Starting phenix.real_space_refine on Tue Apr 7 07:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9piv_71678/04_2026/9piv_71678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9piv_71678/04_2026/9piv_71678.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9piv_71678/04_2026/9piv_71678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9piv_71678/04_2026/9piv_71678.map" model { file = "/net/cci-nas-00/data/ceres_data/9piv_71678/04_2026/9piv_71678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9piv_71678/04_2026/9piv_71678.cif" } 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= 0.007 sd= 0.051 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 135 5.16 5 C 15855 2.51 5 N 4290 2.21 5 O 5058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25338 Number of models: 1 Model: "" Number of chains: 45 Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 95} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "B" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3534 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 966 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "I" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 95} Chain: "O" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "Q" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "E" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3534 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "C" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 966 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 95} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "F" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3534 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "D" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 966 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" 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: "l" 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.85, per 1000 atoms: 0.23 Number of scatterers: 25338 At special positions: 0 Unit cell: (137.94, 144.21, 152.57, 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 135 16.00 O 5058 8.00 N 4290 7.00 C 15855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN V 4 " - " MAN V 5 " " MAN c 4 " - " MAN c 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA V 3 " - " MAN V 6 " " BMA W 3 " - " MAN W 5 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA j 3 " - " MAN j 6 " " BMA k 3 " - " MAN k 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 611 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 156 " " NAG B 602 " - " ASN B 160 " " NAG B 603 " - " ASN B 295 " " NAG B 604 " - " ASN B 332 " " NAG B 605 " - " ASN B 339 " " NAG B 606 " - " ASN B 448 " " NAG B 607 " - " ASN B 133 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 611 " " NAG C 703 " - " ASN C 637 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 611 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 156 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 332 " " NAG E 605 " - " ASN E 339 " " NAG E 606 " - " ASN E 448 " " NAG E 607 " - " ASN E 133 " " NAG F 601 " - " ASN F 156 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 295 " " NAG F 604 " - " ASN F 332 " " NAG F 605 " - " ASN F 339 " " NAG F 606 " - " ASN F 448 " " NAG F 607 " - " ASN F 133 " " NAG S 1 " - " ASN B 88 " " NAG T 1 " - " ASN B 197 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 262 " " NAG W 1 " - " ASN B 276 " " NAG X 1 " - " ASN B 386 " " NAG Y 1 " - " ASN B 392 " " NAG Z 1 " - " ASN E 88 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 234 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 276 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 392 " " NAG g 1 " - " ASN F 88 " " NAG h 1 " - " ASN F 197 " " NAG i 1 " - " ASN F 234 " " NAG j 1 " - " ASN F 262 " " NAG k 1 " - " ASN F 276 " " NAG l 1 " - " ASN F 386 " " NAG m 1 " - " ASN F 392 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 949.2 milliseconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5646 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 63 sheets defined 18.3% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.071A pdb=" N VAL G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.695A pdb=" N ASN J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'H' and resid 25 through 30 removed outlier: 3.700A pdb=" N THR H 30 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.743A pdb=" N ARG H 64 " --> pdb=" O ASN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.576A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.949A 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 354 removed outlier: 3.818A 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 475 through 480 removed outlier: 3.533A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 484 removed outlier: 5.091A pdb=" N TYR B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 570 through 596 removed outlier: 4.242A pdb=" N LYS A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 658 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.072A pdb=" N VAL I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.695A pdb=" N ASN O 32 " --> pdb=" O ILE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'M' and resid 25 through 30 removed outlier: 3.700A pdb=" N THR M 30 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.743A pdb=" N ARG M 64 " --> pdb=" O ASN M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.576A pdb=" N THR M 87 " --> pdb=" O SER M 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.628A pdb=" N PHE Q 83 " --> pdb=" O PRO Q 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.949A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.818A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.532A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 484 removed outlier: 5.091A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 481 through 484' Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 570 through 596 removed outlier: 4.242A pdb=" N LYS C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 658 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.071A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.694A pdb=" N ASN P 32 " --> pdb=" O ILE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'N' and resid 25 through 30 removed outlier: 3.700A pdb=" N THR N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.743A pdb=" N ARG N 64 " --> pdb=" O ASN N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 73 through 75 No H-bonds generated for 'chain 'N' and resid 73 through 75' Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.575A pdb=" N THR N 87 " --> pdb=" O SER N 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.628A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 98 through 117 removed outlier: 3.949A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.819A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 480 removed outlier: 3.533A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 484 removed outlier: 5.091A pdb=" N TYR F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.242A pdb=" N LYS D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.426A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.654A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'J' and resid 57 through 58 removed outlier: 5.523A pdb=" N LEU J 45 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 57 through 58 removed outlier: 5.523A pdb=" N LEU J 45 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.451A pdb=" N LEU H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.166A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.512A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.299A pdb=" N VAL A 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR A 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR B 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS A 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.763A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.791A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AB9, first strand: chain 'B' and resid 200 through 203 removed outlier: 5.909A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.604A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N ILE B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 274 removed outlier: 10.511A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N ILE B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 312 removed outlier: 6.892A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.425A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.654A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'O' and resid 57 through 58 removed outlier: 5.524A pdb=" N LEU O 45 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR O 40 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 57 through 58 removed outlier: 5.524A pdb=" N LEU O 45 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR O 40 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.451A pdb=" N LEU M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL M 50 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.166A pdb=" N VAL M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.512A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AD7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.299A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.763A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.791A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AE3, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.908A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.603A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.760A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.511A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.760A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.892A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.425A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.654A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'P' and resid 57 through 58 removed outlier: 5.523A pdb=" N LEU P 45 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR P 40 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 57 through 58 removed outlier: 5.523A pdb=" N LEU P 45 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR P 40 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AF5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.451A pdb=" N LEU N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL N 50 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.166A pdb=" N VAL N 102 " --> pdb=" O ARG N 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.511A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AG1, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.299A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.763A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.791A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AG5, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AG6, first strand: chain 'F' and resid 200 through 203 removed outlier: 5.908A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.604A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 271 through 274 removed outlier: 10.511A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.892A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7921 1.34 - 1.46: 6500 1.46 - 1.59: 11298 1.59 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 25899 Sorted by residual: bond pdb=" N GLY L 99 " pdb=" CA GLY L 99 " ideal model delta sigma weight residual 1.444 1.479 -0.035 9.30e-03 1.16e+04 1.46e+01 bond pdb=" N GLY R 99 " pdb=" CA GLY R 99 " ideal model delta sigma weight residual 1.444 1.479 -0.035 9.30e-03 1.16e+04 1.42e+01 bond pdb=" N GLY Q 99 " pdb=" CA GLY Q 99 " ideal model delta sigma weight residual 1.444 1.479 -0.035 9.30e-03 1.16e+04 1.40e+01 bond pdb=" N ILE O 51 " pdb=" CA ILE O 51 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N ILE J 51 " pdb=" CA ILE J 51 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.12e+01 ... (remaining 25894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 32715 2.03 - 4.06: 2080 4.06 - 6.08: 353 6.08 - 8.11: 24 8.11 - 10.14: 12 Bond angle restraints: 35184 Sorted by residual: angle pdb=" CA TYR Q 91 " pdb=" C TYR Q 91 " pdb=" O TYR Q 91 " ideal model delta sigma weight residual 122.37 115.56 6.81 1.15e+00 7.56e-01 3.51e+01 angle pdb=" CA TYR L 91 " pdb=" C TYR L 91 " pdb=" O TYR L 91 " ideal model delta sigma weight residual 122.37 115.59 6.78 1.15e+00 7.56e-01 3.47e+01 angle pdb=" CA TYR R 91 " pdb=" C TYR R 91 " pdb=" O TYR R 91 " ideal model delta sigma weight residual 122.37 115.59 6.78 1.15e+00 7.56e-01 3.47e+01 angle pdb=" C TYR L 91 " pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " ideal model delta sigma weight residual 112.03 103.20 8.83 1.56e+00 4.11e-01 3.20e+01 angle pdb=" C TYR Q 91 " pdb=" CA TYR Q 91 " pdb=" CB TYR Q 91 " ideal model delta sigma weight residual 112.03 103.23 8.80 1.56e+00 4.11e-01 3.18e+01 ... (remaining 35179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 15864 21.46 - 42.93: 576 42.93 - 64.39: 114 64.39 - 85.85: 69 85.85 - 107.31: 45 Dihedral angle restraints: 16668 sinusoidal: 7878 harmonic: 8790 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.15 37.15 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.14 37.14 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.13 37.13 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 16665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3283 0.075 - 0.150: 772 0.150 - 0.225: 83 0.225 - 0.300: 20 0.300 - 0.375: 9 Chirality restraints: 4167 Sorted by residual: chirality pdb=" C1 NAG k 1 " pdb=" ND2 ASN F 276 " pdb=" C2 NAG k 1 " pdb=" O5 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN E 276 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4164 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 640 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C GLN D 640 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN D 640 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE D 641 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 640 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C GLN C 640 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN C 640 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE C 641 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 640 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C GLN A 640 " 0.065 2.00e-02 2.50e+03 pdb=" O GLN A 640 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 641 " -0.022 2.00e-02 2.50e+03 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6265 2.81 - 3.34: 22469 3.34 - 3.86: 41581 3.86 - 4.38: 48140 4.38 - 4.90: 83542 Nonbonded interactions: 201997 Sorted by model distance: nonbonded pdb=" O PRO Q 8 " pdb=" OG1 THR Q 102 " model vdw 2.292 3.040 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.292 3.040 nonbonded pdb=" O PRO R 8 " pdb=" OG1 THR R 102 " model vdw 2.293 3.040 nonbonded pdb=" O THR F 303 " pdb=" OG1 THR F 303 " model vdw 2.346 3.040 nonbonded pdb=" O THR E 303 " pdb=" OG1 THR E 303 " model vdw 2.346 3.040 ... (remaining 201992 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'm' } ncs_group { reference = chain 'V' selection = chain 'c' selection = chain 'j' } ncs_group { reference = chain 'W' selection = chain 'd' selection = chain 'k' } ncs_group { reference = chain 'X' selection = chain 'e' selection = chain 'l' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.780 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.007 0.055 26040 Z= 0.367 Angle : 1.120 10.140 35562 Z= 0.633 Chirality : 0.065 0.375 4167 Planarity : 0.007 0.102 4377 Dihedral : 13.535 107.314 10887 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.11 % Allowed : 0.79 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.69 (0.15), residues: 3015 helix: 0.17 (0.25), residues: 375 sheet: 0.83 (0.16), residues: 999 loop : 0.43 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG H 100B TYR 0.033 0.003 TYR L 71 PHE 0.040 0.004 PHE F 176 TRP 0.024 0.002 TRP F 479 HIS 0.023 0.003 HIS N 100C Details of bonding type rmsd covalent geometry : bond 0.00703 (25899) covalent geometry : angle 1.10796 (35184) SS BOND : bond 0.00522 ( 45) SS BOND : angle 1.68074 ( 90) hydrogen bonds : bond 0.12523 ( 969) hydrogen bonds : angle 8.20696 ( 2736) link_ALPHA1-2 : bond 0.00717 ( 3) link_ALPHA1-2 : angle 0.96356 ( 9) link_ALPHA1-3 : bond 0.00903 ( 6) link_ALPHA1-3 : angle 2.64416 ( 18) link_ALPHA1-6 : bond 0.01251 ( 6) link_ALPHA1-6 : angle 1.94931 ( 18) link_BETA1-4 : bond 0.00551 ( 30) link_BETA1-4 : angle 1.53127 ( 90) link_NAG-ASN : bond 0.00213 ( 51) link_NAG-ASN : angle 2.25226 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 396 time to evaluate : 0.789 Fit side-chains REVERT: J 24 VAL cc_start: 0.8891 (t) cc_final: 0.8441 (p) REVERT: J 82 ASN cc_start: 0.7492 (p0) cc_final: 0.7236 (p0) REVERT: J 100 LYS cc_start: 0.8539 (ptpt) cc_final: 0.8318 (ptmm) REVERT: B 308 ARG cc_start: 0.7349 (mmm160) cc_final: 0.6989 (mmm160) REVERT: B 326 ILE cc_start: 0.6532 (mm) cc_final: 0.6061 (mm) REVERT: I 5 THR cc_start: 0.6777 (p) cc_final: 0.6397 (p) REVERT: O 24 VAL cc_start: 0.8808 (t) cc_final: 0.8473 (p) REVERT: O 82 ASN cc_start: 0.7757 (p0) cc_final: 0.7445 (p0) REVERT: Q 18 ARG cc_start: 0.6493 (ttp80) cc_final: 0.6176 (mtp180) REVERT: E 95 MET cc_start: 0.9007 (ptm) cc_final: 0.8555 (ptp) REVERT: E 180 ASP cc_start: 0.7571 (m-30) cc_final: 0.7358 (m-30) REVERT: E 308 ARG cc_start: 0.7310 (mmm160) cc_final: 0.7078 (mmm160) REVERT: E 326 ILE cc_start: 0.6464 (mm) cc_final: 0.6248 (mm) REVERT: C 530 MET cc_start: 0.8960 (mtp) cc_final: 0.8382 (mtp) REVERT: K 90 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8180 (pp30) REVERT: P 24 VAL cc_start: 0.8830 (t) cc_final: 0.8410 (p) REVERT: P 82 ASN cc_start: 0.7846 (p0) cc_final: 0.7638 (p0) REVERT: N 58 MET cc_start: 0.8431 (mtp) cc_final: 0.8200 (mtp) REVERT: N 100 ASP cc_start: 0.8021 (m-30) cc_final: 0.7792 (m-30) REVERT: R 75 ILE cc_start: 0.7066 (mt) cc_final: 0.6841 (mt) REVERT: F 161 MET cc_start: 0.6743 (ttm) cc_final: 0.6522 (ttt) REVERT: F 326 ILE cc_start: 0.6414 (mm) cc_final: 0.5670 (mm) REVERT: F 434 MET cc_start: 0.7957 (tmm) cc_final: 0.7365 (ttp) REVERT: D 530 MET cc_start: 0.9040 (mtp) cc_final: 0.8630 (mtt) outliers start: 3 outliers final: 0 residues processed: 399 average time/residue: 0.1914 time to fit residues: 114.1994 Evaluate side-chains 219 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 90 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN H 78 HIS B 462 ASN A 570 HIS A 607 ASN O 64 GLN M 78 HIS Q 89 GLN E 462 ASN C 607 ASN K 90 GLN N 78 HIS R 89 GLN F 462 ASN D 607 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071424 restraints weight = 55125.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073298 restraints weight = 32006.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073416 restraints weight = 22991.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073844 restraints weight = 21730.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074052 restraints weight = 20441.913| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26040 Z= 0.210 Angle : 0.683 6.405 35562 Z= 0.354 Chirality : 0.047 0.220 4167 Planarity : 0.005 0.029 4377 Dihedral : 10.672 93.887 5280 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.94 % Allowed : 5.32 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 1.04 (0.15), residues: 3015 helix: 1.25 (0.27), residues: 378 sheet: 0.81 (0.16), residues: 1020 loop : 0.62 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.018 0.002 TYR O 50 PHE 0.022 0.002 PHE Q 28 TRP 0.017 0.002 TRP B 112 HIS 0.010 0.002 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00479 (25899) covalent geometry : angle 0.66075 (35184) SS BOND : bond 0.00353 ( 45) SS BOND : angle 1.00687 ( 90) hydrogen bonds : bond 0.04792 ( 969) hydrogen bonds : angle 6.31952 ( 2736) link_ALPHA1-2 : bond 0.01074 ( 3) link_ALPHA1-2 : angle 1.93781 ( 9) link_ALPHA1-3 : bond 0.01511 ( 6) link_ALPHA1-3 : angle 1.76395 ( 18) link_ALPHA1-6 : bond 0.00636 ( 6) link_ALPHA1-6 : angle 1.66982 ( 18) link_BETA1-4 : bond 0.00485 ( 30) link_BETA1-4 : angle 1.54092 ( 90) link_NAG-ASN : bond 0.00289 ( 51) link_NAG-ASN : angle 2.27590 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.910 Fit side-chains REVERT: B 308 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7143 (mmm160) REVERT: B 317 PHE cc_start: 0.6696 (t80) cc_final: 0.6434 (t80) REVERT: A 607 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8457 (t0) REVERT: Q 18 ARG cc_start: 0.6688 (ttp80) cc_final: 0.6191 (mtp180) REVERT: C 530 MET cc_start: 0.9200 (mtp) cc_final: 0.8944 (mtp) REVERT: P 82 ASN cc_start: 0.7558 (p0) cc_final: 0.7273 (p0) REVERT: N 58 MET cc_start: 0.8671 (mtp) cc_final: 0.8352 (mtp) REVERT: F 161 MET cc_start: 0.7099 (ttm) cc_final: 0.6774 (ttt) outliers start: 25 outliers final: 13 residues processed: 248 average time/residue: 0.1563 time to fit residues: 63.7583 Evaluate side-chains 207 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain A residue 607 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain D residue 659 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 200 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN A 543 ASN O 82AASN C 543 ASN C 607 ASN R 89 GLN D 543 ASN D 607 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069751 restraints weight = 55529.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.070634 restraints weight = 34239.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071041 restraints weight = 25210.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071388 restraints weight = 23421.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071617 restraints weight = 21850.474| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26040 Z= 0.207 Angle : 0.637 8.193 35562 Z= 0.329 Chirality : 0.046 0.224 4167 Planarity : 0.004 0.035 4377 Dihedral : 9.605 89.436 5277 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.39 % Allowed : 6.85 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.76 (0.15), residues: 3015 helix: 0.89 (0.26), residues: 402 sheet: 0.85 (0.16), residues: 981 loop : 0.30 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 13 TYR 0.014 0.002 TYR P 50 PHE 0.020 0.002 PHE Q 28 TRP 0.020 0.001 TRP E 112 HIS 0.007 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00477 (25899) covalent geometry : angle 0.61426 (35184) SS BOND : bond 0.00411 ( 45) SS BOND : angle 0.77848 ( 90) hydrogen bonds : bond 0.04387 ( 969) hydrogen bonds : angle 5.86831 ( 2736) link_ALPHA1-2 : bond 0.00856 ( 3) link_ALPHA1-2 : angle 1.71149 ( 9) link_ALPHA1-3 : bond 0.01520 ( 6) link_ALPHA1-3 : angle 1.42139 ( 18) link_ALPHA1-6 : bond 0.00843 ( 6) link_ALPHA1-6 : angle 1.55530 ( 18) link_BETA1-4 : bond 0.00436 ( 30) link_BETA1-4 : angle 1.54667 ( 90) link_NAG-ASN : bond 0.00310 ( 51) link_NAG-ASN : angle 2.25055 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: O 3 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7724 (mm-40) REVERT: Q 18 ARG cc_start: 0.6631 (ttp80) cc_final: 0.6153 (mtp180) REVERT: C 530 MET cc_start: 0.9208 (mtp) cc_final: 0.8964 (mtp) REVERT: K 24 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7233 (mtm-85) REVERT: P 82 ASN cc_start: 0.7547 (p0) cc_final: 0.7223 (p0) REVERT: N 58 MET cc_start: 0.8701 (mtp) cc_final: 0.8404 (mtp) REVERT: F 161 MET cc_start: 0.7207 (ttm) cc_final: 0.6372 (tpt) REVERT: F 308 ARG cc_start: 0.7297 (mmm160) cc_final: 0.6942 (mmm160) REVERT: F 434 MET cc_start: 0.8643 (ttp) cc_final: 0.8356 (ttp) REVERT: D 530 MET cc_start: 0.9202 (mtp) cc_final: 0.8581 (mtp) REVERT: D 648 GLU cc_start: 0.7791 (tt0) cc_final: 0.7575 (tt0) outliers start: 37 outliers final: 22 residues processed: 243 average time/residue: 0.1502 time to fit residues: 59.8894 Evaluate side-chains 211 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain D residue 659 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 284 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 100 GLN B 293 GLN Q 89 GLN E 293 GLN C 607 ASN R 89 GLN F 293 GLN D 607 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.100348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.073405 restraints weight = 54437.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074336 restraints weight = 27510.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074821 restraints weight = 22214.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075494 restraints weight = 19985.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075624 restraints weight = 18255.678| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26040 Z= 0.117 Angle : 0.564 6.727 35562 Z= 0.287 Chirality : 0.044 0.234 4167 Planarity : 0.004 0.038 4377 Dihedral : 8.569 80.873 5277 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.39 % Allowed : 7.94 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.86 (0.16), residues: 3015 helix: 1.14 (0.27), residues: 402 sheet: 0.88 (0.16), residues: 1011 loop : 0.33 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 61 TYR 0.013 0.001 TYR J 50 PHE 0.015 0.002 PHE Q 28 TRP 0.018 0.001 TRP F 112 HIS 0.004 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00252 (25899) covalent geometry : angle 0.54116 (35184) SS BOND : bond 0.00292 ( 45) SS BOND : angle 0.61369 ( 90) hydrogen bonds : bond 0.03753 ( 969) hydrogen bonds : angle 5.42811 ( 2736) link_ALPHA1-2 : bond 0.00864 ( 3) link_ALPHA1-2 : angle 1.66012 ( 9) link_ALPHA1-3 : bond 0.01513 ( 6) link_ALPHA1-3 : angle 1.31277 ( 18) link_ALPHA1-6 : bond 0.01017 ( 6) link_ALPHA1-6 : angle 1.67781 ( 18) link_BETA1-4 : bond 0.00414 ( 30) link_BETA1-4 : angle 1.44975 ( 90) link_NAG-ASN : bond 0.00285 ( 51) link_NAG-ASN : angle 2.13161 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: G 24 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7364 (mtm180) REVERT: H 67 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 161 MET cc_start: 0.6967 (ttm) cc_final: 0.6709 (ttt) REVERT: O 3 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7726 (mm-40) REVERT: Q 18 ARG cc_start: 0.6914 (ttp80) cc_final: 0.6356 (mtp180) REVERT: C 621 GLU cc_start: 0.8415 (tt0) cc_final: 0.8207 (mt-10) REVERT: K 24 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7463 (mtm180) REVERT: P 82 ASN cc_start: 0.7587 (p0) cc_final: 0.7273 (p0) REVERT: N 58 MET cc_start: 0.8657 (mtp) cc_final: 0.8434 (mtp) REVERT: F 100 MET cc_start: 0.8809 (mtm) cc_final: 0.8518 (mtp) REVERT: F 161 MET cc_start: 0.7007 (ttm) cc_final: 0.6328 (tpt) outliers start: 37 outliers final: 17 residues processed: 242 average time/residue: 0.1608 time to fit residues: 63.1303 Evaluate side-chains 205 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 113 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 186 optimal weight: 0.2980 chunk 202 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 274 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 237 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 92 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AASN H 3 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN C 607 ASN K 92 ASN N 3 GLN D 577 GLN D 607 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.098840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069987 restraints weight = 55014.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071045 restraints weight = 33923.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.071594 restraints weight = 24768.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.072010 restraints weight = 22209.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072149 restraints weight = 20895.935| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26040 Z= 0.164 Angle : 0.578 5.691 35562 Z= 0.294 Chirality : 0.045 0.230 4167 Planarity : 0.004 0.039 4377 Dihedral : 8.183 74.700 5277 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.69 % Allowed : 8.73 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.77 (0.16), residues: 3015 helix: 1.07 (0.27), residues: 402 sheet: 0.85 (0.16), residues: 975 loop : 0.27 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 61 TYR 0.013 0.001 TYR P 50 PHE 0.017 0.002 PHE E 382 TRP 0.017 0.001 TRP F 112 HIS 0.009 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00374 (25899) covalent geometry : angle 0.55543 (35184) SS BOND : bond 0.00345 ( 45) SS BOND : angle 0.66207 ( 90) hydrogen bonds : bond 0.03848 ( 969) hydrogen bonds : angle 5.29877 ( 2736) link_ALPHA1-2 : bond 0.00728 ( 3) link_ALPHA1-2 : angle 1.68542 ( 9) link_ALPHA1-3 : bond 0.01485 ( 6) link_ALPHA1-3 : angle 1.41373 ( 18) link_ALPHA1-6 : bond 0.00880 ( 6) link_ALPHA1-6 : angle 1.92894 ( 18) link_BETA1-4 : bond 0.00410 ( 30) link_BETA1-4 : angle 1.40933 ( 90) link_NAG-ASN : bond 0.00302 ( 51) link_NAG-ASN : angle 2.12121 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 24 ARG cc_start: 0.7719 (mtm180) cc_final: 0.7368 (mtm180) REVERT: J 3 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7620 (mm-40) REVERT: J 38 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7480 (ptt180) REVERT: H 67 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8548 (mp) REVERT: I 18 ARG cc_start: 0.6519 (tpp80) cc_final: 0.6227 (mmm-85) REVERT: O 38 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7926 (ptp90) REVERT: Q 18 ARG cc_start: 0.6912 (ttp80) cc_final: 0.6295 (mtp180) REVERT: E 180 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: K 24 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7435 (mtm180) REVERT: P 82 ASN cc_start: 0.7687 (p0) cc_final: 0.7369 (p0) REVERT: N 58 MET cc_start: 0.8681 (mtp) cc_final: 0.8460 (mtp) REVERT: R 89 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: F 308 ARG cc_start: 0.7124 (mmm160) cc_final: 0.6827 (mmm160) REVERT: F 434 MET cc_start: 0.8601 (ttp) cc_final: 0.8354 (ttt) outliers start: 45 outliers final: 27 residues processed: 234 average time/residue: 0.1522 time to fit residues: 57.8886 Evaluate side-chains 219 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 293 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 92 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN L 89 GLN M 3 GLN C 607 ASN K 92 ASN K 100 GLN N 3 GLN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 607 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073355 restraints weight = 55040.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073506 restraints weight = 27331.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073689 restraints weight = 28833.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074376 restraints weight = 23287.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074646 restraints weight = 20906.627| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26040 Z= 0.132 Angle : 0.559 6.099 35562 Z= 0.283 Chirality : 0.044 0.234 4167 Planarity : 0.004 0.040 4377 Dihedral : 7.520 62.765 5277 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.61 % Allowed : 9.21 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.84 (0.16), residues: 3015 helix: 1.18 (0.27), residues: 402 sheet: 0.94 (0.17), residues: 972 loop : 0.26 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 94 TYR 0.013 0.001 TYR P 50 PHE 0.014 0.002 PHE E 382 TRP 0.016 0.001 TRP F 112 HIS 0.006 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00295 (25899) covalent geometry : angle 0.53560 (35184) SS BOND : bond 0.00266 ( 45) SS BOND : angle 0.60608 ( 90) hydrogen bonds : bond 0.03672 ( 969) hydrogen bonds : angle 5.14082 ( 2736) link_ALPHA1-2 : bond 0.00707 ( 3) link_ALPHA1-2 : angle 1.67344 ( 9) link_ALPHA1-3 : bond 0.01506 ( 6) link_ALPHA1-3 : angle 1.35730 ( 18) link_ALPHA1-6 : bond 0.00872 ( 6) link_ALPHA1-6 : angle 2.31378 ( 18) link_BETA1-4 : bond 0.00430 ( 30) link_BETA1-4 : angle 1.37856 ( 90) link_NAG-ASN : bond 0.00281 ( 51) link_NAG-ASN : angle 2.09407 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 24 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7380 (mtm180) REVERT: J 3 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7559 (mm-40) REVERT: J 38 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8166 (ptp90) REVERT: H 67 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8443 (mp) REVERT: L 61 ARG cc_start: 0.5704 (mtm-85) cc_final: 0.5404 (mtm-85) REVERT: L 89 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7099 (pt0) REVERT: A 648 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7492 (tt0) REVERT: I 24 ARG cc_start: 0.7472 (mtm180) cc_final: 0.7265 (mtm180) REVERT: O 38 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7954 (ptp90) REVERT: Q 18 ARG cc_start: 0.6703 (ttp80) cc_final: 0.6330 (mtp180) REVERT: E 180 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: C 621 GLU cc_start: 0.8450 (tt0) cc_final: 0.7869 (mt-10) REVERT: K 92 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8522 (m110) REVERT: P 3 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7640 (mm-40) REVERT: P 82 ASN cc_start: 0.7585 (p0) cc_final: 0.7255 (p0) REVERT: N 3 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7443 (mm-40) REVERT: N 58 MET cc_start: 0.8655 (mtp) cc_final: 0.8444 (mtp) REVERT: R 89 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: F 434 MET cc_start: 0.8582 (ttp) cc_final: 0.8282 (ttt) outliers start: 43 outliers final: 28 residues processed: 235 average time/residue: 0.1544 time to fit residues: 59.6863 Evaluate side-chains 223 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 193 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN A 577 GLN I 100 GLN C 577 GLN C 607 ASN K 92 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN D 577 GLN D 607 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068355 restraints weight = 55561.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.070731 restraints weight = 29604.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072377 restraints weight = 19513.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072514 restraints weight = 18413.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072463 restraints weight = 16054.236| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26040 Z= 0.212 Angle : 0.608 7.176 35562 Z= 0.309 Chirality : 0.045 0.237 4167 Planarity : 0.004 0.040 4377 Dihedral : 6.662 56.679 5277 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 1.99 % Allowed : 9.63 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.66 (0.16), residues: 3015 helix: 1.05 (0.27), residues: 402 sheet: 0.73 (0.17), residues: 984 loop : 0.20 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 94 TYR 0.013 0.001 TYR O 50 PHE 0.016 0.002 PHE E 382 TRP 0.015 0.001 TRP F 112 HIS 0.005 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00492 (25899) covalent geometry : angle 0.58652 (35184) SS BOND : bond 0.00340 ( 45) SS BOND : angle 0.68815 ( 90) hydrogen bonds : bond 0.03958 ( 969) hydrogen bonds : angle 5.18636 ( 2736) link_ALPHA1-2 : bond 0.00639 ( 3) link_ALPHA1-2 : angle 1.69056 ( 9) link_ALPHA1-3 : bond 0.01384 ( 6) link_ALPHA1-3 : angle 1.50416 ( 18) link_ALPHA1-6 : bond 0.00725 ( 6) link_ALPHA1-6 : angle 1.77067 ( 18) link_BETA1-4 : bond 0.00409 ( 30) link_BETA1-4 : angle 1.43933 ( 90) link_NAG-ASN : bond 0.00329 ( 51) link_NAG-ASN : angle 2.14845 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7362 (mtm180) REVERT: J 1 GLU cc_start: 0.7547 (tt0) cc_final: 0.7269 (tt0) REVERT: J 3 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7442 (mm-40) REVERT: J 38 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7508 (ptt180) REVERT: H 67 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 648 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7729 (tm-30) REVERT: O 38 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8017 (ptp90) REVERT: Q 18 ARG cc_start: 0.6650 (ttp80) cc_final: 0.6371 (mtp180) REVERT: E 180 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7793 (t0) REVERT: E 207 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7021 (tptt) REVERT: K 92 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8359 (m110) REVERT: P 3 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7803 (mm-40) REVERT: P 38 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7483 (ptt180) REVERT: P 82 ASN cc_start: 0.7633 (p0) cc_final: 0.7310 (p0) REVERT: N 58 MET cc_start: 0.8705 (mtp) cc_final: 0.8475 (mtp) REVERT: R 89 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7145 (pt0) REVERT: F 308 ARG cc_start: 0.7332 (mmm160) cc_final: 0.7017 (mmm160) REVERT: D 648 GLU cc_start: 0.7837 (tt0) cc_final: 0.7623 (tt0) outliers start: 53 outliers final: 35 residues processed: 231 average time/residue: 0.1568 time to fit residues: 59.3222 Evaluate side-chains 221 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 40 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 226 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 282 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN K 92 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073744 restraints weight = 54845.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073831 restraints weight = 27194.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074033 restraints weight = 28793.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074722 restraints weight = 23237.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074978 restraints weight = 20859.110| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26040 Z= 0.107 Angle : 0.545 6.856 35562 Z= 0.277 Chirality : 0.043 0.236 4167 Planarity : 0.004 0.042 4377 Dihedral : 6.112 56.409 5277 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.57 % Allowed : 10.15 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.77 (0.16), residues: 3015 helix: 1.23 (0.27), residues: 402 sheet: 0.85 (0.17), residues: 1008 loop : 0.20 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.014 0.001 TYR P 50 PHE 0.011 0.001 PHE F 382 TRP 0.016 0.001 TRP F 112 HIS 0.006 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00233 (25899) covalent geometry : angle 0.52239 (35184) SS BOND : bond 0.00250 ( 45) SS BOND : angle 0.57446 ( 90) hydrogen bonds : bond 0.03542 ( 969) hydrogen bonds : angle 5.00713 ( 2736) link_ALPHA1-2 : bond 0.00658 ( 3) link_ALPHA1-2 : angle 1.68576 ( 9) link_ALPHA1-3 : bond 0.01586 ( 6) link_ALPHA1-3 : angle 1.32743 ( 18) link_ALPHA1-6 : bond 0.00723 ( 6) link_ALPHA1-6 : angle 1.70039 ( 18) link_BETA1-4 : bond 0.00413 ( 30) link_BETA1-4 : angle 1.34986 ( 90) link_NAG-ASN : bond 0.00288 ( 51) link_NAG-ASN : angle 2.06043 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 24 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7335 (mtm180) REVERT: J 1 GLU cc_start: 0.7571 (tt0) cc_final: 0.7237 (tt0) REVERT: J 3 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7264 (mm-40) REVERT: H 67 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8476 (mp) REVERT: B 180 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: O 38 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8003 (ptp90) REVERT: Q 18 ARG cc_start: 0.6756 (ttp80) cc_final: 0.6347 (mtp180) REVERT: E 207 LYS cc_start: 0.8158 (ttpp) cc_final: 0.6879 (tptt) REVERT: C 621 GLU cc_start: 0.8434 (tt0) cc_final: 0.7929 (mt-10) REVERT: P 3 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7512 (mm-40) REVERT: P 38 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7924 (ptp90) REVERT: P 82 ASN cc_start: 0.7617 (p0) cc_final: 0.7297 (p0) REVERT: R 89 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: F 161 MET cc_start: 0.6905 (ttp) cc_final: 0.6083 (tpt) REVERT: F 308 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6825 (mmm160) REVERT: F 434 MET cc_start: 0.8480 (ttp) cc_final: 0.8225 (ttt) outliers start: 42 outliers final: 26 residues processed: 231 average time/residue: 0.1603 time to fit residues: 60.4400 Evaluate side-chains 215 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain F residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 207 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 117 optimal weight: 0.0570 chunk 277 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 274 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 100 GLN L 89 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN C 607 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN D 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074257 restraints weight = 54577.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074402 restraints weight = 26226.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075395 restraints weight = 24273.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075917 restraints weight = 19265.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.076234 restraints weight = 17992.319| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26040 Z= 0.103 Angle : 0.544 7.842 35562 Z= 0.276 Chirality : 0.043 0.236 4167 Planarity : 0.004 0.042 4377 Dihedral : 5.909 55.849 5277 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 1.35 % Allowed : 10.26 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.79 (0.16), residues: 3015 helix: 1.34 (0.27), residues: 402 sheet: 0.90 (0.17), residues: 1014 loop : 0.16 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 94 TYR 0.014 0.001 TYR P 50 PHE 0.022 0.001 PHE F 317 TRP 0.015 0.001 TRP F 112 HIS 0.008 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00224 (25899) covalent geometry : angle 0.52103 (35184) SS BOND : bond 0.00275 ( 45) SS BOND : angle 0.94069 ( 90) hydrogen bonds : bond 0.03406 ( 969) hydrogen bonds : angle 4.89316 ( 2736) link_ALPHA1-2 : bond 0.00619 ( 3) link_ALPHA1-2 : angle 1.67950 ( 9) link_ALPHA1-3 : bond 0.01387 ( 6) link_ALPHA1-3 : angle 1.33967 ( 18) link_ALPHA1-6 : bond 0.00737 ( 6) link_ALPHA1-6 : angle 1.65838 ( 18) link_BETA1-4 : bond 0.00433 ( 30) link_BETA1-4 : angle 1.34674 ( 90) link_NAG-ASN : bond 0.00281 ( 51) link_NAG-ASN : angle 2.03745 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4 MET cc_start: 0.6785 (mtp) cc_final: 0.6560 (mtp) REVERT: G 24 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7403 (mtm180) REVERT: J 1 GLU cc_start: 0.7739 (tt0) cc_final: 0.7462 (tt0) REVERT: J 3 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7236 (mm-40) REVERT: H 67 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8627 (mp) REVERT: L 89 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: B 180 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: O 38 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8073 (ptp90) REVERT: Q 18 ARG cc_start: 0.6650 (ttp80) cc_final: 0.6387 (mtp180) REVERT: E 207 LYS cc_start: 0.8197 (ttpp) cc_final: 0.6889 (tptt) REVERT: E 475 MET cc_start: 0.8926 (tpp) cc_final: 0.8585 (tpp) REVERT: C 621 GLU cc_start: 0.8319 (tt0) cc_final: 0.7885 (mt-10) REVERT: P 3 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7632 (mm-40) REVERT: P 38 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8040 (ptp90) REVERT: F 95 MET cc_start: 0.9095 (ptm) cc_final: 0.8864 (ptm) REVERT: F 161 MET cc_start: 0.6763 (ttp) cc_final: 0.6099 (tpt) REVERT: F 308 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6805 (mmm160) REVERT: F 434 MET cc_start: 0.8499 (ttp) cc_final: 0.8203 (ttt) outliers start: 36 outliers final: 30 residues processed: 224 average time/residue: 0.1534 time to fit residues: 56.4005 Evaluate side-chains 219 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain C residue 607 ASN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain D residue 607 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 140 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 275 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069966 restraints weight = 55427.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.070612 restraints weight = 35727.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071239 restraints weight = 26517.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071602 restraints weight = 22802.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071867 restraints weight = 21287.401| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26040 Z= 0.180 Angle : 0.591 9.360 35562 Z= 0.299 Chirality : 0.045 0.234 4167 Planarity : 0.004 0.045 4377 Dihedral : 5.962 56.053 5277 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.46 % Allowed : 10.26 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.73 (0.16), residues: 3015 helix: 1.48 (0.27), residues: 384 sheet: 0.71 (0.16), residues: 1056 loop : 0.18 (0.17), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.012 0.001 TYR P 50 PHE 0.018 0.002 PHE F 317 TRP 0.012 0.001 TRP F 112 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00418 (25899) covalent geometry : angle 0.56773 (35184) SS BOND : bond 0.00289 ( 45) SS BOND : angle 1.03214 ( 90) hydrogen bonds : bond 0.03739 ( 969) hydrogen bonds : angle 4.97339 ( 2736) link_ALPHA1-2 : bond 0.00549 ( 3) link_ALPHA1-2 : angle 1.67087 ( 9) link_ALPHA1-3 : bond 0.01426 ( 6) link_ALPHA1-3 : angle 1.41469 ( 18) link_ALPHA1-6 : bond 0.00670 ( 6) link_ALPHA1-6 : angle 1.74511 ( 18) link_BETA1-4 : bond 0.00408 ( 30) link_BETA1-4 : angle 1.36016 ( 90) link_NAG-ASN : bond 0.00278 ( 51) link_NAG-ASN : angle 2.12703 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7385 (mtm180) REVERT: J 3 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7516 (mm-40) REVERT: H 67 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 180 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: A 648 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7712 (tm-30) REVERT: O 3 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7865 (mm-40) REVERT: O 38 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8060 (ptp90) REVERT: Q 18 ARG cc_start: 0.6629 (ttp80) cc_final: 0.6402 (mtp180) REVERT: E 207 LYS cc_start: 0.8203 (ttpp) cc_final: 0.6907 (tptt) REVERT: E 475 MET cc_start: 0.8995 (tpp) cc_final: 0.8707 (tpp) REVERT: P 3 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7689 (mm-40) REVERT: P 38 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8162 (ptp90) REVERT: R 89 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7202 (pt0) REVERT: F 161 MET cc_start: 0.6758 (ttp) cc_final: 0.6121 (tpt) REVERT: F 434 MET cc_start: 0.8612 (ttp) cc_final: 0.8334 (ttt) REVERT: D 648 GLU cc_start: 0.7781 (tt0) cc_final: 0.7567 (tt0) outliers start: 39 outliers final: 33 residues processed: 218 average time/residue: 0.1449 time to fit residues: 52.3594 Evaluate side-chains 217 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain D residue 607 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 196 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 251 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 2 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072889 restraints weight = 54730.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072960 restraints weight = 27205.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074031 restraints weight = 23647.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074788 restraints weight = 19028.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074928 restraints weight = 17412.485| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26040 Z= 0.123 Angle : 0.556 9.862 35562 Z= 0.281 Chirality : 0.043 0.234 4167 Planarity : 0.004 0.049 4377 Dihedral : 5.882 56.159 5277 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 1.57 % Allowed : 10.34 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 0.77 (0.16), residues: 3015 helix: 1.54 (0.27), residues: 384 sheet: 0.77 (0.16), residues: 1053 loop : 0.17 (0.17), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.014 0.001 TYR P 50 PHE 0.018 0.001 PHE F 317 TRP 0.014 0.001 TRP F 112 HIS 0.005 0.001 HIS N 74 Details of bonding type rmsd covalent geometry : bond 0.00276 (25899) covalent geometry : angle 0.53312 (35184) SS BOND : bond 0.00243 ( 45) SS BOND : angle 0.85870 ( 90) hydrogen bonds : bond 0.03567 ( 969) hydrogen bonds : angle 4.90936 ( 2736) link_ALPHA1-2 : bond 0.00584 ( 3) link_ALPHA1-2 : angle 1.69883 ( 9) link_ALPHA1-3 : bond 0.01405 ( 6) link_ALPHA1-3 : angle 1.35881 ( 18) link_ALPHA1-6 : bond 0.00712 ( 6) link_ALPHA1-6 : angle 1.70525 ( 18) link_BETA1-4 : bond 0.00410 ( 30) link_BETA1-4 : angle 1.35225 ( 90) link_NAG-ASN : bond 0.00262 ( 51) link_NAG-ASN : angle 2.07348 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.58 seconds wall clock time: 60 minutes 56.63 seconds (3656.63 seconds total)