Starting phenix.real_space_refine on Mon Aug 25 11:55:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ogl_70469/08_2025/9ogl_70469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ogl_70469/08_2025/9ogl_70469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ogl_70469/08_2025/9ogl_70469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ogl_70469/08_2025/9ogl_70469.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ogl_70469/08_2025/9ogl_70469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ogl_70469/08_2025/9ogl_70469.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 16986 2.51 5 N 4556 2.21 5 O 5471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27177 Number of models: 1 Model: "" Number of chains: 38 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "F" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "K" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "M" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 751 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "N" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "O" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 758 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "P" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "Q" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 751 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4464 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 21, 'TRANS': 544} Chain breaks: 6 Chain: "B" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4393 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 21, 'TRANS': 535} Chain breaks: 5 Chain: "C" Number of atoms: 4374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4374 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 21, 'TRANS': 532} Chain breaks: 6 Chain: "R" 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: "S" 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: "T" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "U" 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: "V" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "c" 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: "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: "e" 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: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "h" 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: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.59, per 1000 atoms: 0.24 Number of scatterers: 27177 At special positions: 0 Unit cell: (153.017, 161.288, 151.983, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 5471 8.00 N 4556 7.00 C 16986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 32 " - pdb=" SG CYS N 98 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 32 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.05 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN U 5 " - " MAN U 6 " " MAN Z 4 " - " MAN Z 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN c 5 " - " MAN c 6 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN g 8 " - " MAN g 9 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 10 " " MAN U 4 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 7 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " MAN c 4 " - " MAN c 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " " MAN g 7 " - " MAN g 8 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 8 " " BMA U 3 " - " MAN U 4 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 7 " " MAN g 7 " - " MAN g 10 " BETA1-4 " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " BETA1-6 " NAG V 1 " - " FUC V 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 234 " " NAG A 703 " - " ASN A 301 " " NAG A 704 " - " ASN A 133 " " NAG A 705 " - " ASN A 156 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 339 " " NAG A 708 " - " ASN A 386 " " NAG A 709 " - " ASN A 448 " " NAG A 710 " - " ASN A 295 " " NAG A 711 " - " ASN A 241 " " NAG A 712 " - " ASN A 289 " " NAG A 713 " - " ASN A 611 " " NAG A 714 " - " ASN A 625 " " NAG A 715 " - " ASN A 637 " " NAG B 701 " - " ASN B 133 " " NAG B 702 " - " ASN B 160 " " NAG B 703 " - " ASN B 234 " " NAG B 704 " - " ASN B 295 " " NAG B 705 " - " ASN B 301 " " NAG B 706 " - " ASN B 339 " " NAG B 707 " - " ASN B 448 " " NAG B 708 " - " ASN B 88 " " NAG B 709 " - " ASN B 241 " " NAG B 710 " - " ASN B 289 " " NAG B 711 " - " ASN B 611 " " NAG C 701 " - " ASN C 133 " " NAG C 702 " - " ASN C 160 " " NAG C 703 " - " ASN C 197 " " NAG C 704 " - " ASN C 234 " " NAG C 705 " - " ASN C 295 " " NAG C 706 " - " ASN C 301 " " NAG C 707 " - " ASN C 448 " " NAG C 708 " - " ASN C 88 " " NAG C 709 " - " ASN C 241 " " NAG C 710 " - " ASN C 289 " " NAG C 711 " - " ASN C 339 " " NAG C 712 " - " ASN C 611 " " NAG C 713 " - " ASN C 637 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN B 156 " " NAG X 1 " - " ASN B 197 " " NAG Y 1 " - " ASN B 262 " " NAG Z 1 " - " ASN B 276 " " NAG a 1 " - " ASN B 332 " " NAG b 1 " - " ASN B 386 " " NAG c 1 " - " ASN B 392 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 262 " " NAG f 1 " - " ASN C 276 " " NAG g 1 " - " ASN C 332 " " NAG h 1 " - " ASN C 386 " " NAG i 1 " - " ASN C 392 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 51 sheets defined 17.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 100B through 100F Processing helix chain 'E' and resid 26 through 30 removed outlier: 3.570A pdb=" N SER E 30 " --> pdb=" O PRO E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 100B through 100F Processing helix chain 'G' and resid 26 through 30 removed outlier: 3.819A pdb=" N SER G 30 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'I' and resid 29 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 100B through 100F Processing helix chain 'J' and resid 26 through 29 removed outlier: 3.758A pdb=" N THR J 29 " --> pdb=" O ALA J 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 26 through 29' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.540A pdb=" N THR N 87 " --> pdb=" O VAL N 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.567A pdb=" N THR P 87 " --> pdb=" O VAL P 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.503A pdb=" N THR H 87 " --> pdb=" O PHE H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100E through 100I removed outlier: 3.936A pdb=" N PHE H 100I" --> pdb=" O SER H 100F" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.825A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.533A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.578A pdb=" N MET A 535 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 649 through 659 Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.568A pdb=" N ASN B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.135A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.242A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.792A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.708A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.941A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.687A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.576A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 536 removed outlier: 3.564A pdb=" N MET C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 536 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 571 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 653 Processing helix chain 'C' and resid 653 through 661 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 5.252A pdb=" N GLU D 16 " --> pdb=" O SER D 82B" (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 82B" --> pdb=" O GLU D 16 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.962A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP D 50 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP D 35 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS D 92 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL D 102 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG D 94 " --> pdb=" O MET D 100M" (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET D 100M" --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA D 96 " --> pdb=" O TYR D 100K" (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 9 through 13 current: chain 'E' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 48 current: chain 'E' and resid 96 through 98 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AA5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'F' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 11 through 12 current: chain 'F' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 51 current: chain 'F' and resid 100H through 103 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 9 through 13 current: chain 'G' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 96 through 98 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'I' and resid 34 through 39 removed outlier: 5.906A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100H through 103 Processing sheet with id=AB2, first strand: chain 'J' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 9 through 13 current: chain 'J' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 45 through 48 current: chain 'J' and resid 96 through 98 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 11 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 11 current: chain 'M' and resid 45 through 49 removed outlier: 3.565A pdb=" N TYR M 49 " --> pdb=" O THR M 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 53 through 54 current: chain 'M' and resid 97 through 98 Processing sheet with id=AB8, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 11 current: chain 'N' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 56 through 59 current: chain 'N' and resid 102 through 103 Processing sheet with id=AC1, first strand: chain 'O' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.745A pdb=" N LEU O 11 " --> pdb=" O GLN O 105 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP O 35 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'P' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 11 current: chain 'P' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 56 through 59 current: chain 'P' and resid 100 through 103 Processing sheet with id=AC5, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'Q' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 12 current: chain 'Q' and resid 44 through 49 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 53 through 54 current: chain 'Q' and resid 97 through 98 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 11 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 59 current: chain 'H' and resid 100K through 103 Processing sheet with id=AC9, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AD2, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.022A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.518A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.975A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AD6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AD7, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AD8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.902A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AD9, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.684A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 45 through 46 removed outlier: 4.616A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AE3, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AE4, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AE5, first strand: chain 'B' and resid 200 through 203 removed outlier: 5.930A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 298 removed outlier: 6.343A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 329 through 334 current: chain 'B' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 381 through 385 current: chain 'B' and resid 465 through 470 Processing sheet with id=AE7, first strand: chain 'B' and resid 303 through 312 removed outlier: 6.888A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.946A pdb=" N VAL C 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL C 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR C 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR C 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N CYS C 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.632A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AF2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AF3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AF4, first strand: chain 'C' and resid 200 through 203 Processing sheet with id=AF5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.464A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 329 through 334 current: chain 'C' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 382 through 386 current: chain 'C' and resid 466 through 470 Processing sheet with id=AF6, first strand: chain 'C' and resid 302 through 312 removed outlier: 6.715A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1848 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: 5.59 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8555 1.35 - 1.49: 7840 1.49 - 1.63: 11132 1.63 - 1.76: 1 1.76 - 1.90: 226 Bond restraints: 27754 Sorted by residual: bond pdb=" N ILE C 277 " pdb=" CA ILE C 277 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" CA SER E 55 " pdb=" CB SER E 55 " ideal model delta sigma weight residual 1.533 1.471 0.062 1.82e-02 3.02e+03 1.16e+01 bond pdb=" N ARG E 54 " pdb=" CA ARG E 54 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.00e+00 bond pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " ideal model delta sigma weight residual 1.808 1.897 -0.089 3.30e-02 9.18e+02 7.33e+00 bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.02e+00 ... (remaining 27749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 37144 3.34 - 6.68: 513 6.68 - 10.02: 21 10.02 - 13.36: 4 13.36 - 16.70: 2 Bond angle restraints: 37684 Sorted by residual: angle pdb=" N SER E 56 " pdb=" CA SER E 56 " pdb=" C SER E 56 " ideal model delta sigma weight residual 112.72 96.02 16.70 1.28e+00 6.10e-01 1.70e+02 angle pdb=" N ASP C 659 " pdb=" CA ASP C 659 " pdb=" C ASP C 659 " ideal model delta sigma weight residual 113.88 103.21 10.67 1.23e+00 6.61e-01 7.52e+01 angle pdb=" N ASN C 276 " pdb=" CA ASN C 276 " pdb=" C ASN C 276 " ideal model delta sigma weight residual 111.02 102.06 8.96 1.25e+00 6.40e-01 5.14e+01 angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 130.15 -15.75 2.30e+00 1.89e-01 4.69e+01 angle pdb=" C SER E 55 " pdb=" N SER E 56 " pdb=" CA SER E 56 " ideal model delta sigma weight residual 122.46 111.15 11.31 1.80e+00 3.09e-01 3.95e+01 ... (remaining 37679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 17388 23.47 - 46.94: 473 46.94 - 70.41: 146 70.41 - 93.88: 79 93.88 - 117.35: 51 Dihedral angle restraints: 18137 sinusoidal: 8801 harmonic: 9336 Sorted by residual: dihedral pdb=" CD ARG E 61 " pdb=" NE ARG E 61 " pdb=" CZ ARG E 61 " pdb=" NH1 ARG E 61 " ideal model delta sinusoidal sigma weight residual 0.00 65.59 -65.59 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CD ARG E 54 " pdb=" NE ARG E 54 " pdb=" CZ ARG E 54 " pdb=" NH1 ARG E 54 " ideal model delta sinusoidal sigma weight residual 0.00 61.88 -61.88 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS A 605 " pdb=" CB CYS A 605 " ideal model delta sinusoidal sigma weight residual 93.00 35.92 57.08 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 18134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4041 0.096 - 0.192: 458 0.192 - 0.287: 29 0.287 - 0.383: 6 0.383 - 0.479: 1 Chirality restraints: 4535 Sorted by residual: chirality pdb=" C1 NAG C 705 " pdb=" ND2 ASN C 295 " pdb=" C2 NAG C 705 " pdb=" O5 NAG C 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG A 706 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG A 706 " pdb=" O5 NAG A 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 4532 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 54 " 0.967 9.50e-02 1.11e+02 4.33e-01 1.14e+02 pdb=" NE ARG E 54 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG E 54 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 54 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 54 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 61 " -0.852 9.50e-02 1.11e+02 3.83e-01 9.72e+01 pdb=" NE ARG E 61 " 0.070 2.00e-02 2.50e+03 pdb=" CZ ARG E 61 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG E 61 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG E 61 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 61 " -0.696 9.50e-02 1.11e+02 3.13e-01 6.78e+01 pdb=" NE ARG J 61 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG J 61 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG J 61 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG J 61 " -0.005 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 408 2.63 - 3.20: 23738 3.20 - 3.77: 43103 3.77 - 4.33: 61647 4.33 - 4.90: 100743 Nonbonded interactions: 229639 Sorted by model distance: nonbonded pdb=" O ASP G 95 " pdb=" O3 MAN c 5 " model vdw 2.063 3.040 nonbonded pdb=" OD2 ASP B 325 " pdb=" O4 MAN a 5 " model vdw 2.073 3.040 nonbonded pdb=" OD2 ASP C 325 " pdb=" O4 MAN g 5 " model vdw 2.092 3.040 nonbonded pdb=" N VAL D 2 " pdb=" OD1 ASN D 26 " model vdw 2.155 3.120 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP C 632 " model vdw 2.181 3.120 ... (remaining 229634 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 139 or resid 153 through \ 184 or resid 189 through 502 or resid 520 through 546 or resid 574 through 658 \ or resid 705 through 714)) selection = (chain 'B' and (resid 33 through 57 or resid 66 through 139 or resid 153 through \ 502 or resid 520 through 546 or resid 574 through 710)) selection = (chain 'C' and (resid 33 through 139 or resid 153 through 546 or resid 574 throu \ gh 658 or resid 704 through 713)) } ncs_group { reference = chain 'D' selection = (chain 'F' and resid 2 through 111) selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'M' selection = (chain 'O' and resid 3 through 105) selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'e' } ncs_group { reference = chain 'T' selection = chain 'a' selection = chain 'g' } ncs_group { reference = (chain 'U' and (resid 1 or resid 4 through 6)) selection = (chain 'Z' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 6)) selection = (chain 'i' and (resid 1 or resid 4 through 6)) } ncs_group { reference = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'h' and resid 1) } ncs_group { reference = chain 'Y' selection = chain 'f' } 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: 4.530 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 26.600 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 27930 Z= 0.254 Angle : 1.041 16.702 38162 Z= 0.556 Chirality : 0.061 0.479 4535 Planarity : 0.011 0.433 4623 Dihedral : 14.296 117.352 12005 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.46 % Allowed : 1.95 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3193 helix: -0.31 (0.24), residues: 406 sheet: 0.49 (0.14), residues: 1106 loop : 0.44 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG J 61 TYR 0.037 0.003 TYR A 191 PHE 0.064 0.004 PHE J 98 TRP 0.040 0.003 TRP P 50 HIS 0.028 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00567 (27754) covalent geometry : angle 0.99752 (37684) SS BOND : bond 0.00519 ( 50) SS BOND : angle 2.14919 ( 100) hydrogen bonds : bond 0.13620 ( 726) hydrogen bonds : angle 7.35276 ( 1848) link_ALPHA1-2 : bond 0.00372 ( 14) link_ALPHA1-2 : angle 2.17564 ( 42) link_ALPHA1-3 : bond 0.00369 ( 13) link_ALPHA1-3 : angle 1.96461 ( 39) link_ALPHA1-6 : bond 0.00704 ( 12) link_ALPHA1-6 : angle 2.47580 ( 36) link_BETA1-4 : bond 0.01412 ( 29) link_BETA1-4 : angle 4.05201 ( 87) link_BETA1-6 : bond 0.00027 ( 1) link_BETA1-6 : angle 2.15869 ( 3) link_NAG-ASN : bond 0.00533 ( 57) link_NAG-ASN : angle 2.80759 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 805 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 PRO cc_start: 0.8228 (Cg_endo) cc_final: 0.7756 (Cg_exo) REVERT: D 35 TRP cc_start: 0.7336 (m100) cc_final: 0.6778 (m100) REVERT: D 53 TYR cc_start: 0.7195 (m-80) cc_final: 0.6903 (m-10) REVERT: D 82 MET cc_start: 0.4747 (mmp) cc_final: 0.2950 (ptp) REVERT: E 87 TYR cc_start: 0.7045 (m-80) cc_final: 0.6382 (m-10) REVERT: F 35 TRP cc_start: 0.6547 (m100) cc_final: 0.6246 (m100) REVERT: F 68 ARG cc_start: 0.7905 (mmt-90) cc_final: 0.7436 (mtp85) REVERT: F 97 ILE cc_start: 0.8179 (mt) cc_final: 0.7772 (pt) REVERT: G 34 TYR cc_start: 0.7050 (m-80) cc_final: 0.6807 (m-80) REVERT: G 72 THR cc_start: 0.8147 (m) cc_final: 0.7904 (m) REVERT: G 73 LEU cc_start: 0.7265 (tp) cc_final: 0.6872 (tp) REVERT: G 90 SER cc_start: 0.8289 (p) cc_final: 0.7792 (m) REVERT: J 35 TRP cc_start: 0.8150 (m100) cc_final: 0.7433 (m100) REVERT: J 72 THR cc_start: 0.8053 (m) cc_final: 0.7768 (p) REVERT: J 97 MET cc_start: 0.6853 (ptp) cc_final: 0.6337 (ptp) REVERT: K 3 GLN cc_start: 0.7701 (tt0) cc_final: 0.7441 (pm20) REVERT: O 96 GLU cc_start: 0.8431 (mp0) cc_final: 0.7945 (mp0) REVERT: P 12 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7597 (mmtm) REVERT: H 18 VAL cc_start: 0.4036 (p) cc_final: 0.3669 (p) REVERT: H 70 THR cc_start: 0.7001 (t) cc_final: 0.6792 (t) REVERT: H 110 THR cc_start: 0.6523 (m) cc_final: 0.6250 (m) REVERT: A 232 LYS cc_start: 0.8205 (mttp) cc_final: 0.7800 (mtmm) REVERT: A 368 ASP cc_start: 0.8158 (m-30) cc_final: 0.7916 (m-30) REVERT: A 370 GLU cc_start: 0.7770 (mp0) cc_final: 0.7445 (mt-10) REVERT: A 479 TRP cc_start: 0.8171 (m-10) cc_final: 0.7774 (m-10) REVERT: A 584 GLU cc_start: 0.7829 (tt0) cc_final: 0.7603 (tt0) REVERT: B 166 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7846 (mtm110) REVERT: B 308 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7818 (mmt180) REVERT: B 375 SER cc_start: 0.8915 (t) cc_final: 0.8710 (p) REVERT: B 419 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7955 (mtm-85) REVERT: B 425 ASN cc_start: 0.8834 (t0) cc_final: 0.8568 (t0) REVERT: B 439 ILE cc_start: 0.8588 (mm) cc_final: 0.8321 (mm) REVERT: B 625 ASN cc_start: 0.7190 (m-40) cc_final: 0.6981 (t0) REVERT: B 632 ASP cc_start: 0.8022 (t70) cc_final: 0.7806 (t70) REVERT: C 82 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6904 (tp-100) REVERT: C 255 VAL cc_start: 0.9078 (t) cc_final: 0.8875 (m) REVERT: C 309 ILE cc_start: 0.7983 (mm) cc_final: 0.7757 (mt) REVERT: C 479 TRP cc_start: 0.8252 (m-10) cc_final: 0.7073 (m-10) REVERT: C 530 MET cc_start: 0.7185 (mtm) cc_final: 0.6838 (mtp) REVERT: C 618 ASN cc_start: 0.7142 (t0) cc_final: 0.6900 (t0) REVERT: C 622 ILE cc_start: 0.7651 (mt) cc_final: 0.7200 (mt) REVERT: C 625 ASN cc_start: 0.7464 (m-40) cc_final: 0.7216 (m-40) outliers start: 13 outliers final: 6 residues processed: 816 average time/residue: 0.2043 time to fit residues: 255.8311 Evaluate side-chains 532 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 526 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 161 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 HIS K 102 HIS ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN O 77 ASN P 102 HIS L 38 GLN A 280 ASN A 591 GLN A 630 GLN B 85 HIS ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 577 GLN B 607 ASN C 85 HIS C 249 HIS C 279 ASN C 348 GLN C 352 HIS C 570 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.188990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149888 restraints weight = 36091.489| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.62 r_work: 0.3659 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27930 Z= 0.182 Angle : 0.744 23.071 38162 Z= 0.361 Chirality : 0.048 0.347 4535 Planarity : 0.005 0.088 4623 Dihedral : 10.989 95.153 6085 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 2.41 % Allowed : 9.14 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3193 helix: 0.13 (0.25), residues: 402 sheet: 0.32 (0.15), residues: 1079 loop : 0.12 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 61 TYR 0.025 0.002 TYR C 217 PHE 0.024 0.002 PHE J 62 TRP 0.023 0.002 TRP P 50 HIS 0.011 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00408 (27754) covalent geometry : angle 0.68503 (37684) SS BOND : bond 0.00370 ( 50) SS BOND : angle 1.54326 ( 100) hydrogen bonds : bond 0.04295 ( 726) hydrogen bonds : angle 6.20963 ( 1848) link_ALPHA1-2 : bond 0.00560 ( 14) link_ALPHA1-2 : angle 2.07811 ( 42) link_ALPHA1-3 : bond 0.00619 ( 13) link_ALPHA1-3 : angle 2.43752 ( 39) link_ALPHA1-6 : bond 0.00480 ( 12) link_ALPHA1-6 : angle 1.73075 ( 36) link_BETA1-4 : bond 0.00953 ( 29) link_BETA1-4 : angle 2.85941 ( 87) link_BETA1-6 : bond 0.00897 ( 1) link_BETA1-6 : angle 2.11382 ( 3) link_NAG-ASN : bond 0.00433 ( 57) link_NAG-ASN : angle 3.38380 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 567 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7088 (ttp-170) REVERT: D 68 ARG cc_start: 0.7214 (mmp80) cc_final: 0.6939 (mmp80) REVERT: D 82 MET cc_start: 0.4890 (mmp) cc_final: 0.4116 (mmm) REVERT: D 105 GLN cc_start: 0.5861 (mp10) cc_final: 0.5508 (mp10) REVERT: E 71 VAL cc_start: 0.8717 (t) cc_final: 0.8449 (p) REVERT: E 95 ASP cc_start: 0.7511 (t0) cc_final: 0.7156 (t70) REVERT: F 35 TRP cc_start: 0.6776 (m100) cc_final: 0.6195 (m100) REVERT: F 68 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.7556 (mtp-110) REVERT: G 34 TYR cc_start: 0.7239 (m-80) cc_final: 0.6736 (m-80) REVERT: G 89 GLN cc_start: 0.6751 (tt0) cc_final: 0.6503 (pt0) REVERT: G 90 SER cc_start: 0.8384 (p) cc_final: 0.8062 (m) REVERT: J 53 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7417 (tt0) REVERT: K 66 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8254 (mtp85) REVERT: M 61 ARG cc_start: 0.7149 (ptp90) cc_final: 0.6945 (ptp-170) REVERT: H 70 THR cc_start: 0.6981 (t) cc_final: 0.6766 (t) REVERT: H 72 ASP cc_start: 0.6851 (t70) cc_final: 0.6620 (t0) REVERT: H 89 MET cc_start: 0.7048 (tpp) cc_final: 0.6759 (tpp) REVERT: L 67 SER cc_start: 0.7963 (t) cc_final: 0.7564 (m) REVERT: A 125 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 232 LYS cc_start: 0.8366 (mttp) cc_final: 0.7813 (mtmm) REVERT: A 267 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7128 (mp0) REVERT: A 368 ASP cc_start: 0.8262 (m-30) cc_final: 0.7948 (m-30) REVERT: A 370 GLU cc_start: 0.7814 (mp0) cc_final: 0.7374 (mt-10) REVERT: A 412 ASP cc_start: 0.7608 (t0) cc_final: 0.7220 (p0) REVERT: A 479 TRP cc_start: 0.7994 (m-10) cc_final: 0.7577 (m-10) REVERT: B 104 MET cc_start: 0.8516 (mtp) cc_final: 0.8274 (ttt) REVERT: B 121 LYS cc_start: 0.8507 (mptt) cc_final: 0.8079 (mmtm) REVERT: B 166 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7907 (mtp-110) REVERT: B 189 LYS cc_start: 0.7317 (mttt) cc_final: 0.6991 (tppt) REVERT: B 217 TYR cc_start: 0.7824 (m-80) cc_final: 0.7194 (m-80) REVERT: B 308 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7787 (mmt180) REVERT: B 419 ARG cc_start: 0.8372 (mtm180) cc_final: 0.8030 (mtm-85) REVERT: B 425 ASN cc_start: 0.8714 (t0) cc_final: 0.8263 (t0) REVERT: B 439 ILE cc_start: 0.8970 (mm) cc_final: 0.8475 (mm) REVERT: B 457 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7915 (t0) REVERT: B 545 LEU cc_start: 0.7774 (mt) cc_final: 0.7520 (mt) REVERT: B 625 ASN cc_start: 0.7593 (m-40) cc_final: 0.7104 (t0) REVERT: B 632 ASP cc_start: 0.7967 (t70) cc_final: 0.7587 (t70) REVERT: C 618 ASN cc_start: 0.7131 (t0) cc_final: 0.6824 (t0) REVERT: C 622 ILE cc_start: 0.7568 (mt) cc_final: 0.7027 (mp) outliers start: 68 outliers final: 35 residues processed: 605 average time/residue: 0.1766 time to fit residues: 165.9412 Evaluate side-chains 531 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 494 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 639 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 258 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 GLN J 89 GLN M 89 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 658 GLN B 67 ASN B 82 GLN B 355 ASN C 280 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.183962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144274 restraints weight = 35947.528| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.72 r_work: 0.3611 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27930 Z= 0.239 Angle : 0.737 14.061 38162 Z= 0.363 Chirality : 0.049 0.461 4535 Planarity : 0.005 0.052 4623 Dihedral : 9.540 88.341 6080 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 2.97 % Allowed : 11.01 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 3193 helix: 0.08 (0.26), residues: 408 sheet: 0.15 (0.15), residues: 1069 loop : -0.06 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 61 TYR 0.020 0.002 TYR C 217 PHE 0.021 0.002 PHE J 62 TRP 0.026 0.002 TRP G 35 HIS 0.008 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00552 (27754) covalent geometry : angle 0.69324 (37684) SS BOND : bond 0.00708 ( 50) SS BOND : angle 1.87434 ( 100) hydrogen bonds : bond 0.04220 ( 726) hydrogen bonds : angle 6.08780 ( 1848) link_ALPHA1-2 : bond 0.00493 ( 14) link_ALPHA1-2 : angle 2.10550 ( 42) link_ALPHA1-3 : bond 0.00658 ( 13) link_ALPHA1-3 : angle 2.12673 ( 39) link_ALPHA1-6 : bond 0.00491 ( 12) link_ALPHA1-6 : angle 1.77187 ( 36) link_BETA1-4 : bond 0.00901 ( 29) link_BETA1-4 : angle 2.82951 ( 87) link_BETA1-6 : bond 0.00279 ( 1) link_BETA1-6 : angle 2.35511 ( 3) link_NAG-ASN : bond 0.00762 ( 57) link_NAG-ASN : angle 2.53621 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 519 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.7846 (mtp85) cc_final: 0.6817 (ttp-170) REVERT: D 36 TRP cc_start: 0.7455 (m100) cc_final: 0.7021 (m100) REVERT: D 82 MET cc_start: 0.4427 (mmp) cc_final: 0.2707 (mtp) REVERT: E 33 THR cc_start: 0.7334 (m) cc_final: 0.6940 (t) REVERT: E 71 VAL cc_start: 0.8749 (t) cc_final: 0.8549 (p) REVERT: E 82 ASP cc_start: 0.7192 (m-30) cc_final: 0.6919 (m-30) REVERT: E 86 TYR cc_start: 0.8403 (m-80) cc_final: 0.8202 (m-80) REVERT: E 89 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: E 95 ASP cc_start: 0.7619 (t0) cc_final: 0.7337 (t70) REVERT: F 35 TRP cc_start: 0.7271 (m100) cc_final: 0.6089 (m100) REVERT: F 68 ARG cc_start: 0.8055 (mmt-90) cc_final: 0.7342 (mtp85) REVERT: F 98 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6826 (ttm-80) REVERT: G 72 THR cc_start: 0.7941 (m) cc_final: 0.7714 (p) REVERT: I 36 TRP cc_start: 0.7640 (m100) cc_final: 0.7352 (m100) REVERT: I 89 MET cc_start: 0.7659 (tpp) cc_final: 0.7407 (tpp) REVERT: J 35 TRP cc_start: 0.8033 (m100) cc_final: 0.7507 (m100) REVERT: J 53 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7833 (tt0) REVERT: J 62 PHE cc_start: 0.6651 (m-80) cc_final: 0.6450 (m-80) REVERT: M 45 ARG cc_start: 0.8840 (ptt180) cc_final: 0.8496 (ptt90) REVERT: M 61 ARG cc_start: 0.7256 (ptp90) cc_final: 0.6821 (ptp90) REVERT: N 48 MET cc_start: 0.8647 (mmm) cc_final: 0.8112 (mtp) REVERT: N 80 LEU cc_start: 0.8954 (tp) cc_final: 0.8750 (tp) REVERT: O 71 TYR cc_start: 0.7732 (m-80) cc_final: 0.7384 (m-80) REVERT: P 12 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8543 (mmtm) REVERT: P 34 LEU cc_start: 0.8869 (mp) cc_final: 0.8546 (tp) REVERT: H 34 MET cc_start: 0.7476 (mmm) cc_final: 0.7256 (tpp) REVERT: H 70 THR cc_start: 0.7101 (t) cc_final: 0.6876 (t) REVERT: H 72 ASP cc_start: 0.6805 (t70) cc_final: 0.6557 (t0) REVERT: H 89 MET cc_start: 0.7159 (tpp) cc_final: 0.6864 (tpp) REVERT: L 67 SER cc_start: 0.7972 (t) cc_final: 0.7602 (m) REVERT: A 159 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8783 (p90) REVERT: A 232 LYS cc_start: 0.8671 (mttp) cc_final: 0.8193 (mtmm) REVERT: A 356 ASN cc_start: 0.8397 (p0) cc_final: 0.8086 (m-40) REVERT: A 412 ASP cc_start: 0.7652 (t0) cc_final: 0.7339 (p0) REVERT: A 479 TRP cc_start: 0.8223 (m-10) cc_final: 0.7325 (m-10) REVERT: A 650 GLN cc_start: 0.7062 (pp30) cc_final: 0.6522 (pp30) REVERT: B 104 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8223 (ttt) REVERT: B 189 LYS cc_start: 0.7547 (mttt) cc_final: 0.7326 (tppt) REVERT: B 195 ASN cc_start: 0.8035 (m110) cc_final: 0.7719 (m-40) REVERT: B 217 TYR cc_start: 0.7882 (m-80) cc_final: 0.7295 (m-80) REVERT: B 268 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7314 (tp30) REVERT: B 419 ARG cc_start: 0.8346 (mtm180) cc_final: 0.8039 (mtm-85) REVERT: B 425 ASN cc_start: 0.8824 (t0) cc_final: 0.8435 (t0) REVERT: B 439 ILE cc_start: 0.9272 (mm) cc_final: 0.8920 (mm) REVERT: B 457 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7835 (t0) REVERT: B 632 ASP cc_start: 0.8038 (t70) cc_final: 0.7697 (t70) REVERT: C 35 TRP cc_start: 0.7836 (m100) cc_final: 0.7602 (m100) REVERT: C 54 CYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6534 (p) REVERT: C 283 ASN cc_start: 0.8612 (m-40) cc_final: 0.8365 (m-40) REVERT: C 475 MET cc_start: 0.8129 (mmt) cc_final: 0.7764 (mmt) REVERT: C 618 ASN cc_start: 0.7301 (t0) cc_final: 0.6880 (t0) REVERT: C 625 ASN cc_start: 0.7547 (m-40) cc_final: 0.7336 (m-40) outliers start: 84 outliers final: 58 residues processed: 567 average time/residue: 0.1850 time to fit residues: 164.2787 Evaluate side-chains 544 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 480 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 208 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 304 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN O 89 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS B 355 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.184323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145180 restraints weight = 35848.332| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.68 r_work: 0.3590 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27930 Z= 0.203 Angle : 0.698 16.284 38162 Z= 0.339 Chirality : 0.047 0.464 4535 Planarity : 0.004 0.045 4623 Dihedral : 8.758 78.198 6077 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 2.83 % Allowed : 12.71 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.15), residues: 3193 helix: 0.12 (0.26), residues: 406 sheet: 0.04 (0.15), residues: 1060 loop : -0.11 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 61 TYR 0.037 0.002 TYR D 53 PHE 0.017 0.002 PHE D 78 TRP 0.022 0.002 TRP P 50 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00471 (27754) covalent geometry : angle 0.65060 (37684) SS BOND : bond 0.00441 ( 50) SS BOND : angle 1.76898 ( 100) hydrogen bonds : bond 0.03874 ( 726) hydrogen bonds : angle 6.00566 ( 1848) link_ALPHA1-2 : bond 0.00489 ( 14) link_ALPHA1-2 : angle 2.05765 ( 42) link_ALPHA1-3 : bond 0.00743 ( 13) link_ALPHA1-3 : angle 2.19798 ( 39) link_ALPHA1-6 : bond 0.00488 ( 12) link_ALPHA1-6 : angle 1.83202 ( 36) link_BETA1-4 : bond 0.00849 ( 29) link_BETA1-4 : angle 2.72200 ( 87) link_BETA1-6 : bond 0.00369 ( 1) link_BETA1-6 : angle 1.56643 ( 3) link_NAG-ASN : bond 0.00430 ( 57) link_NAG-ASN : angle 2.65192 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 506 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7527 (mtp180) REVERT: D 36 TRP cc_start: 0.7366 (m100) cc_final: 0.6846 (m100) REVERT: D 68 ARG cc_start: 0.7457 (mmp80) cc_final: 0.7127 (mmp80) REVERT: D 82 MET cc_start: 0.4303 (mmp) cc_final: 0.2718 (mtp) REVERT: E 71 VAL cc_start: 0.8743 (t) cc_final: 0.8480 (p) REVERT: E 82 ASP cc_start: 0.7163 (m-30) cc_final: 0.6943 (m-30) REVERT: E 89 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: E 95 ASP cc_start: 0.7763 (t0) cc_final: 0.7424 (t70) REVERT: F 35 TRP cc_start: 0.7334 (m100) cc_final: 0.6049 (m100) REVERT: F 68 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.7400 (mtp85) REVERT: F 98 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6845 (ttm-80) REVERT: G 72 THR cc_start: 0.8093 (m) cc_final: 0.7787 (p) REVERT: I 36 TRP cc_start: 0.7463 (m100) cc_final: 0.6913 (m100) REVERT: J 35 TRP cc_start: 0.8039 (m100) cc_final: 0.7525 (m100) REVERT: J 53 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7777 (tt0) REVERT: K 64 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7732 (mm-40) REVERT: M 61 ARG cc_start: 0.7154 (ptp90) cc_final: 0.6695 (ptp90) REVERT: O 11 LEU cc_start: 0.6585 (tp) cc_final: 0.6347 (tp) REVERT: O 71 TYR cc_start: 0.7890 (m-80) cc_final: 0.7383 (m-80) REVERT: P 11 MET cc_start: 0.7798 (mtm) cc_final: 0.7526 (mmp) REVERT: H 70 THR cc_start: 0.7137 (t) cc_final: 0.6915 (t) REVERT: H 72 ASP cc_start: 0.6941 (t70) cc_final: 0.6618 (t70) REVERT: H 89 MET cc_start: 0.7138 (tpp) cc_final: 0.6775 (tpp) REVERT: L 50 GLU cc_start: 0.7965 (mp0) cc_final: 0.7507 (mp0) REVERT: L 67 SER cc_start: 0.8110 (t) cc_final: 0.7712 (m) REVERT: A 267 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7309 (mp0) REVERT: A 356 ASN cc_start: 0.8552 (p0) cc_final: 0.8320 (m-40) REVERT: A 412 ASP cc_start: 0.7811 (t0) cc_final: 0.7357 (p0) REVERT: A 475 MET cc_start: 0.8425 (tpp) cc_final: 0.8071 (tpp) REVERT: A 479 TRP cc_start: 0.8208 (m-10) cc_final: 0.7661 (m-10) REVERT: B 104 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8226 (ttt) REVERT: B 121 LYS cc_start: 0.8655 (mptt) cc_final: 0.8184 (mmtm) REVERT: B 189 LYS cc_start: 0.7510 (mttt) cc_final: 0.7200 (tppt) REVERT: B 217 TYR cc_start: 0.7911 (m-80) cc_final: 0.7295 (m-80) REVERT: B 268 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7303 (tp30) REVERT: B 419 ARG cc_start: 0.8407 (mtm180) cc_final: 0.8041 (mtm-85) REVERT: B 425 ASN cc_start: 0.8891 (t0) cc_final: 0.8430 (t0) REVERT: B 444 ARG cc_start: 0.8007 (tpt-90) cc_final: 0.7791 (mtp-110) REVERT: B 632 ASP cc_start: 0.8092 (t70) cc_final: 0.7730 (t70) REVERT: C 35 TRP cc_start: 0.7803 (m100) cc_final: 0.7567 (m100) REVERT: C 283 ASN cc_start: 0.8635 (m-40) cc_final: 0.8395 (m-40) REVERT: C 618 ASN cc_start: 0.7265 (t0) cc_final: 0.6719 (t0) outliers start: 80 outliers final: 59 residues processed: 550 average time/residue: 0.1780 time to fit residues: 153.8625 Evaluate side-chains 536 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 474 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 641 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 201 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN A 103 GLN A 130 GLN A 246 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 658 GLN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 352 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.183991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.144597 restraints weight = 35795.456| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.57 r_work: 0.3606 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27930 Z= 0.184 Angle : 0.683 16.794 38162 Z= 0.330 Chirality : 0.046 0.385 4535 Planarity : 0.004 0.053 4623 Dihedral : 8.207 76.104 6075 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 2.83 % Allowed : 13.77 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.15), residues: 3193 helix: 0.13 (0.26), residues: 410 sheet: -0.06 (0.15), residues: 1069 loop : -0.18 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 76 TYR 0.019 0.002 TYR D 53 PHE 0.022 0.002 PHE J 62 TRP 0.021 0.002 TRP N 50 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00425 (27754) covalent geometry : angle 0.63489 (37684) SS BOND : bond 0.00407 ( 50) SS BOND : angle 1.81644 ( 100) hydrogen bonds : bond 0.03743 ( 726) hydrogen bonds : angle 5.94296 ( 1848) link_ALPHA1-2 : bond 0.00490 ( 14) link_ALPHA1-2 : angle 2.03598 ( 42) link_ALPHA1-3 : bond 0.00845 ( 13) link_ALPHA1-3 : angle 2.13102 ( 39) link_ALPHA1-6 : bond 0.00509 ( 12) link_ALPHA1-6 : angle 1.83568 ( 36) link_BETA1-4 : bond 0.00852 ( 29) link_BETA1-4 : angle 2.64132 ( 87) link_BETA1-6 : bond 0.00186 ( 1) link_BETA1-6 : angle 1.68541 ( 3) link_NAG-ASN : bond 0.00435 ( 57) link_NAG-ASN : angle 2.66233 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 495 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 TRP cc_start: 0.7297 (m100) cc_final: 0.6781 (m100) REVERT: D 53 TYR cc_start: 0.7117 (m-80) cc_final: 0.6533 (m-10) REVERT: D 105 GLN cc_start: 0.5493 (mp10) cc_final: 0.5228 (mp10) REVERT: E 71 VAL cc_start: 0.8798 (t) cc_final: 0.8510 (p) REVERT: E 95 ASP cc_start: 0.7833 (t0) cc_final: 0.7476 (t70) REVERT: F 35 TRP cc_start: 0.7391 (m100) cc_final: 0.6189 (m100) REVERT: F 68 ARG cc_start: 0.8011 (mmt-90) cc_final: 0.7398 (mtp85) REVERT: I 36 TRP cc_start: 0.7581 (m100) cc_final: 0.6844 (m100) REVERT: I 59 TYR cc_start: 0.6968 (p90) cc_final: 0.6438 (p90) REVERT: I 80 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6026 (tt) REVERT: I 89 MET cc_start: 0.7695 (tpp) cc_final: 0.7488 (tpp) REVERT: J 35 TRP cc_start: 0.8067 (m100) cc_final: 0.7580 (m100) REVERT: J 53 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7799 (tt0) REVERT: K 43 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7684 (pttt) REVERT: K 64 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7732 (mm-40) REVERT: M 61 ARG cc_start: 0.7183 (ptp90) cc_final: 0.6980 (ptp-170) REVERT: M 89 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: N 48 MET cc_start: 0.8631 (mmm) cc_final: 0.8177 (mtt) REVERT: O 11 LEU cc_start: 0.6694 (tp) cc_final: 0.6462 (tp) REVERT: O 71 TYR cc_start: 0.7937 (m-80) cc_final: 0.7356 (m-80) REVERT: P 34 LEU cc_start: 0.8853 (mp) cc_final: 0.8543 (tp) REVERT: H 34 MET cc_start: 0.7423 (tpt) cc_final: 0.7215 (tpt) REVERT: H 70 THR cc_start: 0.7110 (t) cc_final: 0.6889 (t) REVERT: H 72 ASP cc_start: 0.6905 (t70) cc_final: 0.6595 (t70) REVERT: H 89 MET cc_start: 0.7205 (tpp) cc_final: 0.6789 (tpp) REVERT: L 30 TYR cc_start: 0.7724 (m-80) cc_final: 0.7390 (m-80) REVERT: L 50 GLU cc_start: 0.7928 (mp0) cc_final: 0.7474 (mp0) REVERT: L 67 SER cc_start: 0.8063 (t) cc_final: 0.7682 (m) REVERT: A 267 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7366 (mp0) REVERT: A 356 ASN cc_start: 0.8530 (p0) cc_final: 0.8280 (m-40) REVERT: A 412 ASP cc_start: 0.7890 (t0) cc_final: 0.7469 (p0) REVERT: A 475 MET cc_start: 0.8432 (tpp) cc_final: 0.8190 (tpp) REVERT: A 479 TRP cc_start: 0.8220 (m-10) cc_final: 0.7695 (m-10) REVERT: A 650 GLN cc_start: 0.6995 (pp30) cc_final: 0.6448 (pp30) REVERT: B 104 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8142 (ttt) REVERT: B 189 LYS cc_start: 0.7570 (mttt) cc_final: 0.7268 (tppt) REVERT: B 217 TYR cc_start: 0.7897 (m-80) cc_final: 0.7212 (m-80) REVERT: B 425 ASN cc_start: 0.8885 (t0) cc_final: 0.8463 (t0) REVERT: B 543 ASN cc_start: 0.7928 (m110) cc_final: 0.7673 (m110) REVERT: B 632 ASP cc_start: 0.7984 (t70) cc_final: 0.7624 (t70) REVERT: C 102 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8216 (mm-30) REVERT: C 125 LEU cc_start: 0.8994 (tp) cc_final: 0.8791 (tp) REVERT: C 264 SER cc_start: 0.9134 (m) cc_final: 0.8880 (p) REVERT: C 283 ASN cc_start: 0.8637 (m-40) cc_final: 0.8401 (m-40) REVERT: C 475 MET cc_start: 0.8509 (tpp) cc_final: 0.8000 (mmt) REVERT: C 640 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7942 (mm110) outliers start: 80 outliers final: 67 residues processed: 538 average time/residue: 0.1796 time to fit residues: 153.9398 Evaluate side-chains 537 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 466 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 530 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 87 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 72 ASN ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN B 82 GLN B 352 HIS B 355 ASN B 607 ASN C 72 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.180070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140138 restraints weight = 35746.367| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.64 r_work: 0.3563 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 27930 Z= 0.281 Angle : 0.757 17.286 38162 Z= 0.367 Chirality : 0.050 0.784 4535 Planarity : 0.005 0.063 4623 Dihedral : 8.296 78.249 6075 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 3.97 % Allowed : 13.63 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 3193 helix: -0.19 (0.26), residues: 412 sheet: -0.22 (0.15), residues: 1054 loop : -0.33 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 166 TYR 0.019 0.002 TYR D 53 PHE 0.021 0.002 PHE A 159 TRP 0.024 0.002 TRP A 427 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00660 (27754) covalent geometry : angle 0.70717 (37684) SS BOND : bond 0.00574 ( 50) SS BOND : angle 1.88961 ( 100) hydrogen bonds : bond 0.04095 ( 726) hydrogen bonds : angle 6.14137 ( 1848) link_ALPHA1-2 : bond 0.00492 ( 14) link_ALPHA1-2 : angle 2.29292 ( 42) link_ALPHA1-3 : bond 0.00675 ( 13) link_ALPHA1-3 : angle 2.36486 ( 39) link_ALPHA1-6 : bond 0.00500 ( 12) link_ALPHA1-6 : angle 1.91320 ( 36) link_BETA1-4 : bond 0.00853 ( 29) link_BETA1-4 : angle 2.79007 ( 87) link_BETA1-6 : bond 0.00356 ( 1) link_BETA1-6 : angle 2.16462 ( 3) link_NAG-ASN : bond 0.00589 ( 57) link_NAG-ASN : angle 2.84895 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 495 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 TRP cc_start: 0.7364 (m100) cc_final: 0.6904 (m100) REVERT: D 53 TYR cc_start: 0.7386 (m-80) cc_final: 0.7016 (m-10) REVERT: D 82 MET cc_start: 0.3621 (mmm) cc_final: 0.2591 (mtp) REVERT: D 89 MET cc_start: 0.5732 (ttt) cc_final: 0.5477 (ttm) REVERT: D 91 TYR cc_start: 0.6789 (m-80) cc_final: 0.6054 (m-80) REVERT: D 105 GLN cc_start: 0.5674 (mp10) cc_final: 0.5361 (mp10) REVERT: E 71 VAL cc_start: 0.8796 (t) cc_final: 0.8512 (p) REVERT: E 95 ASP cc_start: 0.8088 (t0) cc_final: 0.7767 (t70) REVERT: F 68 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7432 (mtp85) REVERT: I 36 TRP cc_start: 0.7738 (m100) cc_final: 0.7288 (m100) REVERT: I 59 TYR cc_start: 0.6961 (p90) cc_final: 0.6461 (p90) REVERT: I 80 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6099 (tt) REVERT: J 53 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8113 (tt0) REVERT: M 45 ARG cc_start: 0.8901 (ptt180) cc_final: 0.8603 (ptt90) REVERT: M 77 ASN cc_start: 0.7548 (t0) cc_final: 0.7228 (t0) REVERT: M 89 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: N 48 MET cc_start: 0.8698 (mmm) cc_final: 0.8190 (mtt) REVERT: O 11 LEU cc_start: 0.6822 (tp) cc_final: 0.6605 (tp) REVERT: H 70 THR cc_start: 0.7300 (t) cc_final: 0.7061 (t) REVERT: H 72 ASP cc_start: 0.6957 (t70) cc_final: 0.6706 (t70) REVERT: H 89 MET cc_start: 0.7232 (tpp) cc_final: 0.6828 (tpp) REVERT: L 50 GLU cc_start: 0.7938 (mp0) cc_final: 0.7614 (mp0) REVERT: L 67 SER cc_start: 0.8099 (t) cc_final: 0.7729 (m) REVERT: A 189 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6721 (tttp) REVERT: A 267 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7504 (mp0) REVERT: A 475 MET cc_start: 0.8455 (tpp) cc_final: 0.8170 (tpp) REVERT: A 479 TRP cc_start: 0.8325 (m-10) cc_final: 0.7578 (m-10) REVERT: B 104 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8140 (ttt) REVERT: B 129 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8962 (mp) REVERT: B 189 LYS cc_start: 0.7571 (mttt) cc_final: 0.7252 (tppt) REVERT: B 217 TYR cc_start: 0.7960 (m-80) cc_final: 0.7511 (m-80) REVERT: B 323 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8166 (pt) REVERT: B 439 ILE cc_start: 0.9428 (mm) cc_final: 0.9042 (mm) REVERT: B 632 ASP cc_start: 0.8095 (t70) cc_final: 0.7717 (t70) REVERT: C 102 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8229 (mm-30) REVERT: C 164 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: C 264 SER cc_start: 0.9168 (m) cc_final: 0.8948 (p) REVERT: C 485 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7478 (ptmt) outliers start: 112 outliers final: 86 residues processed: 559 average time/residue: 0.1584 time to fit residues: 140.7116 Evaluate side-chains 559 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 465 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 604 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 chunk 124 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 ASN ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 ASN ** P 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN B 352 HIS B 355 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.184511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145349 restraints weight = 35639.065| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.55 r_work: 0.3613 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27930 Z= 0.149 Angle : 0.674 20.719 38162 Z= 0.325 Chirality : 0.047 0.743 4535 Planarity : 0.004 0.061 4623 Dihedral : 7.826 74.638 6073 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 2.58 % Allowed : 16.36 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 3193 helix: 0.08 (0.26), residues: 408 sheet: -0.16 (0.16), residues: 1042 loop : -0.31 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 166 TYR 0.016 0.001 TYR H 27 PHE 0.025 0.002 PHE J 62 TRP 0.023 0.002 TRP N 50 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00338 (27754) covalent geometry : angle 0.61699 (37684) SS BOND : bond 0.00373 ( 50) SS BOND : angle 1.55626 ( 100) hydrogen bonds : bond 0.03607 ( 726) hydrogen bonds : angle 5.93220 ( 1848) link_ALPHA1-2 : bond 0.00499 ( 14) link_ALPHA1-2 : angle 2.02796 ( 42) link_ALPHA1-3 : bond 0.00782 ( 13) link_ALPHA1-3 : angle 2.16821 ( 39) link_ALPHA1-6 : bond 0.00528 ( 12) link_ALPHA1-6 : angle 1.82616 ( 36) link_BETA1-4 : bond 0.00817 ( 29) link_BETA1-4 : angle 2.62569 ( 87) link_BETA1-6 : bond 0.00327 ( 1) link_BETA1-6 : angle 1.10596 ( 3) link_NAG-ASN : bond 0.00628 ( 57) link_NAG-ASN : angle 3.13624 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 505 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 TRP cc_start: 0.7230 (m100) cc_final: 0.6804 (m100) REVERT: D 53 TYR cc_start: 0.7387 (m-80) cc_final: 0.7151 (m-10) REVERT: D 82 MET cc_start: 0.3994 (mmm) cc_final: 0.2734 (mtp) REVERT: D 89 MET cc_start: 0.5575 (ttt) cc_final: 0.5229 (ttm) REVERT: D 91 TYR cc_start: 0.6708 (m-80) cc_final: 0.5858 (m-80) REVERT: E 71 VAL cc_start: 0.8779 (t) cc_final: 0.8477 (p) REVERT: E 95 ASP cc_start: 0.7880 (t0) cc_final: 0.7628 (t70) REVERT: F 47 TRP cc_start: 0.7076 (t60) cc_final: 0.6874 (t60) REVERT: F 68 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7403 (mtp85) REVERT: I 36 TRP cc_start: 0.7684 (m100) cc_final: 0.7288 (m100) REVERT: I 59 TYR cc_start: 0.7020 (p90) cc_final: 0.6481 (p90) REVERT: J 35 TRP cc_start: 0.8006 (m100) cc_final: 0.7559 (m100) REVERT: J 53 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8060 (tt0) REVERT: J 89 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: K 43 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7749 (pttt) REVERT: M 45 ARG cc_start: 0.8914 (ptt180) cc_final: 0.8679 (ptt-90) REVERT: M 77 ASN cc_start: 0.7376 (t0) cc_final: 0.7148 (t0) REVERT: M 89 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: M 96 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6274 (pm20) REVERT: O 11 LEU cc_start: 0.6654 (tp) cc_final: 0.6443 (tp) REVERT: P 34 LEU cc_start: 0.8784 (mp) cc_final: 0.8510 (tp) REVERT: P 61 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7754 (mtm110) REVERT: P 82 ARG cc_start: 0.8513 (mpp80) cc_final: 0.8204 (mtp180) REVERT: H 34 MET cc_start: 0.7525 (tpt) cc_final: 0.6772 (tpt) REVERT: H 70 THR cc_start: 0.7190 (t) cc_final: 0.6968 (t) REVERT: H 89 MET cc_start: 0.7143 (tpp) cc_final: 0.6711 (tpp) REVERT: L 30 TYR cc_start: 0.7941 (m-80) cc_final: 0.7691 (m-80) REVERT: L 50 GLU cc_start: 0.7829 (mp0) cc_final: 0.7608 (mp0) REVERT: L 67 SER cc_start: 0.8080 (t) cc_final: 0.7691 (m) REVERT: A 51 THR cc_start: 0.9294 (m) cc_final: 0.9071 (p) REVERT: A 267 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7333 (mp0) REVERT: A 351 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7834 (mttp) REVERT: A 479 TRP cc_start: 0.8228 (m-10) cc_final: 0.7787 (m-10) REVERT: B 189 LYS cc_start: 0.7552 (mttt) cc_final: 0.7325 (tppt) REVERT: B 191 TYR cc_start: 0.9128 (m-80) cc_final: 0.8911 (m-80) REVERT: B 217 TYR cc_start: 0.7823 (m-80) cc_final: 0.7153 (m-80) REVERT: B 439 ILE cc_start: 0.9326 (mm) cc_final: 0.8938 (mm) REVERT: B 632 ASP cc_start: 0.7865 (t70) cc_final: 0.7498 (t70) REVERT: C 102 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8239 (mm-30) REVERT: C 264 SER cc_start: 0.9145 (m) cc_final: 0.8939 (p) REVERT: C 283 ASN cc_start: 0.8624 (m-40) cc_final: 0.8386 (m-40) REVERT: C 475 MET cc_start: 0.8474 (tpp) cc_final: 0.8089 (mmt) REVERT: C 485 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7336 (ptmt) outliers start: 73 outliers final: 52 residues processed: 548 average time/residue: 0.1689 time to fit residues: 145.7251 Evaluate side-chains 537 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 480 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 485 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 160 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 299 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 312 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 313 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 72 ASN ** P 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN B 352 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.184597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.144977 restraints weight = 35906.104| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.66 r_work: 0.3632 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27930 Z= 0.173 Angle : 0.674 16.591 38162 Z= 0.325 Chirality : 0.046 0.445 4535 Planarity : 0.004 0.067 4623 Dihedral : 7.603 72.536 6073 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 2.62 % Allowed : 16.22 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3193 helix: 0.15 (0.26), residues: 408 sheet: -0.23 (0.16), residues: 1061 loop : -0.27 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 61 TYR 0.015 0.001 TYR O 86 PHE 0.022 0.002 PHE D 78 TRP 0.025 0.002 TRP N 50 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00402 (27754) covalent geometry : angle 0.62163 (37684) SS BOND : bond 0.00398 ( 50) SS BOND : angle 1.63891 ( 100) hydrogen bonds : bond 0.03623 ( 726) hydrogen bonds : angle 5.90239 ( 1848) link_ALPHA1-2 : bond 0.00477 ( 14) link_ALPHA1-2 : angle 2.07842 ( 42) link_ALPHA1-3 : bond 0.00721 ( 13) link_ALPHA1-3 : angle 2.14554 ( 39) link_ALPHA1-6 : bond 0.00522 ( 12) link_ALPHA1-6 : angle 1.85468 ( 36) link_BETA1-4 : bond 0.00805 ( 29) link_BETA1-4 : angle 2.60945 ( 87) link_BETA1-6 : bond 0.00580 ( 1) link_BETA1-6 : angle 1.34454 ( 3) link_NAG-ASN : bond 0.00440 ( 57) link_NAG-ASN : angle 2.87198 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 487 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 TRP cc_start: 0.7291 (m100) cc_final: 0.6916 (m100) REVERT: D 82 MET cc_start: 0.3905 (mmm) cc_final: 0.2752 (mtp) REVERT: D 91 TYR cc_start: 0.6730 (m-80) cc_final: 0.5835 (m-80) REVERT: E 71 VAL cc_start: 0.8764 (t) cc_final: 0.8508 (p) REVERT: E 89 GLN cc_start: 0.7176 (pt0) cc_final: 0.6942 (pt0) REVERT: E 95 ASP cc_start: 0.7909 (t0) cc_final: 0.7678 (t70) REVERT: E 96 LYS cc_start: 0.8015 (mmmm) cc_final: 0.7791 (mttp) REVERT: F 47 TRP cc_start: 0.7174 (t60) cc_final: 0.6964 (t60) REVERT: F 68 ARG cc_start: 0.8168 (mmt-90) cc_final: 0.7476 (mtp85) REVERT: I 36 TRP cc_start: 0.7750 (m100) cc_final: 0.7316 (m100) REVERT: I 59 TYR cc_start: 0.7108 (p90) cc_final: 0.6618 (p90) REVERT: I 66 ARG cc_start: 0.6251 (mtp-110) cc_final: 0.5356 (tmm-80) REVERT: I 80 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6106 (tt) REVERT: J 53 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8163 (tt0) REVERT: J 89 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: K 43 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7805 (pttt) REVERT: K 64 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7590 (mt0) REVERT: M 89 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: M 96 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6273 (pm20) REVERT: N 48 MET cc_start: 0.8914 (mtp) cc_final: 0.8237 (mtt) REVERT: O 11 LEU cc_start: 0.6705 (tp) cc_final: 0.6488 (tp) REVERT: P 61 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7828 (mtm110) REVERT: P 82 ARG cc_start: 0.8487 (mpp80) cc_final: 0.8046 (mtm-85) REVERT: H 34 MET cc_start: 0.7262 (tpt) cc_final: 0.6800 (tpt) REVERT: H 70 THR cc_start: 0.7204 (t) cc_final: 0.6990 (t) REVERT: H 89 MET cc_start: 0.7183 (tpp) cc_final: 0.6822 (tpp) REVERT: H 96 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7904 (ttm) REVERT: L 32 PHE cc_start: 0.7917 (m-10) cc_final: 0.7632 (m-10) REVERT: L 67 SER cc_start: 0.7946 (t) cc_final: 0.7586 (m) REVERT: A 267 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7361 (mp0) REVERT: A 351 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7860 (mttp) REVERT: A 479 TRP cc_start: 0.8197 (m-10) cc_final: 0.7832 (m-10) REVERT: B 104 MET cc_start: 0.8759 (tpp) cc_final: 0.8201 (ttt) REVERT: B 114 GLN cc_start: 0.8263 (mm-40) cc_final: 0.8037 (mt0) REVERT: B 173 TYR cc_start: 0.7528 (m-80) cc_final: 0.7245 (m-80) REVERT: B 189 LYS cc_start: 0.7685 (mttt) cc_final: 0.7473 (tppt) REVERT: B 217 TYR cc_start: 0.7860 (m-80) cc_final: 0.7338 (m-80) REVERT: B 632 ASP cc_start: 0.7773 (t70) cc_final: 0.7426 (t70) REVERT: C 102 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8224 (mm-30) REVERT: C 283 ASN cc_start: 0.8605 (m-40) cc_final: 0.8385 (m-40) REVERT: C 485 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7440 (ptmt) outliers start: 74 outliers final: 61 residues processed: 531 average time/residue: 0.1673 time to fit residues: 141.3985 Evaluate side-chains 541 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 473 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 485 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 24 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 185 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 294 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 313 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 ASN ** P 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN B 114 GLN B 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.185235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145634 restraints weight = 35925.782| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.58 r_work: 0.3635 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27930 Z= 0.162 Angle : 0.664 15.439 38162 Z= 0.321 Chirality : 0.046 0.352 4535 Planarity : 0.004 0.069 4623 Dihedral : 7.484 71.279 6073 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 2.66 % Allowed : 16.57 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3193 helix: 0.18 (0.26), residues: 408 sheet: -0.25 (0.16), residues: 1068 loop : -0.26 (0.16), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 53 TYR 0.014 0.001 TYR B 217 PHE 0.025 0.002 PHE D 78 TRP 0.026 0.002 TRP N 50 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00377 (27754) covalent geometry : angle 0.61504 (37684) SS BOND : bond 0.00391 ( 50) SS BOND : angle 1.61682 ( 100) hydrogen bonds : bond 0.03552 ( 726) hydrogen bonds : angle 5.85751 ( 1848) link_ALPHA1-2 : bond 0.00492 ( 14) link_ALPHA1-2 : angle 2.02226 ( 42) link_ALPHA1-3 : bond 0.00718 ( 13) link_ALPHA1-3 : angle 2.12501 ( 39) link_ALPHA1-6 : bond 0.00534 ( 12) link_ALPHA1-6 : angle 1.85092 ( 36) link_BETA1-4 : bond 0.00799 ( 29) link_BETA1-4 : angle 2.56540 ( 87) link_BETA1-6 : bond 0.00459 ( 1) link_BETA1-6 : angle 1.28099 ( 3) link_NAG-ASN : bond 0.00409 ( 57) link_NAG-ASN : angle 2.74107 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 495 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 TRP cc_start: 0.7269 (m100) cc_final: 0.6840 (m100) REVERT: D 82 MET cc_start: 0.3682 (mmm) cc_final: 0.2825 (mtp) REVERT: D 91 TYR cc_start: 0.6685 (m-80) cc_final: 0.6074 (m-80) REVERT: E 71 VAL cc_start: 0.8771 (t) cc_final: 0.8507 (p) REVERT: E 97 MET cc_start: 0.7671 (ptp) cc_final: 0.7414 (ptp) REVERT: F 68 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7458 (mtp85) REVERT: I 12 VAL cc_start: 0.6326 (m) cc_final: 0.6081 (t) REVERT: I 36 TRP cc_start: 0.7672 (m100) cc_final: 0.7304 (m100) REVERT: I 59 TYR cc_start: 0.7223 (p90) cc_final: 0.6647 (p90) REVERT: I 66 ARG cc_start: 0.6294 (mtp-110) cc_final: 0.5365 (tmm-80) REVERT: I 80 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6009 (tt) REVERT: J 53 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8111 (tt0) REVERT: J 89 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: K 27 TYR cc_start: 0.8779 (p90) cc_final: 0.8437 (p90) REVERT: K 64 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7557 (mt0) REVERT: M 25 THR cc_start: 0.8940 (m) cc_final: 0.8686 (p) REVERT: M 61 ARG cc_start: 0.7047 (ptp90) cc_final: 0.6625 (ptp90) REVERT: M 89 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: M 96 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: N 48 MET cc_start: 0.8889 (mtp) cc_final: 0.8212 (mtp) REVERT: O 11 LEU cc_start: 0.6654 (tp) cc_final: 0.6440 (tp) REVERT: P 34 LEU cc_start: 0.8752 (mp) cc_final: 0.8521 (tp) REVERT: P 61 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7807 (mtm110) REVERT: P 82 ARG cc_start: 0.8505 (mpp80) cc_final: 0.8075 (mtm-85) REVERT: H 43 GLN cc_start: 0.6884 (pm20) cc_final: 0.6571 (pm20) REVERT: H 70 THR cc_start: 0.7170 (t) cc_final: 0.6960 (t) REVERT: H 89 MET cc_start: 0.7164 (tpp) cc_final: 0.6783 (tpp) REVERT: L 32 PHE cc_start: 0.7904 (m-10) cc_final: 0.7640 (m-10) REVERT: L 67 SER cc_start: 0.7938 (t) cc_final: 0.7574 (m) REVERT: A 267 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7313 (mp0) REVERT: A 351 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7858 (mttp) REVERT: A 370 GLU cc_start: 0.7732 (mp0) cc_final: 0.7192 (mt-10) REVERT: A 479 TRP cc_start: 0.8199 (m-10) cc_final: 0.7888 (m-10) REVERT: A 650 GLN cc_start: 0.7016 (pp30) cc_final: 0.6435 (pp30) REVERT: B 104 MET cc_start: 0.8774 (tpp) cc_final: 0.8236 (ttt) REVERT: B 189 LYS cc_start: 0.7605 (mttt) cc_final: 0.7376 (tppt) REVERT: B 217 TYR cc_start: 0.7882 (m-80) cc_final: 0.7342 (m-80) REVERT: B 268 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6930 (tp30) REVERT: B 323 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8025 (pt) REVERT: B 632 ASP cc_start: 0.7735 (t70) cc_final: 0.7384 (t70) REVERT: C 102 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8236 (mm-30) REVERT: C 485 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7391 (ptmt) outliers start: 75 outliers final: 62 residues processed: 538 average time/residue: 0.1581 time to fit residues: 135.0032 Evaluate side-chains 547 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 479 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 604 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 266 optimal weight: 0.0370 chunk 37 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 ASN ** P 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN B 352 HIS B 607 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.185151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145276 restraints weight = 35894.079| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.48 r_work: 0.3639 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27930 Z= 0.169 Angle : 0.675 14.581 38162 Z= 0.325 Chirality : 0.046 0.309 4535 Planarity : 0.004 0.073 4623 Dihedral : 7.417 69.720 6073 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 2.73 % Allowed : 16.54 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3193 helix: 0.24 (0.26), residues: 408 sheet: -0.25 (0.16), residues: 1056 loop : -0.27 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 61 TYR 0.021 0.001 TYR D 53 PHE 0.025 0.002 PHE D 78 TRP 0.027 0.002 TRP N 50 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00393 (27754) covalent geometry : angle 0.62702 (37684) SS BOND : bond 0.00385 ( 50) SS BOND : angle 1.61795 ( 100) hydrogen bonds : bond 0.03552 ( 726) hydrogen bonds : angle 5.84842 ( 1848) link_ALPHA1-2 : bond 0.00488 ( 14) link_ALPHA1-2 : angle 2.03552 ( 42) link_ALPHA1-3 : bond 0.00695 ( 13) link_ALPHA1-3 : angle 2.07830 ( 39) link_ALPHA1-6 : bond 0.00537 ( 12) link_ALPHA1-6 : angle 1.86126 ( 36) link_BETA1-4 : bond 0.00782 ( 29) link_BETA1-4 : angle 2.56391 ( 87) link_BETA1-6 : bond 0.00427 ( 1) link_BETA1-6 : angle 1.30966 ( 3) link_NAG-ASN : bond 0.00417 ( 57) link_NAG-ASN : angle 2.69552 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 481 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6607 (ttp-170) REVERT: D 36 TRP cc_start: 0.7317 (m100) cc_final: 0.6870 (m100) REVERT: D 82 MET cc_start: 0.3844 (mmm) cc_final: 0.3131 (mtp) REVERT: D 91 TYR cc_start: 0.6680 (m-80) cc_final: 0.5914 (m-80) REVERT: E 71 VAL cc_start: 0.8768 (t) cc_final: 0.8507 (p) REVERT: E 97 MET cc_start: 0.8021 (ptp) cc_final: 0.7601 (ptp) REVERT: F 68 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7425 (mtp85) REVERT: I 12 VAL cc_start: 0.6383 (m) cc_final: 0.6137 (t) REVERT: I 36 TRP cc_start: 0.7696 (m100) cc_final: 0.7327 (m100) REVERT: I 59 TYR cc_start: 0.7135 (p90) cc_final: 0.6609 (p90) REVERT: I 66 ARG cc_start: 0.6302 (mtp-110) cc_final: 0.5310 (ttm-80) REVERT: I 80 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6156 (tt) REVERT: J 53 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8113 (tt0) REVERT: K 27 TYR cc_start: 0.8762 (p90) cc_final: 0.8448 (p90) REVERT: K 64 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7593 (mt0) REVERT: M 25 THR cc_start: 0.8955 (m) cc_final: 0.8700 (p) REVERT: M 61 ARG cc_start: 0.7092 (ptp90) cc_final: 0.6632 (ptp90) REVERT: M 89 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: M 96 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: N 48 MET cc_start: 0.8861 (mtp) cc_final: 0.8167 (mtp) REVERT: O 11 LEU cc_start: 0.6694 (tp) cc_final: 0.6476 (tp) REVERT: P 34 LEU cc_start: 0.8749 (mp) cc_final: 0.8518 (tp) REVERT: P 61 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7763 (mtm110) REVERT: H 43 GLN cc_start: 0.6852 (pm20) cc_final: 0.6556 (pm20) REVERT: H 70 THR cc_start: 0.7125 (t) cc_final: 0.6918 (t) REVERT: H 89 MET cc_start: 0.7147 (tpp) cc_final: 0.6763 (tpp) REVERT: H 97 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8266 (mtm180) REVERT: L 67 SER cc_start: 0.7905 (t) cc_final: 0.7544 (m) REVERT: A 267 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7295 (mp0) REVERT: A 370 GLU cc_start: 0.7722 (mp0) cc_final: 0.7194 (mt-10) REVERT: A 479 TRP cc_start: 0.8213 (m-10) cc_final: 0.7875 (m-10) REVERT: A 650 GLN cc_start: 0.7013 (pp30) cc_final: 0.6443 (pp30) REVERT: B 104 MET cc_start: 0.8792 (tpp) cc_final: 0.8359 (ttt) REVERT: B 189 LYS cc_start: 0.7606 (mttt) cc_final: 0.7385 (tppt) REVERT: B 217 TYR cc_start: 0.7924 (m-80) cc_final: 0.7495 (m-80) REVERT: B 268 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6887 (tp30) REVERT: B 323 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8038 (pt) REVERT: B 632 ASP cc_start: 0.7698 (t70) cc_final: 0.7363 (t70) REVERT: C 102 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8191 (mm-30) REVERT: C 444 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: C 485 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7402 (ptmt) REVERT: C 636 SER cc_start: 0.8600 (t) cc_final: 0.8347 (t) REVERT: C 658 GLN cc_start: 0.6995 (mp10) cc_final: 0.6728 (tt0) outliers start: 77 outliers final: 65 residues processed: 528 average time/residue: 0.1592 time to fit residues: 133.0809 Evaluate side-chains 544 residues out of total 2824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 473 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 98 CYS Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 604 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 26 optimal weight: 10.0000 chunk 250 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 201 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 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 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 ASN ** P 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN B 66 HIS B 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.184231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145911 restraints weight = 35483.716| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.36 r_work: 0.3668 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27930 Z= 0.158 Angle : 0.668 17.846 38162 Z= 0.322 Chirality : 0.046 0.396 4535 Planarity : 0.004 0.074 4623 Dihedral : 7.349 68.409 6073 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 2.66 % Allowed : 16.86 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 3193 helix: 0.22 (0.26), residues: 410 sheet: -0.22 (0.16), residues: 1054 loop : -0.28 (0.16), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 45 TYR 0.021 0.001 TYR L 49 PHE 0.030 0.002 PHE D 78 TRP 0.028 0.002 TRP N 50 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00367 (27754) covalent geometry : angle 0.61824 (37684) SS BOND : bond 0.00380 ( 50) SS BOND : angle 1.52747 ( 100) hydrogen bonds : bond 0.03517 ( 726) hydrogen bonds : angle 5.79737 ( 1848) link_ALPHA1-2 : bond 0.00483 ( 14) link_ALPHA1-2 : angle 2.00744 ( 42) link_ALPHA1-3 : bond 0.00689 ( 13) link_ALPHA1-3 : angle 2.06641 ( 39) link_ALPHA1-6 : bond 0.00541 ( 12) link_ALPHA1-6 : angle 1.85311 ( 36) link_BETA1-4 : bond 0.00772 ( 29) link_BETA1-4 : angle 2.53876 ( 87) link_BETA1-6 : bond 0.00336 ( 1) link_BETA1-6 : angle 1.37161 ( 3) link_NAG-ASN : bond 0.00474 ( 57) link_NAG-ASN : angle 2.81787 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7947.25 seconds wall clock time: 136 minutes 50.32 seconds (8210.32 seconds total)