Starting phenix.real_space_refine on Mon Aug 25 11:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ogm_70471/08_2025/9ogm_70471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ogm_70471/08_2025/9ogm_70471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ogm_70471/08_2025/9ogm_70471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ogm_70471/08_2025/9ogm_70471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ogm_70471/08_2025/9ogm_70471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ogm_70471/08_2025/9ogm_70471.map" } resolution = 3.5 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= 0.011 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 161 5.16 5 C 16937 2.51 5 N 4539 2.21 5 O 5416 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: 27053 Number of models: 1 Model: "" Number of chains: 40 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: "H" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 122} 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: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} 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: "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: "A" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4318 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 23, 'TRANS': 523} Chain breaks: 6 Chain: "B" Number of atoms: 4610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4610 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 23, 'TRANS': 556} Chain breaks: 5 Chain: "C" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4304 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 23, 'TRANS': 521} Chain breaks: 6 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: "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: 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: "V" 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: "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: 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: "Y" 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: "Z" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.75, per 1000 atoms: 0.21 Number of scatterers: 27053 At special positions: 0 Unit cell: (165.858, 162.986, 173.038, 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 161 16.00 O 5416 8.00 N 4539 7.00 C 16937 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=2.03 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 H 22 " - pdb=" SG CYS H 92 " distance=1.95 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 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=1.78 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 32 " - pdb=" SG CYS N 98 " distance=1.47 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=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 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=2.03 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=2.02 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=2.03 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=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=1.68 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.15 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=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 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 Y 4 " - " MAN Y 5 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 5 " - " MAN Z 6 " " MAN Z 8 " - " MAN Z 9 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN f 8 " - " MAN f 9 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 10 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 7 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 7 " - " MAN Z 10 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 8 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 6 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 7 " - " MAN Z 8 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 7 " " MAN f 7 " - " MAN f 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " NAG-ASN " NAG A 801 " - " ASN A 137 " " NAG A 802 " - " ASN A 160 " " NAG A 803 " - " ASN A 234 " " NAG A 804 " - " ASN A 301 " " NAG A 805 " - " ASN A 133 " " NAG A 806 " - " ASN A 156 " " NAG A 807 " - " ASN A 197 " " NAG A 808 " - " ASN A 339 " " NAG A 809 " - " ASN A 386 " " NAG A 810 " - " ASN A 448 " " NAG A 811 " - " ASN A 295 " " NAG B 801 " - " ASN B 133 " " NAG B 802 " - " ASN B 137 " " NAG B 803 " - " ASN B 160 " " NAG B 804 " - " ASN B 234 " " NAG B 805 " - " ASN B 295 " " NAG B 806 " - " ASN B 301 " " NAG B 807 " - " ASN B 339 " " NAG B 808 " - " ASN B 448 " " NAG C 801 " - " ASN C 133 " " NAG C 802 " - " ASN C 137 " " NAG C 803 " - " ASN C 160 " " NAG C 804 " - " ASN C 197 " " NAG C 805 " - " ASN C 234 " " NAG C 806 " - " ASN C 295 " " NAG C 807 " - " ASN C 301 " " NAG C 808 " - " ASN C 448 " " NAG D 301 " - " ASN D 26 " " NAG F 301 " - " ASN F 26 " " NAG I 301 " - " ASN I 26 " " 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 B 156 " " NAG W 1 " - " ASN B 197 " " NAG X 1 " - " ASN B 262 " " NAG Y 1 " - " ASN B 276 " " NAG Z 1 " - " ASN B 332 " " NAG a 1 " - " ASN B 386 " " NAG b 1 " - " ASN B 392 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 262 " " NAG e 1 " - " ASN C 276 " " NAG f 1 " - " ASN C 332 " " NAG g 1 " - " ASN C 386 " " NAG h 1 " - " ASN C 392 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 56 sheets defined 16.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.533A pdb=" N ASP D 32 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS D 33 " --> pdb=" O PRO D 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 33' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 100B through 100F Processing helix chain 'E' and resid 26 through 31 removed outlier: 3.770A pdb=" N ARG E 31 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 61 through 64 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 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.565A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 100B through 100F Processing helix chain 'J' and resid 26 through 30 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.070A pdb=" N CYS K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 26 through 31 removed outlier: 3.891A pdb=" N SER L 30 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 84 removed outlier: 4.575A pdb=" N ALA L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.798A pdb=" N THR P 87 " --> pdb=" O VAL P 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.463A 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 removed outlier: 3.919A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.976A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.606A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 646 removed outlier: 3.620A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.886A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.134A 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 removed outlier: 3.718A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.634A pdb=" N PHE B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.790A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.615A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 531 through 536' Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.335A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 620 through 625 removed outlier: 3.971A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 650 Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.117A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.811A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.524A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.662A pdb=" N MET C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 574 through 596 Processing helix chain 'C' and resid 618 through 626 removed outlier: 3.529A pdb=" N MET C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) 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 659 Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 34 through 39 removed outlier: 6.225A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 59 current: chain 'D' and resid 100H through 103 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 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 44 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 removed outlier: 3.636A pdb=" N ARG F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) 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 57 through 59 current: chain 'F' and resid 100H through 103 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 'H' and resid 11 through 12 removed outlier: 3.724A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 17 through 22 Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.653A pdb=" N ASP H 58 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG H 50 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'I' and resid 33 through 39 removed outlier: 6.589A pdb=" N TRP I 35 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (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 100J Processing sheet with id=AB5, 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=AB5 Processing sheet with id=AB6, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AB7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AB8, 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 100D through 103 Processing sheet with id=AB9, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AC1, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.824A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY L 100 " --> pdb=" O CYS L 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.503A pdb=" N SER M 63 " --> pdb=" O THR M 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.390A pdb=" N TRP M 35 " --> pdb=" O VAL M 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.518A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 34 through 39 removed outlier: 3.671A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 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=AC6, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AC7, 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 102 through 103 Processing sheet with id=AC8, first strand: chain 'Q' and resid 5 through 7 Processing sheet with id=AC9, first strand: chain 'Q' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 11 current: chain 'Q' and resid 45 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=AD1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.610A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AD3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AD4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AD5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AD6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AD7, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.373A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AD9, 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 298 removed outlier: 7.130A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 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=AE1, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.699A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 495 through 499 removed outlier: 4.900A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.708A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.748A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AE6, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AE7, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AE8, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.774A pdb=" N ALA B 433 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 260 current: chain 'B' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 287 current: chain 'B' and resid 394 through 395 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 394 through 395 current: chain 'B' and resid 465 through 470 No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.485A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 298 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 303 through 312 removed outlier: 6.904A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 495 through 499 removed outlier: 4.996A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AF5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AF6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AF7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AF8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.412A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AF9, 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 308 removed outlier: 6.982A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AG1, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'O' and resid 10 through 12 removed outlier: 7.058A pdb=" N LEU O 11 " --> pdb=" O GLN O 105 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP O 35 " --> pdb=" O VAL O 47 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8376 1.34 - 1.47: 7323 1.47 - 1.60: 11722 1.60 - 1.72: 1 1.72 - 1.85: 222 Bond restraints: 27644 Sorted by residual: bond pdb=" N ASP B 618 " pdb=" CA ASP B 618 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.32e-02 5.74e+03 1.03e+01 bond pdb=" N PHE B 391 " pdb=" CA PHE B 391 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.00e-02 1.00e+04 9.79e+00 bond pdb=" N PHE O 97 " pdb=" CA PHE O 97 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.32e-02 5.74e+03 9.49e+00 bond pdb=" N ASN C 607 " pdb=" CA ASN C 607 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.46e+00 ... (remaining 27639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 34851 1.74 - 3.48: 2140 3.48 - 5.22: 436 5.22 - 6.96: 99 6.96 - 8.71: 10 Bond angle restraints: 37536 Sorted by residual: angle pdb=" CA ASP A 47 " pdb=" C ASP A 47 " pdb=" O ASP A 47 " ideal model delta sigma weight residual 122.03 117.16 4.87 1.13e+00 7.83e-01 1.85e+01 angle pdb=" N CYS C 54 " pdb=" CA CYS C 54 " pdb=" C CYS C 54 " ideal model delta sigma weight residual 110.55 116.04 -5.49 1.35e+00 5.49e-01 1.66e+01 angle pdb=" N PHE O 97 " pdb=" CA PHE O 97 " pdb=" C PHE O 97 " ideal model delta sigma weight residual 110.43 115.61 -5.18 1.31e+00 5.83e-01 1.56e+01 angle pdb=" N ASP P 99 " pdb=" CA ASP P 99 " pdb=" C ASP P 99 " ideal model delta sigma weight residual 112.93 107.69 5.24 1.33e+00 5.65e-01 1.55e+01 angle pdb=" N ARG A 579 " pdb=" CA ARG A 579 " pdb=" C ARG A 579 " ideal model delta sigma weight residual 111.36 107.07 4.29 1.09e+00 8.42e-01 1.55e+01 ... (remaining 37531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16046 17.93 - 35.85: 1378 35.85 - 53.78: 362 53.78 - 71.70: 108 71.70 - 89.63: 40 Dihedral angle restraints: 17934 sinusoidal: 8606 harmonic: 9328 Sorted by residual: dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual 93.00 171.71 -78.71 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CB CYS N 32 " pdb=" SG CYS N 32 " pdb=" SG CYS N 98 " pdb=" CB CYS N 98 " ideal model delta sinusoidal sigma weight residual 93.00 15.00 78.00 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS C 598 " pdb=" SG CYS C 598 " pdb=" SG CYS C 604 " pdb=" CB CYS C 604 " ideal model delta sinusoidal sigma weight residual 93.00 155.75 -62.75 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 17931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4181 0.110 - 0.219: 271 0.219 - 0.329: 6 0.329 - 0.438: 4 0.438 - 0.548: 2 Chirality restraints: 4464 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 392 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.44e+00 chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 4461 not shown) Planarity restraints: 4667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 617 " 0.643 9.50e-02 1.11e+02 2.88e-01 5.07e+01 pdb=" NE ARG B 617 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 617 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 617 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 617 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 576 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C LEU A 576 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU A 576 " 0.029 2.00e-02 2.50e+03 pdb=" N GLN A 577 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 39 " -0.024 2.00e-02 2.50e+03 2.97e-02 1.76e+01 pdb=" CG TYR C 39 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR C 39 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR C 39 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 39 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 39 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 39 " -0.004 2.00e-02 2.50e+03 ... (remaining 4664 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 133 2.47 - 3.08: 18543 3.08 - 3.69: 39380 3.69 - 4.29: 58600 4.29 - 4.90: 98664 Nonbonded interactions: 215320 Sorted by model distance: nonbonded pdb=" O PHE C 522 " pdb=" NE2 GLN C 540 " model vdw 1.863 3.120 nonbonded pdb=" CG2 THR L 20 " pdb=" OG SER L 72 " model vdw 1.946 3.460 nonbonded pdb=" O GLU H 6 " pdb=" OG1 THR H 107 " model vdw 2.071 3.040 nonbonded pdb=" OE1 GLU H 100J" pdb=" NH1 ARG L 91 " model vdw 2.098 3.120 nonbonded pdb=" OG1 THR A 303 " pdb=" OD1 ASP A 322 " model vdw 2.101 3.040 ... (remaining 215315 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 522 through 537 or resid 573 through 659 \ or resid 804 through 811)) selection = (chain 'B' and (resid 33 through 57 or resid 66 through 139 or resid 153 through \ 502 or resid 522 through 537 or resid 573 through 659 or resid 801 through 808) \ ) selection = (chain 'C' and (resid 33 through 537 or resid 573 through 808)) } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 2 through 111 or resid 301)) 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 'S' selection = chain 'b' selection = chain 'd' } ncs_group { reference = chain 'T' selection = chain 'Z' selection = chain 'f' } ncs_group { reference = (chain 'U' and (resid 2 or resid 5 through 7)) selection = (chain 'Y' and (resid 2 or resid 5 through 7)) selection = (chain 'h' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'X' selection = chain 'e' } 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 group one per residue 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: 9.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.920 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.008 0.560 27809 Z= 0.359 Angle : 1.078 41.733 37981 Z= 0.549 Chirality : 0.056 0.548 4464 Planarity : 0.008 0.288 4620 Dihedral : 14.838 89.627 11808 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.74 % Allowed : 14.07 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.58 (0.14), residues: 3190 helix: 0.09 (0.27), residues: 401 sheet: 0.02 (0.15), residues: 1030 loop : -0.69 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG B 444 TYR 0.072 0.003 TYR C 39 PHE 0.044 0.003 PHE P 100D TRP 0.025 0.002 TRP N 50 HIS 0.008 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00634 (27644) covalent geometry : angle 0.97724 (37536) SS BOND : bond 0.10223 ( 50) SS BOND : angle 7.53950 ( 100) hydrogen bonds : bond 0.14604 ( 697) hydrogen bonds : angle 7.16510 ( 1761) link_ALPHA1-2 : bond 0.00444 ( 13) link_ALPHA1-2 : angle 2.28749 ( 39) link_ALPHA1-3 : bond 0.00687 ( 13) link_ALPHA1-3 : angle 2.66758 ( 39) link_ALPHA1-6 : bond 0.00420 ( 13) link_ALPHA1-6 : angle 1.91476 ( 39) link_BETA1-4 : bond 0.01142 ( 29) link_BETA1-4 : angle 3.50785 ( 87) link_NAG-ASN : bond 0.00500 ( 47) link_NAG-ASN : angle 2.50122 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 645 time to evaluate : 0.976 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ASN cc_start: 0.7313 (t0) cc_final: 0.6816 (t0) REVERT: D 91 TYR cc_start: 0.7566 (m-80) cc_final: 0.7143 (m-10) REVERT: E 75 ILE cc_start: 0.8516 (tp) cc_final: 0.8304 (mt) REVERT: E 95 ASP cc_start: 0.8190 (t0) cc_final: 0.7956 (t70) REVERT: F 100 MET cc_start: 0.7970 (mtm) cc_final: 0.6999 (mpp) REVERT: G 20 ARG cc_start: 0.8744 (mmt90) cc_final: 0.8403 (mpt-90) REVERT: G 21 ILE cc_start: 0.8744 (mp) cc_final: 0.8438 (mt) REVERT: I 39 GLN cc_start: 0.7206 (tt0) cc_final: 0.6970 (tt0) REVERT: I 47 TRP cc_start: 0.8223 (t60) cc_final: 0.7921 (t60) REVERT: L 48 PHE cc_start: 0.4222 (OUTLIER) cc_final: 0.4003 (t80) REVERT: L 73 LEU cc_start: 0.7162 (pp) cc_final: 0.6642 (pp) REVERT: M 14 SER cc_start: 0.7480 (m) cc_final: 0.7276 (p) REVERT: M 36 TYR cc_start: 0.8157 (m-80) cc_final: 0.7821 (m-80) REVERT: M 37 GLN cc_start: 0.7668 (tt0) cc_final: 0.7402 (tt0) REVERT: Q 36 TYR cc_start: 0.7553 (m-80) cc_final: 0.7220 (m-80) REVERT: B 107 ASP cc_start: 0.7495 (t0) cc_final: 0.7126 (t0) REVERT: B 115 SER cc_start: 0.8560 (t) cc_final: 0.8313 (m) REVERT: B 411 ASN cc_start: 0.7703 (m-40) cc_final: 0.7029 (t0) REVERT: C 35 TRP cc_start: 0.7885 (m100) cc_final: 0.7142 (m-10) REVERT: C 67 ASN cc_start: 0.7596 (t0) cc_final: 0.7228 (t0) REVERT: C 486 TYR cc_start: 0.7508 (m-80) cc_final: 0.7179 (m-80) REVERT: O 61 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7439 (mtm110) outliers start: 21 outliers final: 10 residues processed: 658 average time/residue: 0.1703 time to fit residues: 172.8510 Evaluate side-chains 553 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 542 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 680 TRP Chi-restraints excluded: chain C residue 295 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 GLN E 89 GLN J 17 GLN K 102 HIS M 100 GLN A 103 GLN A 136 ASN A 249 HIS A 300 ASN A 577 GLN A 640 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 67 ASN C 249 HIS C 540 GLN O 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113637 restraints weight = 42564.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112312 restraints weight = 34450.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113476 restraints weight = 40698.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114231 restraints weight = 27079.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115320 restraints weight = 23887.585| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 27809 Z= 0.251 Angle : 0.789 15.035 37981 Z= 0.383 Chirality : 0.050 0.374 4464 Planarity : 0.005 0.060 4620 Dihedral : 9.415 86.932 5869 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 4.11 % Allowed : 15.13 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.63 (0.14), residues: 3190 helix: 0.33 (0.26), residues: 401 sheet: -0.09 (0.15), residues: 1051 loop : -0.77 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 94 TYR 0.028 0.002 TYR F 53 PHE 0.029 0.002 PHE P 100D TRP 0.036 0.002 TRP B 35 HIS 0.007 0.002 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00589 (27644) covalent geometry : angle 0.74775 (37536) SS BOND : bond 0.00449 ( 50) SS BOND : angle 1.42016 ( 100) hydrogen bonds : bond 0.04579 ( 697) hydrogen bonds : angle 5.80989 ( 1761) link_ALPHA1-2 : bond 0.00525 ( 13) link_ALPHA1-2 : angle 2.30613 ( 39) link_ALPHA1-3 : bond 0.00785 ( 13) link_ALPHA1-3 : angle 2.65494 ( 39) link_ALPHA1-6 : bond 0.00581 ( 13) link_ALPHA1-6 : angle 1.97901 ( 39) link_BETA1-4 : bond 0.00897 ( 29) link_BETA1-4 : angle 3.01948 ( 87) link_NAG-ASN : bond 0.00562 ( 47) link_NAG-ASN : angle 2.71508 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 558 time to evaluate : 1.092 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: symmetry clash revert: symmetry clash REVERT: D 5 ARG cc_start: 0.7156 (mpp80) cc_final: 0.6857 (ttp80) REVERT: D 91 TYR cc_start: 0.7512 (m-80) cc_final: 0.7199 (m-80) REVERT: F 82 MET cc_start: 0.6559 (tmm) cc_final: 0.6173 (tpp) REVERT: G 20 ARG cc_start: 0.8798 (mmt90) cc_final: 0.8390 (mpt-90) REVERT: G 21 ILE cc_start: 0.8822 (mp) cc_final: 0.8616 (mt) REVERT: H 19 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7521 (ttm110) REVERT: I 5 ARG cc_start: 0.7390 (mmp-170) cc_final: 0.6730 (mmp-170) REVERT: I 47 TRP cc_start: 0.8434 (t60) cc_final: 0.8010 (t60) REVERT: J 42 GLN cc_start: 0.7213 (mt0) cc_final: 0.6748 (mp10) REVERT: L 48 PHE cc_start: 0.4528 (OUTLIER) cc_final: 0.3960 (t80) REVERT: Q 37 GLN cc_start: 0.7752 (tt0) cc_final: 0.7465 (tt0) REVERT: Q 86 TYR cc_start: 0.8467 (m-80) cc_final: 0.7924 (m-80) REVERT: B 107 ASP cc_start: 0.7581 (t0) cc_final: 0.7153 (t0) REVERT: B 115 SER cc_start: 0.8662 (t) cc_final: 0.8232 (m) REVERT: B 190 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: B 211 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: B 411 ASN cc_start: 0.7799 (m-40) cc_final: 0.7086 (t0) REVERT: B 657 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: C 35 TRP cc_start: 0.7811 (m100) cc_final: 0.7411 (m100) REVERT: C 67 ASN cc_start: 0.7771 (t0) cc_final: 0.7269 (t0) REVERT: C 161 MET cc_start: 0.7431 (tpt) cc_final: 0.6882 (tpt) REVERT: C 486 TYR cc_start: 0.7770 (m-80) cc_final: 0.7325 (m-80) REVERT: C 584 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7407 (tm-30) outliers start: 116 outliers final: 75 residues processed: 622 average time/residue: 0.2028 time to fit residues: 193.4599 Evaluate side-chains 591 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 511 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain B residue 680 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 214 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN G 17 GLN G 42 GLN J 17 GLN N 35 ASN N 100AASN P 100AASN Q 42 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 195 ASN C 577 GLN C 590 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114861 restraints weight = 42389.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113644 restraints weight = 34224.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114916 restraints weight = 37885.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115553 restraints weight = 26859.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116094 restraints weight = 23950.415| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27809 Z= 0.165 Angle : 0.715 13.622 37981 Z= 0.343 Chirality : 0.047 0.375 4464 Planarity : 0.005 0.052 4620 Dihedral : 8.814 85.370 5863 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 3.61 % Allowed : 16.97 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.55 (0.14), residues: 3190 helix: 0.61 (0.27), residues: 407 sheet: -0.08 (0.15), residues: 1081 loop : -0.74 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 53 TYR 0.032 0.002 TYR F 53 PHE 0.021 0.002 PHE B 53 TRP 0.033 0.002 TRP H 55 HIS 0.006 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00378 (27644) covalent geometry : angle 0.67283 (37536) SS BOND : bond 0.00333 ( 50) SS BOND : angle 1.26987 ( 100) hydrogen bonds : bond 0.03898 ( 697) hydrogen bonds : angle 5.47988 ( 1761) link_ALPHA1-2 : bond 0.00573 ( 13) link_ALPHA1-2 : angle 2.17254 ( 39) link_ALPHA1-3 : bond 0.00861 ( 13) link_ALPHA1-3 : angle 2.52538 ( 39) link_ALPHA1-6 : bond 0.00593 ( 13) link_ALPHA1-6 : angle 1.83139 ( 39) link_BETA1-4 : bond 0.00935 ( 29) link_BETA1-4 : angle 2.86060 ( 87) link_NAG-ASN : bond 0.00414 ( 47) link_NAG-ASN : angle 2.64910 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 551 time to evaluate : 1.118 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 GLU cc_start: 0.7741 (pp20) cc_final: 0.7334 (pp20) REVERT: D 66 ARG cc_start: 0.6993 (mtp-110) cc_final: 0.6749 (mtp-110) REVERT: G 20 ARG cc_start: 0.8730 (mmt90) cc_final: 0.8392 (mpt-90) REVERT: H 19 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7516 (ttm110) REVERT: I 47 TRP cc_start: 0.8349 (t60) cc_final: 0.7965 (t60) REVERT: J 42 GLN cc_start: 0.7252 (mt0) cc_final: 0.6789 (mp10) REVERT: J 95 TYR cc_start: 0.7594 (p90) cc_final: 0.6991 (p90) REVERT: K 82 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8502 (tp) REVERT: L 48 PHE cc_start: 0.4530 (OUTLIER) cc_final: 0.3917 (t80) REVERT: L 74 THR cc_start: 0.8062 (m) cc_final: 0.7824 (p) REVERT: L 87 TYR cc_start: 0.7219 (m-80) cc_final: 0.7014 (m-80) REVERT: N 39 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8010 (mm) REVERT: Q 37 GLN cc_start: 0.7762 (tt0) cc_final: 0.7487 (tt0) REVERT: Q 86 TYR cc_start: 0.8402 (m-80) cc_final: 0.7878 (m-80) REVERT: B 107 ASP cc_start: 0.7485 (t0) cc_final: 0.7068 (t0) REVERT: B 115 SER cc_start: 0.8569 (t) cc_final: 0.8183 (m) REVERT: B 190 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: B 411 ASN cc_start: 0.7841 (m-40) cc_final: 0.7187 (t0) REVERT: C 35 TRP cc_start: 0.7877 (m100) cc_final: 0.7037 (m-10) REVERT: C 67 ASN cc_start: 0.7745 (t0) cc_final: 0.7243 (t0) REVERT: C 161 MET cc_start: 0.7326 (tpt) cc_final: 0.6938 (tpt) outliers start: 102 outliers final: 70 residues processed: 607 average time/residue: 0.1990 time to fit residues: 187.5483 Evaluate side-chains 581 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 507 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain B residue 680 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 225 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 202 optimal weight: 0.6980 chunk 256 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 42 GLN J 17 GLN J 38 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100AASN P 64 GLN P 100AASN A 651 ASN C 67 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115499 restraints weight = 42219.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114411 restraints weight = 33268.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115457 restraints weight = 39357.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116208 restraints weight = 26775.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116634 restraints weight = 23542.356| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27809 Z= 0.142 Angle : 0.711 14.746 37981 Z= 0.338 Chirality : 0.047 0.477 4464 Planarity : 0.005 0.057 4620 Dihedral : 8.458 83.771 5863 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 4.15 % Allowed : 17.65 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.55 (0.14), residues: 3190 helix: 0.70 (0.27), residues: 413 sheet: 0.02 (0.16), residues: 1030 loop : -0.83 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 53 TYR 0.030 0.001 TYR F 53 PHE 0.029 0.002 PHE E 32 TRP 0.045 0.002 TRP B 35 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00325 (27644) covalent geometry : angle 0.66332 (37536) SS BOND : bond 0.00261 ( 50) SS BOND : angle 1.78369 ( 100) hydrogen bonds : bond 0.03580 ( 697) hydrogen bonds : angle 5.25798 ( 1761) link_ALPHA1-2 : bond 0.00577 ( 13) link_ALPHA1-2 : angle 2.16976 ( 39) link_ALPHA1-3 : bond 0.00921 ( 13) link_ALPHA1-3 : angle 2.46597 ( 39) link_ALPHA1-6 : bond 0.00618 ( 13) link_ALPHA1-6 : angle 1.77010 ( 39) link_BETA1-4 : bond 0.00969 ( 29) link_BETA1-4 : angle 2.80446 ( 87) link_NAG-ASN : bond 0.00446 ( 47) link_NAG-ASN : angle 2.83488 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 544 time to evaluate : 1.040 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 ARG cc_start: 0.8666 (mmt90) cc_final: 0.8341 (mpt-90) REVERT: I 47 TRP cc_start: 0.8293 (t60) cc_final: 0.7867 (t60) REVERT: J 42 GLN cc_start: 0.7244 (mt0) cc_final: 0.6828 (mp10) REVERT: L 48 PHE cc_start: 0.4463 (OUTLIER) cc_final: 0.3939 (t80) REVERT: N 39 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8045 (mm) REVERT: Q 37 GLN cc_start: 0.7727 (tt0) cc_final: 0.7424 (tt0) REVERT: Q 86 TYR cc_start: 0.8381 (m-80) cc_final: 0.7899 (m-80) REVERT: B 107 ASP cc_start: 0.7464 (t0) cc_final: 0.7052 (t0) REVERT: B 115 SER cc_start: 0.8610 (t) cc_final: 0.8201 (m) REVERT: B 153 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: B 190 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: B 411 ASN cc_start: 0.7820 (m-40) cc_final: 0.7196 (t0) REVERT: C 35 TRP cc_start: 0.7849 (m100) cc_final: 0.7025 (m-10) REVERT: C 67 ASN cc_start: 0.7637 (t0) cc_final: 0.7323 (t0) REVERT: C 161 MET cc_start: 0.7317 (tpt) cc_final: 0.6959 (tpt) REVERT: O 61 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7601 (mtm110) outliers start: 117 outliers final: 79 residues processed: 609 average time/residue: 0.2026 time to fit residues: 191.6550 Evaluate side-chains 601 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 518 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 25 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 170 optimal weight: 5.9990 chunk 313 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 274 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 151 optimal weight: 0.4980 chunk 295 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 17 GLN J 17 GLN ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN P 100AASN A 114 GLN ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 607 ASN C 67 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094728 restraints weight = 44412.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098347 restraints weight = 23247.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100596 restraints weight = 16046.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101986 restraints weight = 12899.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102776 restraints weight = 11355.141| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 27809 Z= 0.324 Angle : 0.838 17.401 37981 Z= 0.404 Chirality : 0.051 0.434 4464 Planarity : 0.005 0.064 4620 Dihedral : 8.927 86.597 5861 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 5.35 % Allowed : 18.57 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.93 (0.14), residues: 3190 helix: 0.47 (0.26), residues: 405 sheet: -0.28 (0.15), residues: 1062 loop : -1.07 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 53 TYR 0.026 0.003 TYR C 39 PHE 0.025 0.003 PHE P 100D TRP 0.060 0.002 TRP B 35 HIS 0.008 0.002 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00765 (27644) covalent geometry : angle 0.79039 (37536) SS BOND : bond 0.00594 ( 50) SS BOND : angle 2.06475 ( 100) hydrogen bonds : bond 0.04258 ( 697) hydrogen bonds : angle 5.50674 ( 1761) link_ALPHA1-2 : bond 0.00517 ( 13) link_ALPHA1-2 : angle 2.32803 ( 39) link_ALPHA1-3 : bond 0.00731 ( 13) link_ALPHA1-3 : angle 2.60125 ( 39) link_ALPHA1-6 : bond 0.00604 ( 13) link_ALPHA1-6 : angle 1.95215 ( 39) link_BETA1-4 : bond 0.00887 ( 29) link_BETA1-4 : angle 3.10035 ( 87) link_NAG-ASN : bond 0.00571 ( 47) link_NAG-ASN : angle 3.07594 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 524 time to evaluate : 1.129 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: D 5 ARG cc_start: 0.7691 (mpp80) cc_final: 0.6980 (ttp80) REVERT: D 38 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.4669 (ptm-80) REVERT: D 46 GLU cc_start: 0.7934 (pp20) cc_final: 0.7543 (pp20) REVERT: E 85 ASP cc_start: 0.7701 (m-30) cc_final: 0.7332 (m-30) REVERT: H 34 MET cc_start: 0.7275 (mmm) cc_final: 0.6649 (mmt) REVERT: H 39 GLN cc_start: 0.6888 (tm-30) cc_final: 0.6675 (tm-30) REVERT: H 59 TYR cc_start: 0.6673 (m-10) cc_final: 0.6296 (m-10) REVERT: I 47 TRP cc_start: 0.8248 (t60) cc_final: 0.7431 (t60) REVERT: I 100 MET cc_start: 0.8489 (mtt) cc_final: 0.8241 (mtt) REVERT: J 42 GLN cc_start: 0.7316 (mt0) cc_final: 0.6393 (mp10) REVERT: M 14 SER cc_start: 0.7743 (m) cc_final: 0.7417 (p) REVERT: M 32 SER cc_start: 0.8968 (t) cc_final: 0.8525 (p) REVERT: N 38 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6429 (ptm160) REVERT: N 39 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7579 (mm) REVERT: Q 37 GLN cc_start: 0.8173 (tt0) cc_final: 0.7779 (tt0) REVERT: Q 52 SER cc_start: 0.8426 (p) cc_final: 0.7955 (m) REVERT: Q 86 TYR cc_start: 0.8742 (m-80) cc_final: 0.8243 (m-80) REVERT: B 49 GLU cc_start: 0.8267 (pp20) cc_final: 0.7984 (pp20) REVERT: B 107 ASP cc_start: 0.7975 (t0) cc_final: 0.7469 (t0) REVERT: B 115 SER cc_start: 0.8630 (t) cc_final: 0.8053 (m) REVERT: B 153 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 190 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: B 411 ASN cc_start: 0.7793 (m-40) cc_final: 0.7208 (t0) REVERT: C 35 TRP cc_start: 0.8448 (m100) cc_final: 0.7771 (m100) REVERT: C 67 ASN cc_start: 0.8234 (t0) cc_final: 0.7415 (t0) REVERT: C 161 MET cc_start: 0.8027 (tpt) cc_final: 0.7422 (tpt) REVERT: C 486 TYR cc_start: 0.8489 (m-80) cc_final: 0.7838 (m-80) outliers start: 151 outliers final: 114 residues processed: 615 average time/residue: 0.2005 time to fit residues: 191.8904 Evaluate side-chains 616 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 497 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 58 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 234 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 291 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 73 GLN G 42 GLN J 17 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100AASN N 102 HIS P 100AASN Q 89 GLN A 114 GLN A 302 ASN C 280 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113817 restraints weight = 42179.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112719 restraints weight = 33099.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114589 restraints weight = 30436.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114777 restraints weight = 23011.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115225 restraints weight = 21545.158| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27809 Z= 0.141 Angle : 0.710 16.214 37981 Z= 0.336 Chirality : 0.047 0.413 4464 Planarity : 0.004 0.058 4620 Dihedral : 8.441 85.382 5859 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 3.76 % Allowed : 20.27 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.77 (0.14), residues: 3190 helix: 0.77 (0.27), residues: 405 sheet: -0.18 (0.15), residues: 1058 loop : -1.01 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 82A TYR 0.022 0.001 TYR L 87 PHE 0.017 0.002 PHE B 53 TRP 0.035 0.002 TRP B 35 HIS 0.006 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00319 (27644) covalent geometry : angle 0.66505 (37536) SS BOND : bond 0.00370 ( 50) SS BOND : angle 1.44651 ( 100) hydrogen bonds : bond 0.03554 ( 697) hydrogen bonds : angle 5.21589 ( 1761) link_ALPHA1-2 : bond 0.00577 ( 13) link_ALPHA1-2 : angle 2.14411 ( 39) link_ALPHA1-3 : bond 0.00893 ( 13) link_ALPHA1-3 : angle 2.39047 ( 39) link_ALPHA1-6 : bond 0.00617 ( 13) link_ALPHA1-6 : angle 1.76319 ( 39) link_BETA1-4 : bond 0.00940 ( 29) link_BETA1-4 : angle 2.80623 ( 87) link_NAG-ASN : bond 0.00423 ( 47) link_NAG-ASN : angle 2.83711 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 535 time to evaluate : 1.032 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: symmetry clash revert: symmetry clash REVERT: D 38 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.5530 (ptm-80) REVERT: D 100 MET cc_start: 0.7986 (mtt) cc_final: 0.7582 (mtt) REVERT: E 85 ASP cc_start: 0.7165 (m-30) cc_final: 0.6870 (m-30) REVERT: E 89 GLN cc_start: 0.7712 (pt0) cc_final: 0.7310 (pt0) REVERT: I 47 TRP cc_start: 0.8402 (t60) cc_final: 0.8050 (t60) REVERT: I 86 ASP cc_start: 0.6376 (OUTLIER) cc_final: 0.6054 (t70) REVERT: J 42 GLN cc_start: 0.7259 (mt0) cc_final: 0.6839 (mp10) REVERT: K 82 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8543 (tp) REVERT: M 32 SER cc_start: 0.8782 (t) cc_final: 0.8504 (p) REVERT: N 39 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8023 (mm) REVERT: Q 37 GLN cc_start: 0.7802 (tt0) cc_final: 0.7482 (tt0) REVERT: Q 52 SER cc_start: 0.8268 (p) cc_final: 0.7988 (m) REVERT: Q 86 TYR cc_start: 0.8467 (m-80) cc_final: 0.7873 (m-80) REVERT: B 107 ASP cc_start: 0.7481 (t0) cc_final: 0.7120 (t0) REVERT: B 115 SER cc_start: 0.8652 (t) cc_final: 0.8229 (m) REVERT: B 190 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: B 411 ASN cc_start: 0.7779 (m-40) cc_final: 0.7203 (t0) REVERT: C 35 TRP cc_start: 0.7957 (m100) cc_final: 0.7408 (m100) REVERT: C 67 ASN cc_start: 0.7723 (t0) cc_final: 0.7210 (t0) REVERT: C 486 TYR cc_start: 0.7899 (m-80) cc_final: 0.7521 (m-80) REVERT: O 61 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7655 (mtm110) outliers start: 106 outliers final: 80 residues processed: 592 average time/residue: 0.2070 time to fit residues: 188.5638 Evaluate side-chains 594 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 509 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 238 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 100 optimal weight: 0.0170 chunk 80 optimal weight: 6.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 GLN A 114 GLN C 67 ASN ** C 374 HIS ** 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 = 0.3833 r_free = 0.3833 target = 0.146223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113877 restraints weight = 42241.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111916 restraints weight = 35376.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112986 restraints weight = 43700.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114190 restraints weight = 27916.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114914 restraints weight = 23956.630| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27809 Z= 0.155 Angle : 0.717 15.929 37981 Z= 0.341 Chirality : 0.047 0.403 4464 Planarity : 0.004 0.059 4620 Dihedral : 8.301 84.644 5859 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 4.04 % Allowed : 20.66 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.77 (0.15), residues: 3190 helix: 0.76 (0.27), residues: 407 sheet: -0.20 (0.15), residues: 1075 loop : -1.01 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 82A TYR 0.023 0.001 TYR L 87 PHE 0.018 0.002 PHE C 53 TRP 0.063 0.002 TRP B 35 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00361 (27644) covalent geometry : angle 0.67226 (37536) SS BOND : bond 0.00297 ( 50) SS BOND : angle 1.80659 ( 100) hydrogen bonds : bond 0.03497 ( 697) hydrogen bonds : angle 5.19701 ( 1761) link_ALPHA1-2 : bond 0.00549 ( 13) link_ALPHA1-2 : angle 2.12808 ( 39) link_ALPHA1-3 : bond 0.00850 ( 13) link_ALPHA1-3 : angle 2.36877 ( 39) link_ALPHA1-6 : bond 0.00606 ( 13) link_ALPHA1-6 : angle 1.76582 ( 39) link_BETA1-4 : bond 0.00925 ( 29) link_BETA1-4 : angle 2.79011 ( 87) link_NAG-ASN : bond 0.00452 ( 47) link_NAG-ASN : angle 2.71050 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 523 time to evaluate : 1.140 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 82 MET cc_start: 0.6410 (ttm) cc_final: 0.6000 (mtm) REVERT: E 85 ASP cc_start: 0.7211 (m-30) cc_final: 0.6951 (m-30) REVERT: G 66 TRP cc_start: 0.5866 (t60) cc_final: 0.5609 (t60) REVERT: H 34 MET cc_start: 0.6605 (mmm) cc_final: 0.6401 (mmt) REVERT: I 47 TRP cc_start: 0.8396 (t60) cc_final: 0.8028 (t60) REVERT: I 86 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.6080 (t70) REVERT: J 42 GLN cc_start: 0.7234 (mt0) cc_final: 0.6814 (mp10) REVERT: K 82 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8574 (tp) REVERT: K 82 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8025 (mtm110) REVERT: L 98 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: M 32 SER cc_start: 0.8763 (t) cc_final: 0.8489 (p) REVERT: M 37 GLN cc_start: 0.7985 (tt0) cc_final: 0.7713 (tt0) REVERT: N 39 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7992 (mm) REVERT: P 100 ASN cc_start: 0.7215 (OUTLIER) cc_final: 0.6614 (t0) REVERT: Q 37 GLN cc_start: 0.7811 (tt0) cc_final: 0.7513 (tt0) REVERT: Q 52 SER cc_start: 0.8270 (p) cc_final: 0.8017 (m) REVERT: Q 86 TYR cc_start: 0.8468 (m-80) cc_final: 0.7957 (m-80) REVERT: B 107 ASP cc_start: 0.7490 (t0) cc_final: 0.7095 (t0) REVERT: B 115 SER cc_start: 0.8640 (t) cc_final: 0.8218 (m) REVERT: B 190 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: B 411 ASN cc_start: 0.7810 (m-40) cc_final: 0.7243 (t0) REVERT: B 646 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 35 TRP cc_start: 0.8007 (m100) cc_final: 0.7459 (m100) REVERT: C 67 ASN cc_start: 0.7690 (t0) cc_final: 0.7269 (t0) REVERT: C 161 MET cc_start: 0.7409 (tpt) cc_final: 0.7075 (tpt) REVERT: C 486 TYR cc_start: 0.7908 (m-80) cc_final: 0.7579 (m-80) outliers start: 114 outliers final: 88 residues processed: 588 average time/residue: 0.2045 time to fit residues: 185.7651 Evaluate side-chains 602 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 507 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 287 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 23 optimal weight: 0.0040 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 GLN K 6 GLN B 203 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120027 restraints weight = 41918.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118189 restraints weight = 40846.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119835 restraints weight = 39734.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120376 restraints weight = 26576.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120656 restraints weight = 24721.134| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27809 Z= 0.136 Angle : 0.699 16.088 37981 Z= 0.331 Chirality : 0.046 0.397 4464 Planarity : 0.004 0.054 4620 Dihedral : 8.078 83.044 5859 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 3.97 % Allowed : 20.84 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.72 (0.15), residues: 3190 helix: 0.87 (0.27), residues: 404 sheet: -0.13 (0.16), residues: 1060 loop : -1.02 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 37 TYR 0.025 0.001 TYR L 87 PHE 0.019 0.001 PHE C 53 TRP 0.060 0.002 TRP B 35 HIS 0.004 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00312 (27644) covalent geometry : angle 0.65944 (37536) SS BOND : bond 0.00229 ( 50) SS BOND : angle 1.22322 ( 100) hydrogen bonds : bond 0.03303 ( 697) hydrogen bonds : angle 5.11612 ( 1761) link_ALPHA1-2 : bond 0.00564 ( 13) link_ALPHA1-2 : angle 2.07746 ( 39) link_ALPHA1-3 : bond 0.00848 ( 13) link_ALPHA1-3 : angle 2.29986 ( 39) link_ALPHA1-6 : bond 0.00619 ( 13) link_ALPHA1-6 : angle 1.71431 ( 39) link_BETA1-4 : bond 0.00927 ( 29) link_BETA1-4 : angle 2.72727 ( 87) link_NAG-ASN : bond 0.00403 ( 47) link_NAG-ASN : angle 2.61877 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 532 time to evaluate : 1.107 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: symmetry clash REVERT: D 100 MET cc_start: 0.7802 (mtt) cc_final: 0.7487 (mtt) REVERT: E 20 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7416 (mmm160) REVERT: E 85 ASP cc_start: 0.7200 (m-30) cc_final: 0.6946 (m-30) REVERT: G 66 TRP cc_start: 0.5913 (t60) cc_final: 0.5711 (t60) REVERT: H 34 MET cc_start: 0.6602 (mmm) cc_final: 0.6391 (mmt) REVERT: I 47 TRP cc_start: 0.8286 (t60) cc_final: 0.8015 (t60) REVERT: I 86 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.6186 (t70) REVERT: J 42 GLN cc_start: 0.7240 (mt0) cc_final: 0.6841 (mp10) REVERT: K 82 ARG cc_start: 0.8430 (mtm110) cc_final: 0.7768 (mtm110) REVERT: L 98 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: N 39 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8007 (mm) REVERT: Q 33 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8052 (tp) REVERT: Q 37 GLN cc_start: 0.7802 (tt0) cc_final: 0.7502 (tt0) REVERT: Q 52 SER cc_start: 0.8289 (p) cc_final: 0.8031 (m) REVERT: Q 86 TYR cc_start: 0.8478 (m-80) cc_final: 0.7945 (m-80) REVERT: B 107 ASP cc_start: 0.7502 (t0) cc_final: 0.7132 (t0) REVERT: B 115 SER cc_start: 0.8684 (t) cc_final: 0.8240 (m) REVERT: B 190 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: B 411 ASN cc_start: 0.7786 (m-40) cc_final: 0.7271 (t0) REVERT: C 35 TRP cc_start: 0.8039 (m100) cc_final: 0.7489 (m100) REVERT: C 67 ASN cc_start: 0.7715 (t0) cc_final: 0.7301 (t0) REVERT: C 161 MET cc_start: 0.7465 (tpt) cc_final: 0.7049 (tpt) REVERT: O 61 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7557 (mtm110) outliers start: 112 outliers final: 91 residues processed: 594 average time/residue: 0.2007 time to fit residues: 184.7889 Evaluate side-chains 608 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 512 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 25 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 210 optimal weight: 0.5980 chunk 156 optimal weight: 0.4980 chunk 189 optimal weight: 4.9990 chunk 294 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 262 optimal weight: 0.6980 chunk 276 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 GLN A 114 GLN C 249 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121374 restraints weight = 41648.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119307 restraints weight = 40367.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121203 restraints weight = 38545.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121718 restraints weight = 26587.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121956 restraints weight = 25168.540| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.003 0.068 27809 Z= 0.131 Angle : 0.705 16.439 37981 Z= 0.334 Chirality : 0.046 0.394 4464 Planarity : 0.004 0.054 4620 Dihedral : 7.917 81.684 5859 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 3.76 % Allowed : 21.19 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.72 (0.15), residues: 3190 helix: 0.82 (0.27), residues: 405 sheet: -0.11 (0.16), residues: 1054 loop : -1.00 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 166 TYR 0.020 0.001 TYR H 98 PHE 0.017 0.001 PHE C 53 TRP 0.066 0.002 TRP B 35 HIS 0.004 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00301 (27644) covalent geometry : angle 0.66686 (37536) SS BOND : bond 0.00262 ( 50) SS BOND : angle 1.58074 ( 100) hydrogen bonds : bond 0.03266 ( 697) hydrogen bonds : angle 5.07891 ( 1761) link_ALPHA1-2 : bond 0.00544 ( 13) link_ALPHA1-2 : angle 2.05832 ( 39) link_ALPHA1-3 : bond 0.00856 ( 13) link_ALPHA1-3 : angle 2.25816 ( 39) link_ALPHA1-6 : bond 0.00613 ( 13) link_ALPHA1-6 : angle 1.69140 ( 39) link_BETA1-4 : bond 0.00913 ( 29) link_BETA1-4 : angle 2.68289 ( 87) link_NAG-ASN : bond 0.00436 ( 47) link_NAG-ASN : angle 2.39819 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 523 time to evaluate : 1.173 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: E 85 ASP cc_start: 0.7128 (m-30) cc_final: 0.6881 (m-30) REVERT: H 67 PHE cc_start: 0.5770 (m-10) cc_final: 0.4288 (m-10) REVERT: I 5 ARG cc_start: 0.7375 (mmp-170) cc_final: 0.5483 (mmm160) REVERT: I 47 TRP cc_start: 0.8199 (t60) cc_final: 0.7975 (t60) REVERT: I 86 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6112 (t70) REVERT: I 100 TYR cc_start: 0.8868 (t80) cc_final: 0.8569 (t80) REVERT: J 42 GLN cc_start: 0.7182 (mt0) cc_final: 0.6835 (mp10) REVERT: K 82 ARG cc_start: 0.8441 (mtm110) cc_final: 0.7790 (mtm110) REVERT: L 98 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: M 37 GLN cc_start: 0.7956 (tt0) cc_final: 0.7702 (tt0) REVERT: N 38 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7679 (ptm160) REVERT: N 39 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8001 (mm) REVERT: Q 33 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8017 (tp) REVERT: Q 37 GLN cc_start: 0.7768 (tt0) cc_final: 0.7458 (tt0) REVERT: Q 52 SER cc_start: 0.8256 (p) cc_final: 0.8026 (m) REVERT: Q 86 TYR cc_start: 0.8447 (m-80) cc_final: 0.7925 (m-80) REVERT: B 107 ASP cc_start: 0.7493 (t0) cc_final: 0.7141 (t0) REVERT: B 115 SER cc_start: 0.8691 (t) cc_final: 0.8239 (m) REVERT: B 190 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: B 411 ASN cc_start: 0.7763 (m-40) cc_final: 0.7257 (t0) REVERT: C 35 TRP cc_start: 0.7991 (m100) cc_final: 0.7453 (m100) REVERT: C 67 ASN cc_start: 0.7674 (t0) cc_final: 0.7260 (t0) REVERT: C 161 MET cc_start: 0.7404 (tpt) cc_final: 0.6997 (tpt) REVERT: O 61 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7560 (mtm110) outliers start: 106 outliers final: 88 residues processed: 583 average time/residue: 0.2066 time to fit residues: 185.8153 Evaluate side-chains 601 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 507 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 24 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 238 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 GLN F 73 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN A 114 GLN ** C 374 HIS ** 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 = 0.3915 r_free = 0.3915 target = 0.152166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120589 restraints weight = 41832.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118885 restraints weight = 35281.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120252 restraints weight = 39557.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120934 restraints weight = 27295.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121199 restraints weight = 24775.514| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27809 Z= 0.159 Angle : 0.717 16.890 37981 Z= 0.341 Chirality : 0.047 0.392 4464 Planarity : 0.004 0.057 4620 Dihedral : 7.912 81.485 5859 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 3.61 % Allowed : 21.44 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.73 (0.15), residues: 3190 helix: 0.81 (0.27), residues: 399 sheet: -0.16 (0.15), residues: 1087 loop : -0.99 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 5 TYR 0.021 0.001 TYR H 90 PHE 0.014 0.001 PHE C 53 TRP 0.073 0.002 TRP B 35 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00373 (27644) covalent geometry : angle 0.68012 (37536) SS BOND : bond 0.00355 ( 50) SS BOND : angle 1.23199 ( 100) hydrogen bonds : bond 0.03361 ( 697) hydrogen bonds : angle 5.09887 ( 1761) link_ALPHA1-2 : bond 0.00513 ( 13) link_ALPHA1-2 : angle 2.03463 ( 39) link_ALPHA1-3 : bond 0.00818 ( 13) link_ALPHA1-3 : angle 2.25510 ( 39) link_ALPHA1-6 : bond 0.00595 ( 13) link_ALPHA1-6 : angle 1.70838 ( 39) link_BETA1-4 : bond 0.00900 ( 29) link_BETA1-4 : angle 2.71278 ( 87) link_NAG-ASN : bond 0.00462 ( 47) link_NAG-ASN : angle 2.51844 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 521 time to evaluate : 1.095 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: E 20 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7444 (mmm160) REVERT: H 67 PHE cc_start: 0.5782 (m-10) cc_final: 0.5446 (m-10) REVERT: I 47 TRP cc_start: 0.8241 (t60) cc_final: 0.8014 (t60) REVERT: I 86 ASP cc_start: 0.6447 (OUTLIER) cc_final: 0.6085 (t70) REVERT: J 42 GLN cc_start: 0.7231 (mt0) cc_final: 0.6847 (mp10) REVERT: K 82 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8583 (tp) REVERT: K 82 ARG cc_start: 0.8470 (mtm110) cc_final: 0.7708 (mtm110) REVERT: L 74 THR cc_start: 0.8022 (m) cc_final: 0.7750 (p) REVERT: L 98 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: M 32 SER cc_start: 0.8775 (t) cc_final: 0.8444 (p) REVERT: N 38 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7655 (ptm160) REVERT: N 39 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8010 (mm) REVERT: Q 33 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8030 (tp) REVERT: Q 37 GLN cc_start: 0.7803 (tt0) cc_final: 0.7483 (tt0) REVERT: Q 52 SER cc_start: 0.8300 (p) cc_final: 0.8086 (m) REVERT: Q 86 TYR cc_start: 0.8487 (m-80) cc_final: 0.7951 (m-80) REVERT: B 107 ASP cc_start: 0.7505 (t0) cc_final: 0.7105 (t0) REVERT: B 115 SER cc_start: 0.8721 (t) cc_final: 0.8268 (m) REVERT: B 190 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: B 411 ASN cc_start: 0.7740 (m-40) cc_final: 0.7236 (t0) REVERT: C 35 TRP cc_start: 0.8047 (m100) cc_final: 0.7547 (m100) REVERT: C 67 ASN cc_start: 0.7744 (t0) cc_final: 0.7132 (t0) REVERT: C 161 MET cc_start: 0.7411 (tpt) cc_final: 0.7096 (tpt) REVERT: O 61 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7784 (mtm110) outliers start: 102 outliers final: 91 residues processed: 580 average time/residue: 0.2067 time to fit residues: 184.6108 Evaluate side-chains 604 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 506 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 678 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain O residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 120 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 295 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.151905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120347 restraints weight = 41566.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118012 restraints weight = 41077.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119963 restraints weight = 39204.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120617 restraints weight = 26669.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120824 restraints weight = 24870.809| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.681 27809 Z= 0.283 Angle : 0.913 65.600 37981 Z= 0.452 Chirality : 0.048 0.475 4464 Planarity : 0.005 0.126 4620 Dihedral : 7.913 81.480 5857 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.80 % Rotamer: Outliers : 3.69 % Allowed : 21.72 % Favored : 74.59 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.32 % 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: -0.74 (0.15), residues: 3190 helix: 0.78 (0.27), residues: 399 sheet: -0.17 (0.15), residues: 1087 loop : -0.99 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG I 5 TYR 0.023 0.002 TYR I 100K PHE 0.014 0.001 PHE H 67 TRP 0.070 0.002 TRP B 35 HIS 0.004 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00631 (27644) covalent geometry : angle 0.88562 (37536) SS BOND : bond 0.06253 ( 50) SS BOND : angle 1.54057 ( 100) hydrogen bonds : bond 0.03391 ( 697) hydrogen bonds : angle 5.10488 ( 1761) link_ALPHA1-2 : bond 0.00516 ( 13) link_ALPHA1-2 : angle 2.03550 ( 39) link_ALPHA1-3 : bond 0.00817 ( 13) link_ALPHA1-3 : angle 2.25398 ( 39) link_ALPHA1-6 : bond 0.00594 ( 13) link_ALPHA1-6 : angle 1.71232 ( 39) link_BETA1-4 : bond 0.00901 ( 29) link_BETA1-4 : angle 2.71596 ( 87) link_NAG-ASN : bond 0.00455 ( 47) link_NAG-ASN : angle 2.51948 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6436.94 seconds wall clock time: 112 minutes 1.80 seconds (6721.80 seconds total)