (mmt) cc_final: 0.8397 (mmt) REVERT: C 211 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: C 221 GLU cc_start: 0.8371 (tt0) cc_final: 0.7819 (tp30) REVERT: C 283 ARG cc_start: 0.6868 (mmt180) cc_final: 0.6087 (mmt90) REVERT: C 408 LYS cc_start: 0.6530 (tptp) cc_final: 0.6032 (tppt) REVERT: C 436 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6831 (tmt170) REVERT: C 511 LYS cc_start: 0.8373 (tttt) cc_final: 0.8080 (mptm) REVERT: D 752 CYS cc_start: 0.8577 (t) cc_final: 0.8055 (p) REVERT: D 797 LYS cc_start: 0.8475 (mttt) cc_final: 0.8222 (ttpm) REVERT: D 851 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: G 295 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7302 (mm-40) REVERT: G 341 LEU cc_start: 0.8016 (mm) cc_final: 0.7727 (mp) REVERT: G 408 LYS cc_start: 0.6784 (tptp) cc_final: 0.6244 (ttmm) REVERT: G 511 LYS cc_start: 0.8494 (tttt) cc_final: 0.8149 (mptm) REVERT: H 631 GLU cc_start: 0.7966 (tt0) cc_final: 0.7710 (tt0) REVERT: H 797 LYS cc_start: 0.8548 (mttt) cc_final: 0.8282 (mtpp) REVERT: K 187 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8240 (mp0) REVERT: K 221 GLU cc_start: 0.8363 (tt0) cc_final: 0.7847 (tp30) REVERT: K 338 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6962 (mtm-85) REVERT: K 408 LYS cc_start: 0.7200 (ttmm) cc_final: 0.6544 (tptp) REVERT: K 511 LYS cc_start: 0.8574 (tttt) cc_final: 0.8219 (mptm) REVERT: L 583 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8225 (mmm) REVERT: L 604 ASN cc_start: 0.8839 (p0) cc_final: 0.8512 (p0) REVERT: L 761 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8344 (mt-10) outliers start: 37 outliers final: 30 residues processed: 223 average time/residue: 1.5779 time to fit residues: 395.8332 Evaluate side-chains 231 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 D residue 598 SER Chi-restraints excluded: chain D residue 626 ASP 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 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 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 660 MET Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL 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: 0.9980 chunk 27 optimal weight: 3.9990 chunk 241 optimal weight: 0.0670 chunk 213 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.0770 chunk 198 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.090949 restraints weight = 25958.554| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.89 r_work: 0.2674 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 23484 Z= 0.114 Angle : 0.595 17.355 32106 Z= 0.278 Chirality : 0.045 0.415 3906 Planarity : 0.004 0.033 3792 Dihedral : 8.667 73.553 5349 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.97 % Allowed : 12.88 % Favored : 85.15 % 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: 0.74 (0.17), residues: 2601 helix: 1.89 (0.18), residues: 882 sheet: 0.73 (0.29), residues: 348 loop : -0.50 (0.17), residues: 1371 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 0.009 0.001 PHE L 800 TYR 0.022 0.001 TYR K 470 ARG 0.005 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 33) link_NAG-ASN : angle 2.09633 ( 99) link_ALPHA1-6 : bond 0.00615 ( 15) link_ALPHA1-6 : angle 1.77693 ( 45) link_BETA1-2 : bond 0.00880 ( 3) link_BETA1-2 : angle 3.80946 ( 9) link_BETA1-4 : bond 0.00555 ( 39) link_BETA1-4 : angle 1.67706 ( 117) link_ALPHA1-2 : bond 0.01094 ( 3) link_ALPHA1-2 : angle 2.37612 ( 9) link_ALPHA1-3 : bond 0.01023 ( 15) link_ALPHA1-3 : angle 1.58760 ( 45) hydrogen bonds : bond 0.04341 ( 871) hydrogen bonds : angle 4.25735 ( 2316) SS BOND : bond 0.01040 ( 21) SS BOND : angle 2.18556 ( 42) covalent geometry : bond 0.00256 (23355) covalent geometry : angle 0.56070 (31740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16309.45 seconds wall clock time: 282 minutes 2.90 seconds (16922.90 seconds total)