Starting phenix.real_space_refine on Fri Feb 6 14:43:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ogt_70475/02_2026/9ogt_70475.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ogt_70475/02_2026/9ogt_70475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ogt_70475/02_2026/9ogt_70475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ogt_70475/02_2026/9ogt_70475.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ogt_70475/02_2026/9ogt_70475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ogt_70475/02_2026/9ogt_70475.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 15957 2.51 5 N 4293 2.21 5 O 5016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25401 Number of models: 1 Model: "" Number of chains: 42 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 91} Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3376 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 5 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "K" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 91} Chain: "J" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "C" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3376 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 5 Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "P" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "R" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 91} Chain: "O" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "Q" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3376 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 5 Chain: "F" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} 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: 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "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: 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: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "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: 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: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" 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: "k" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "l" 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: "m" 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.25, per 1000 atoms: 0.25 Number of scatterers: 25401 At special positions: 0 Unit cell: (150.075, 155.875, 147.175, 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 5016 8.00 N 4293 7.00 C 15957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.06 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 445 " distance=2.06 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 100 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.06 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 445 " distance=2.06 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 445 " distance=2.06 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 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 F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 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 W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN d 4 " - " MAN d 5 " " MAN d 5 " - " MAN d 6 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA T 3 " - " MAN T 5 " " BMA W 3 " - " MAN W 7 " " BMA a 3 " - " MAN a 5 " " BMA d 3 " - " MAN d 7 " " BMA h 3 " - " MAN h 5 " " BMA k 3 " - " MAN k 7 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " NAG Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " NAG f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " NAG m 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 234 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 234 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 392 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 234 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 137 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 276 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 386 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 137 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 156 " " NAG h 1 " - " ASN E 137 " " NAG i 1 " - " ASN E 262 " " NAG j 1 " - " ASN E 276 " " NAG k 1 " - " ASN E 332 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 363 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5610 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 57 sheets defined 18.0% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.880A pdb=" N ASP H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.587A pdb=" N GLN H 65 " --> pdb=" O ARG H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 79 removed outlier: 3.633A pdb=" N ASP H 79 " --> pdb=" O TRP H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 79' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.709A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 100D through 100H Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.929A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.739A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.528A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.036A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.709A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.525A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.645A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.731A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.880A pdb=" N ASP K 31 " --> pdb=" O ASN K 28 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.587A pdb=" N GLN K 65 " --> pdb=" O ARG K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 79 removed outlier: 3.634A pdb=" N ASP K 79 " --> pdb=" O TRP K 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 76 through 79' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.709A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 100D through 100H Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.928A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.739A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.528A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.035A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.709A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.525A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.645A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.731A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.880A pdb=" N ASP P 31 " --> pdb=" O ASN P 28 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR P 32 " --> pdb=" O ILE P 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 28 through 32' Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.587A pdb=" N GLN P 65 " --> pdb=" O ARG P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 79 removed outlier: 3.634A pdb=" N ASP P 79 " --> pdb=" O TRP P 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 76 through 79' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.709A pdb=" N ILE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100D through 100H Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.929A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 354 removed outlier: 4.739A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.528A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.035A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.709A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.526A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.645A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.731A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.872A pdb=" N PHE H 83 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.718A pdb=" N ALA H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.546A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.751A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.751A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.526A pdb=" N VAL G 78 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.675A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.591A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 12 through 13 removed outlier: 3.659A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 23 removed outlier: 3.631A pdb=" N ALA I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.711A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AB8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.187A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.447A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 360 Processing sheet with id=AB9, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.087A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.447A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 414 through 421 removed outlier: 4.034A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.770A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.872A pdb=" N PHE K 83 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.718A pdb=" N ALA K 10 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.546A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.751A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE N 48 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.751A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.526A pdb=" N VAL J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.674A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.591A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 12 through 13 removed outlier: 3.659A pdb=" N ALA M 84 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.631A pdb=" N ALA M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AD4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD5, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AD6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.712A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AD9, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.187A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.448A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 360 Processing sheet with id=AE1, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.088A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.448A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 414 through 421 removed outlier: 4.033A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.770A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.872A pdb=" N PHE P 83 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.718A pdb=" N ALA P 10 " --> pdb=" O THR P 120 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.546A pdb=" N THR R 22 " --> pdb=" O SER R 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.751A pdb=" N LEU R 11 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.751A pdb=" N LEU R 11 " --> pdb=" O ASP R 105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.526A pdb=" N VAL O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.674A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.591A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 12 through 13 removed outlier: 3.659A pdb=" N ALA Q 84 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP Q 35 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 19 through 23 removed outlier: 3.631A pdb=" N ALA Q 71 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 494 through 498 Processing sheet with id=AF5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AF6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AF7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.712A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AF9, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AG1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.187A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.447A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 360 Processing sheet with id=AG2, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.087A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.447A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 414 through 421 removed outlier: 4.034A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.770A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2232 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: 7.00 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7971 1.35 - 1.48: 7121 1.48 - 1.61: 10690 1.61 - 1.74: 3 1.74 - 1.88: 177 Bond restraints: 25962 Sorted by residual: bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.702 0.106 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 1.808 1.702 0.106 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.702 0.106 3.30e-02 9.18e+02 1.03e+01 bond pdb=" CA CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sigma weight residual 1.530 1.572 -0.042 1.55e-02 4.16e+03 7.37e+00 bond pdb=" CA CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sigma weight residual 1.530 1.572 -0.042 1.55e-02 4.16e+03 7.27e+00 ... (remaining 25957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 34304 2.38 - 4.76: 801 4.76 - 7.14: 163 7.14 - 9.52: 12 9.52 - 11.90: 3 Bond angle restraints: 35283 Sorted by residual: angle pdb=" CB MET E 161 " pdb=" CG MET E 161 " pdb=" SD MET E 161 " ideal model delta sigma weight residual 112.70 124.60 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB MET C 161 " pdb=" CG MET C 161 " pdb=" SD MET C 161 " ideal model delta sigma weight residual 112.70 124.58 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB MET A 161 " pdb=" CG MET A 161 " pdb=" SD MET A 161 " ideal model delta sigma weight residual 112.70 124.58 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N CYS E 445 " pdb=" CA CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sigma weight residual 110.52 116.83 -6.31 1.65e+00 3.67e-01 1.46e+01 angle pdb=" N CYS A 445 " pdb=" CA CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sigma weight residual 110.52 116.82 -6.30 1.65e+00 3.67e-01 1.46e+01 ... (remaining 35278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14460 17.95 - 35.89: 1620 35.89 - 53.84: 462 53.84 - 71.79: 159 71.79 - 89.73: 69 Dihedral angle restraints: 16770 sinusoidal: 8052 harmonic: 8718 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual -86.00 -165.86 79.86 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -165.85 79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -165.85 79.85 1 1.00e+01 1.00e-02 7.91e+01 ... (remaining 16767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4007 0.111 - 0.223: 190 0.223 - 0.334: 0 0.334 - 0.445: 0 0.445 - 0.557: 9 Chirality restraints: 4206 Sorted by residual: chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-02 2.50e+03 7.10e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-02 2.50e+03 7.09e+02 chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-02 2.50e+03 7.07e+02 ... (remaining 4203 not shown) Planarity restraints: 4398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 2 " -0.070 2.00e-02 2.50e+03 5.93e-02 4.39e+01 pdb=" C7 NAG d 2 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG d 2 " 0.018 2.00e-02 2.50e+03 pdb=" N2 NAG d 2 " 0.096 2.00e-02 2.50e+03 pdb=" O7 NAG d 2 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " -0.070 2.00e-02 2.50e+03 5.92e-02 4.37e+01 pdb=" C7 NAG W 2 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " 0.018 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " 0.096 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG k 2 " -0.070 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" C7 NAG k 2 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG k 2 " 0.018 2.00e-02 2.50e+03 pdb=" N2 NAG k 2 " 0.096 2.00e-02 2.50e+03 pdb=" O7 NAG k 2 " -0.055 2.00e-02 2.50e+03 ... (remaining 4395 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 9038 2.88 - 3.39: 22545 3.39 - 3.89: 42196 3.89 - 4.40: 50558 4.40 - 4.90: 85083 Nonbonded interactions: 209420 Sorted by model distance: nonbonded pdb=" OG SER G 7 " pdb=" CG2 THR G 21 " model vdw 2.376 3.460 nonbonded pdb=" OG SER O 7 " pdb=" CG2 THR O 21 " model vdw 2.376 3.460 nonbonded pdb=" OG SER J 7 " pdb=" CG2 THR J 21 " model vdw 2.376 3.460 nonbonded pdb=" OG SER K 82 " pdb=" OH TYR K 84 " model vdw 2.452 3.040 nonbonded pdb=" OG SER P 82 " pdb=" OH TYR P 84 " model vdw 2.453 3.040 ... (remaining 209415 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'l' } ncs_group { reference = chain 'T' selection = chain 'a' selection = chain 'h' } ncs_group { reference = chain 'U' selection = chain 'b' selection = chain 'i' } ncs_group { reference = chain 'W' selection = chain 'd' selection = chain 'k' } ncs_group { reference = chain 'Y' selection = chain 'f' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.370 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.230 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.005 0.106 26115 Z= 0.226 Angle : 0.968 13.084 35694 Z= 0.481 Chirality : 0.054 0.557 4206 Planarity : 0.007 0.059 4347 Dihedral : 17.204 89.731 11016 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.56 % Allowed : 23.95 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.01 (0.15), residues: 2958 helix: -0.36 (0.26), residues: 387 sheet: -1.79 (0.16), residues: 987 loop : -1.18 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 166 TYR 0.015 0.002 TYR N 49 PHE 0.023 0.002 PHE P 78 TRP 0.022 0.002 TRP K 50 HIS 0.005 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00498 (25962) covalent geometry : angle 0.90556 (35283) SS BOND : bond 0.01145 ( 48) SS BOND : angle 2.97481 ( 96) hydrogen bonds : bond 0.16206 ( 828) hydrogen bonds : angle 8.08917 ( 2232) link_ALPHA1-2 : bond 0.00225 ( 6) link_ALPHA1-2 : angle 1.90519 ( 18) link_ALPHA1-3 : bond 0.01296 ( 9) link_ALPHA1-3 : angle 1.59990 ( 27) link_ALPHA1-6 : bond 0.01014 ( 6) link_ALPHA1-6 : angle 2.91940 ( 18) link_BETA1-4 : bond 0.02069 ( 33) link_BETA1-4 : angle 3.41543 ( 99) link_NAG-ASN : bond 0.00505 ( 51) link_NAG-ASN : angle 3.80254 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 383 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7554 (t80) REVERT: L 5 THR cc_start: 0.7882 (t) cc_final: 0.7565 (p) REVERT: G 11 LEU cc_start: 0.7557 (tt) cc_final: 0.7273 (mt) REVERT: G 90 TYR cc_start: 0.8300 (m-80) cc_final: 0.8032 (m-80) REVERT: G 100 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8302 (mptt) REVERT: A 35 TRP cc_start: 0.6948 (OUTLIER) cc_final: 0.5589 (t-100) REVERT: A 97 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8496 (mmpt) REVERT: A 117 LYS cc_start: 0.8537 (tptt) cc_final: 0.7953 (tppt) REVERT: A 125 LEU cc_start: 0.8917 (tp) cc_final: 0.8575 (mm) REVERT: N 5 THR cc_start: 0.7928 (t) cc_final: 0.7586 (p) REVERT: J 11 LEU cc_start: 0.7478 (tt) cc_final: 0.7218 (mt) REVERT: J 68 HIS cc_start: 0.7742 (t-90) cc_final: 0.7540 (t-90) REVERT: J 100 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8290 (mptp) REVERT: C 35 TRP cc_start: 0.6986 (OUTLIER) cc_final: 0.5800 (t-100) REVERT: C 97 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8484 (mmpt) REVERT: C 117 LYS cc_start: 0.8629 (tptt) cc_final: 0.7979 (tppt) REVERT: C 125 LEU cc_start: 0.8953 (tp) cc_final: 0.8564 (mm) REVERT: R 5 THR cc_start: 0.7814 (t) cc_final: 0.7469 (p) REVERT: O 11 LEU cc_start: 0.7510 (tt) cc_final: 0.7271 (mt) REVERT: O 68 HIS cc_start: 0.7707 (t-90) cc_final: 0.7502 (t-90) REVERT: O 100 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8270 (mptp) REVERT: E 35 TRP cc_start: 0.7001 (OUTLIER) cc_final: 0.5722 (t-100) REVERT: E 97 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8561 (mmpt) REVERT: E 117 LYS cc_start: 0.8604 (tptt) cc_final: 0.7961 (ttmt) REVERT: E 125 LEU cc_start: 0.8993 (tp) cc_final: 0.8585 (mm) outliers start: 15 outliers final: 7 residues processed: 395 average time/residue: 0.6278 time to fit residues: 287.6613 Evaluate side-chains 335 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 324 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 276 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN H 73 HIS L 34 ASN G 58 ASN A 355 ASN B 562 GLN B 577 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN K 73 HIS N 38 GLN J 58 ASN D 562 GLN D 577 GLN ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN E 355 ASN F 562 GLN F 577 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112955 restraints weight = 31271.473| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.40 r_work: 0.3201 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 26115 Z= 0.316 Angle : 0.801 12.059 35694 Z= 0.388 Chirality : 0.050 0.206 4206 Planarity : 0.006 0.042 4347 Dihedral : 10.304 87.264 5437 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.05 % Allowed : 22.82 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.76 (0.15), residues: 2958 helix: -0.35 (0.27), residues: 399 sheet: -1.54 (0.17), residues: 912 loop : -1.07 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 67 TYR 0.021 0.002 TYR L 49 PHE 0.017 0.002 PHE E 383 TRP 0.024 0.002 TRP P 50 HIS 0.003 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00763 (25962) covalent geometry : angle 0.73911 (35283) SS BOND : bond 0.01423 ( 48) SS BOND : angle 3.08784 ( 96) hydrogen bonds : bond 0.05578 ( 828) hydrogen bonds : angle 6.57031 ( 2232) link_ALPHA1-2 : bond 0.00217 ( 6) link_ALPHA1-2 : angle 2.36931 ( 18) link_ALPHA1-3 : bond 0.01198 ( 9) link_ALPHA1-3 : angle 1.46272 ( 27) link_ALPHA1-6 : bond 0.00708 ( 6) link_ALPHA1-6 : angle 1.51919 ( 18) link_BETA1-4 : bond 0.00536 ( 33) link_BETA1-4 : angle 2.46492 ( 99) link_NAG-ASN : bond 0.00845 ( 51) link_NAG-ASN : angle 3.53208 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 348 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7371 (tp40) REVERT: H 72 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7504 (ptt-90) REVERT: H 81 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7540 (t80) REVERT: L 54 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7839 (tp) REVERT: L 55 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: G 11 LEU cc_start: 0.7763 (tt) cc_final: 0.7411 (mt) REVERT: G 100 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: A 35 TRP cc_start: 0.7024 (OUTLIER) cc_final: 0.5926 (t60) REVERT: A 97 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8578 (mmpt) REVERT: A 117 LYS cc_start: 0.8468 (tptt) cc_final: 0.7798 (tppt) REVERT: A 125 LEU cc_start: 0.9055 (tp) cc_final: 0.8616 (mm) REVERT: A 164 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: B 647 GLU cc_start: 0.7230 (pt0) cc_final: 0.6482 (pm20) REVERT: K 25 SER cc_start: 0.8628 (t) cc_final: 0.7870 (m) REVERT: K 72 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7825 (ptt-90) REVERT: N 55 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: J 11 LEU cc_start: 0.7879 (tt) cc_final: 0.7510 (mt) REVERT: J 100 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8670 (mt-10) REVERT: M 95 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7638 (mmp80) REVERT: C 35 TRP cc_start: 0.7065 (OUTLIER) cc_final: 0.5885 (t60) REVERT: C 97 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8630 (mtpp) REVERT: C 117 LYS cc_start: 0.8488 (tptt) cc_final: 0.7818 (tppt) REVERT: C 164 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: D 647 GLU cc_start: 0.7224 (pt0) cc_final: 0.6735 (pm20) REVERT: P 43 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7477 (mm110) REVERT: P 72 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8179 (ptt-90) REVERT: R 54 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7835 (tp) REVERT: O 11 LEU cc_start: 0.7774 (tt) cc_final: 0.7426 (mt) REVERT: O 100 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8810 (mt-10) REVERT: E 35 TRP cc_start: 0.7065 (OUTLIER) cc_final: 0.5956 (t60) REVERT: E 117 LYS cc_start: 0.8501 (tptt) cc_final: 0.7767 (ttmt) REVERT: E 125 LEU cc_start: 0.9088 (tp) cc_final: 0.8610 (mm) REVERT: E 164 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: F 647 GLU cc_start: 0.7296 (pt0) cc_final: 0.7025 (pt0) outliers start: 134 outliers final: 51 residues processed: 441 average time/residue: 0.6237 time to fit residues: 319.2579 Evaluate side-chains 391 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 320 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 46 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 2.9990 chunk 93 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN L 34 ASN P 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116329 restraints weight = 31198.449| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.28 r_work: 0.3234 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26115 Z= 0.148 Angle : 0.676 13.059 35694 Z= 0.328 Chirality : 0.045 0.222 4206 Planarity : 0.004 0.038 4347 Dihedral : 9.609 81.718 5437 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.44 % Allowed : 24.26 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.46 (0.15), residues: 2958 helix: 0.00 (0.27), residues: 399 sheet: -1.32 (0.16), residues: 1014 loop : -0.87 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.017 0.001 TYR N 32 PHE 0.023 0.001 PHE P 78 TRP 0.021 0.001 TRP P 50 HIS 0.002 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00335 (25962) covalent geometry : angle 0.61993 (35283) SS BOND : bond 0.00830 ( 48) SS BOND : angle 2.76016 ( 96) hydrogen bonds : bond 0.04592 ( 828) hydrogen bonds : angle 6.27628 ( 2232) link_ALPHA1-2 : bond 0.00313 ( 6) link_ALPHA1-2 : angle 1.96689 ( 18) link_ALPHA1-3 : bond 0.01208 ( 9) link_ALPHA1-3 : angle 1.47969 ( 27) link_ALPHA1-6 : bond 0.00842 ( 6) link_ALPHA1-6 : angle 1.39462 ( 18) link_BETA1-4 : bond 0.00326 ( 33) link_BETA1-4 : angle 2.31848 ( 99) link_NAG-ASN : bond 0.00454 ( 51) link_NAG-ASN : angle 2.92350 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 348 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.8852 (ttt90) cc_final: 0.8536 (ttm170) REVERT: H 43 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7320 (tp40) REVERT: H 72 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7907 (ptt-90) REVERT: L 45 LYS cc_start: 0.8484 (ttpt) cc_final: 0.7993 (ttmm) REVERT: L 55 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: G 11 LEU cc_start: 0.7691 (tt) cc_final: 0.7331 (mt) REVERT: G 100 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: I 20 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7583 (mtp85) REVERT: A 35 TRP cc_start: 0.7085 (OUTLIER) cc_final: 0.6201 (t60) REVERT: A 97 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8650 (mmpt) REVERT: A 117 LYS cc_start: 0.8589 (tptt) cc_final: 0.7938 (tppt) REVERT: A 125 LEU cc_start: 0.9021 (tp) cc_final: 0.8703 (mm) REVERT: A 164 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: A 346 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 396 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (mt) REVERT: K 72 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7644 (ptt-90) REVERT: N 55 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: J 11 LEU cc_start: 0.7844 (tt) cc_final: 0.7501 (mt) REVERT: J 100 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8704 (mt-10) REVERT: C 35 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.6085 (t60) REVERT: C 97 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8697 (mtpp) REVERT: C 117 LYS cc_start: 0.8637 (tptt) cc_final: 0.7998 (tppt) REVERT: C 164 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: C 166 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8188 (ttp80) REVERT: C 475 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8069 (mpp) REVERT: D 633 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7207 (mtmm) REVERT: D 647 GLU cc_start: 0.7135 (pt0) cc_final: 0.6930 (pt0) REVERT: P 19 ARG cc_start: 0.8795 (ttt90) cc_final: 0.8525 (ttm170) REVERT: P 43 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7471 (mm110) REVERT: P 72 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8081 (ptt-90) REVERT: O 11 LEU cc_start: 0.7758 (tt) cc_final: 0.7382 (mt) REVERT: O 100 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8809 (mt-10) REVERT: E 35 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.6044 (t60) REVERT: E 117 LYS cc_start: 0.8608 (tptt) cc_final: 0.7974 (tppt) REVERT: E 125 LEU cc_start: 0.9044 (tp) cc_final: 0.8655 (mm) REVERT: F 647 GLU cc_start: 0.7295 (pt0) cc_final: 0.7069 (pt0) outliers start: 118 outliers final: 39 residues processed: 429 average time/residue: 0.5769 time to fit residues: 290.2003 Evaluate side-chains 397 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain F residue 538 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 244 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 HIS A 355 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN K 63 GLN J 52 HIS E 355 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117179 restraints weight = 31166.668| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.22 r_work: 0.3237 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26115 Z= 0.186 Angle : 0.679 12.454 35694 Z= 0.328 Chirality : 0.045 0.210 4206 Planarity : 0.004 0.069 4347 Dihedral : 9.521 82.378 5437 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.56 % Allowed : 23.92 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.39 (0.15), residues: 2958 helix: -0.01 (0.26), residues: 417 sheet: -1.23 (0.16), residues: 1014 loop : -0.84 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.013 0.002 TYR N 49 PHE 0.025 0.002 PHE P 78 TRP 0.021 0.002 TRP P 50 HIS 0.002 0.001 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00438 (25962) covalent geometry : angle 0.62435 (35283) SS BOND : bond 0.01006 ( 48) SS BOND : angle 2.73248 ( 96) hydrogen bonds : bond 0.04492 ( 828) hydrogen bonds : angle 6.14579 ( 2232) link_ALPHA1-2 : bond 0.00276 ( 6) link_ALPHA1-2 : angle 1.97722 ( 18) link_ALPHA1-3 : bond 0.01204 ( 9) link_ALPHA1-3 : angle 1.45016 ( 27) link_ALPHA1-6 : bond 0.00762 ( 6) link_ALPHA1-6 : angle 1.45617 ( 18) link_BETA1-4 : bond 0.00364 ( 33) link_BETA1-4 : angle 2.31104 ( 99) link_NAG-ASN : bond 0.00501 ( 51) link_NAG-ASN : angle 2.89943 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 350 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.8854 (ttt90) cc_final: 0.8472 (ttm170) REVERT: H 43 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7492 (mm110) REVERT: H 72 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7836 (ptt-90) REVERT: H 81 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7233 (t80) REVERT: L 54 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7809 (tp) REVERT: L 55 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: G 11 LEU cc_start: 0.7746 (tt) cc_final: 0.7348 (mt) REVERT: G 100 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8637 (mt-10) REVERT: A 35 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6171 (t60) REVERT: A 97 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8644 (mmpt) REVERT: A 117 LYS cc_start: 0.8590 (tptt) cc_final: 0.7942 (tppt) REVERT: A 125 LEU cc_start: 0.9026 (tp) cc_final: 0.8776 (mm) REVERT: A 164 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: A 276 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8295 (t160) REVERT: A 346 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 396 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (mt) REVERT: K 43 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7444 (tp40) REVERT: K 72 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7584 (ptt-90) REVERT: N 55 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: J 11 LEU cc_start: 0.7930 (tt) cc_final: 0.7571 (mt) REVERT: J 100 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8694 (mt-10) REVERT: C 35 TRP cc_start: 0.7230 (OUTLIER) cc_final: 0.6085 (t60) REVERT: C 97 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8691 (mtpp) REVERT: C 117 LYS cc_start: 0.8635 (tptt) cc_final: 0.7993 (tppt) REVERT: C 164 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: C 244 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8434 (t) REVERT: C 396 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7823 (mt) REVERT: C 475 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8107 (mpp) REVERT: D 633 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7118 (mtmm) REVERT: D 647 GLU cc_start: 0.7148 (pt0) cc_final: 0.6901 (pt0) REVERT: P 19 ARG cc_start: 0.8783 (ttt90) cc_final: 0.8456 (ttm170) REVERT: P 43 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7509 (mm110) REVERT: P 72 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8051 (ptt-90) REVERT: O 11 LEU cc_start: 0.7790 (tt) cc_final: 0.7410 (mt) REVERT: O 30 ARG cc_start: 0.8349 (ptm-80) cc_final: 0.8146 (ttp-110) REVERT: O 100 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8794 (mt-10) REVERT: E 35 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.6003 (t60) REVERT: E 117 LYS cc_start: 0.8610 (tptt) cc_final: 0.7974 (tppt) REVERT: E 125 LEU cc_start: 0.9020 (tp) cc_final: 0.8770 (mm) REVERT: E 276 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8363 (t160) REVERT: F 633 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7351 (mtmm) REVERT: F 634 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7283 (mt-10) REVERT: F 647 GLU cc_start: 0.7298 (pt0) cc_final: 0.6996 (pt0) outliers start: 121 outliers final: 49 residues processed: 428 average time/residue: 0.5698 time to fit residues: 283.8831 Evaluate side-chains 420 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 344 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 137 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN N 37 GLN O 52 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118129 restraints weight = 31090.057| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.32 r_work: 0.3251 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26115 Z= 0.156 Angle : 0.649 11.178 35694 Z= 0.315 Chirality : 0.044 0.209 4206 Planarity : 0.004 0.068 4347 Dihedral : 9.293 80.646 5435 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.33 % Allowed : 24.67 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.22 (0.15), residues: 2958 helix: 0.43 (0.26), residues: 399 sheet: -1.16 (0.16), residues: 1017 loop : -0.78 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 30 TYR 0.015 0.001 TYR O 91 PHE 0.023 0.001 PHE P 78 TRP 0.021 0.001 TRP P 50 HIS 0.002 0.000 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00364 (25962) covalent geometry : angle 0.59894 (35283) SS BOND : bond 0.00757 ( 48) SS BOND : angle 2.44794 ( 96) hydrogen bonds : bond 0.04210 ( 828) hydrogen bonds : angle 6.00282 ( 2232) link_ALPHA1-2 : bond 0.00291 ( 6) link_ALPHA1-2 : angle 1.87369 ( 18) link_ALPHA1-3 : bond 0.01199 ( 9) link_ALPHA1-3 : angle 1.49015 ( 27) link_ALPHA1-6 : bond 0.00789 ( 6) link_ALPHA1-6 : angle 1.41138 ( 18) link_BETA1-4 : bond 0.00367 ( 33) link_BETA1-4 : angle 2.29049 ( 99) link_NAG-ASN : bond 0.00398 ( 51) link_NAG-ASN : angle 2.73023 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 359 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.8866 (ttt90) cc_final: 0.8481 (ttm170) REVERT: H 43 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7495 (mm110) REVERT: H 72 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7852 (ptt-90) REVERT: H 81 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7215 (t80) REVERT: L 3 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6704 (pp30) REVERT: L 45 LYS cc_start: 0.8459 (ttpt) cc_final: 0.7966 (ttmm) REVERT: L 55 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: G 11 LEU cc_start: 0.7771 (tt) cc_final: 0.7468 (mt) REVERT: G 70 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.7436 (p) REVERT: G 100 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: A 35 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.6249 (t60) REVERT: A 97 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8636 (mmpt) REVERT: A 117 LYS cc_start: 0.8588 (tptt) cc_final: 0.7947 (tppt) REVERT: A 125 LEU cc_start: 0.9009 (tp) cc_final: 0.8782 (mm) REVERT: A 164 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: A 346 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 396 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7870 (mt) REVERT: B 626 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7986 (ttp) REVERT: K 43 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7480 (tp40) REVERT: K 72 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7548 (ptt-90) REVERT: N 55 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: J 11 LEU cc_start: 0.7976 (tt) cc_final: 0.7586 (mt) REVERT: J 100 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8681 (mt-10) REVERT: C 35 TRP cc_start: 0.7214 (OUTLIER) cc_final: 0.6041 (t60) REVERT: C 97 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8697 (mtpp) REVERT: C 117 LYS cc_start: 0.8633 (tptt) cc_final: 0.7987 (tppt) REVERT: C 164 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: C 396 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7787 (mt) REVERT: D 633 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7147 (mtmm) REVERT: D 647 GLU cc_start: 0.7139 (pt0) cc_final: 0.6904 (pt0) REVERT: P 19 ARG cc_start: 0.8781 (ttt90) cc_final: 0.8449 (ttm170) REVERT: P 43 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7542 (mm110) REVERT: P 72 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7997 (ptt-90) REVERT: R 55 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: O 11 LEU cc_start: 0.7786 (tt) cc_final: 0.7429 (mt) REVERT: O 30 ARG cc_start: 0.8344 (ptm-80) cc_final: 0.8127 (ttp-110) REVERT: O 100 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8797 (mt-10) REVERT: E 35 TRP cc_start: 0.7222 (OUTLIER) cc_final: 0.6146 (t60) REVERT: E 117 LYS cc_start: 0.8618 (tptt) cc_final: 0.7977 (tppt) REVERT: E 125 LEU cc_start: 0.9011 (tp) cc_final: 0.8782 (mm) REVERT: F 542 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.8149 (mtm-85) REVERT: F 633 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7231 (mtmm) REVERT: F 634 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7330 (mt-10) REVERT: F 647 GLU cc_start: 0.7225 (pt0) cc_final: 0.6983 (pt0) outliers start: 115 outliers final: 55 residues processed: 434 average time/residue: 0.5614 time to fit residues: 285.3530 Evaluate side-chains 430 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 349 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 633 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118868 restraints weight = 31318.800| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.21 r_work: 0.3269 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26115 Z= 0.151 Angle : 0.636 10.652 35694 Z= 0.309 Chirality : 0.044 0.210 4206 Planarity : 0.004 0.069 4347 Dihedral : 9.104 80.200 5431 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.37 % Allowed : 24.78 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.15 (0.15), residues: 2958 helix: 0.62 (0.27), residues: 399 sheet: -1.11 (0.16), residues: 1032 loop : -0.77 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 30 TYR 0.016 0.001 TYR O 91 PHE 0.023 0.001 PHE P 78 TRP 0.020 0.001 TRP P 50 HIS 0.002 0.000 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00352 (25962) covalent geometry : angle 0.58773 (35283) SS BOND : bond 0.00778 ( 48) SS BOND : angle 2.34477 ( 96) hydrogen bonds : bond 0.04076 ( 828) hydrogen bonds : angle 5.88821 ( 2232) link_ALPHA1-2 : bond 0.00289 ( 6) link_ALPHA1-2 : angle 1.83364 ( 18) link_ALPHA1-3 : bond 0.01182 ( 9) link_ALPHA1-3 : angle 1.48498 ( 27) link_ALPHA1-6 : bond 0.00780 ( 6) link_ALPHA1-6 : angle 1.41232 ( 18) link_BETA1-4 : bond 0.00380 ( 33) link_BETA1-4 : angle 2.27074 ( 99) link_NAG-ASN : bond 0.00400 ( 51) link_NAG-ASN : angle 2.64847 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 355 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.8838 (ttt90) cc_final: 0.8443 (ttm170) REVERT: H 43 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7532 (mm110) REVERT: H 72 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7797 (ptt-90) REVERT: H 81 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7139 (t80) REVERT: L 55 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: G 11 LEU cc_start: 0.7778 (tt) cc_final: 0.7447 (mt) REVERT: G 100 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8631 (mt-10) REVERT: A 35 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.6234 (t60) REVERT: A 97 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8640 (mmpt) REVERT: A 117 LYS cc_start: 0.8588 (tptt) cc_final: 0.7989 (tppt) REVERT: A 125 LEU cc_start: 0.9005 (tp) cc_final: 0.8755 (mm) REVERT: A 164 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: A 346 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 396 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7887 (mt) REVERT: B 626 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7926 (ttp) REVERT: K 43 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7484 (tp40) REVERT: K 72 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7458 (ptt-90) REVERT: K 91 ARG cc_start: 0.8482 (mpp80) cc_final: 0.8206 (mpp80) REVERT: N 55 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: J 11 LEU cc_start: 0.7957 (tt) cc_final: 0.7560 (mt) REVERT: J 100 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: M 20 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7583 (mtp85) REVERT: C 35 TRP cc_start: 0.7093 (OUTLIER) cc_final: 0.5916 (t60) REVERT: C 97 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8705 (mtpp) REVERT: C 117 LYS cc_start: 0.8636 (tptt) cc_final: 0.7990 (tppt) REVERT: C 164 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: D 626 MET cc_start: 0.8070 (ttp) cc_final: 0.7754 (ttm) REVERT: D 633 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7007 (mtmm) REVERT: D 647 GLU cc_start: 0.7164 (pt0) cc_final: 0.6940 (pt0) REVERT: P 19 ARG cc_start: 0.8777 (ttt90) cc_final: 0.8429 (ttm170) REVERT: P 43 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: P 72 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7995 (ptt-90) REVERT: R 55 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: O 11 LEU cc_start: 0.7790 (tt) cc_final: 0.7435 (mt) REVERT: O 100 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8794 (mt-10) REVERT: E 35 TRP cc_start: 0.7199 (OUTLIER) cc_final: 0.6118 (t60) REVERT: E 117 LYS cc_start: 0.8619 (tptt) cc_final: 0.7979 (tppt) REVERT: E 125 LEU cc_start: 0.9006 (tp) cc_final: 0.8775 (mm) REVERT: F 633 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7261 (mtmm) REVERT: F 647 GLU cc_start: 0.7180 (pt0) cc_final: 0.6947 (pt0) outliers start: 116 outliers final: 58 residues processed: 435 average time/residue: 0.5667 time to fit residues: 289.4022 Evaluate side-chains 432 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 351 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 633 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 206 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 249 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 230 optimal weight: 0.0010 chunk 121 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 HIS A 355 ASN A 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118029 restraints weight = 31252.801| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.48 r_work: 0.3232 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 26115 Z= 0.186 Angle : 0.703 17.934 35694 Z= 0.333 Chirality : 0.051 0.911 4206 Planarity : 0.004 0.071 4347 Dihedral : 9.230 81.039 5431 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.39 % Favored : 95.54 % Rotamer: Outliers : 4.18 % Allowed : 24.63 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.16 (0.15), residues: 2958 helix: 0.60 (0.27), residues: 399 sheet: -1.19 (0.16), residues: 987 loop : -0.75 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 30 TYR 0.018 0.002 TYR O 91 PHE 0.017 0.002 PHE P 78 TRP 0.020 0.001 TRP P 50 HIS 0.002 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00437 (25962) covalent geometry : angle 0.62816 (35283) SS BOND : bond 0.00904 ( 48) SS BOND : angle 2.47610 ( 96) hydrogen bonds : bond 0.04266 ( 828) hydrogen bonds : angle 5.88829 ( 2232) link_ALPHA1-2 : bond 0.00271 ( 6) link_ALPHA1-2 : angle 1.86732 ( 18) link_ALPHA1-3 : bond 0.01148 ( 9) link_ALPHA1-3 : angle 1.45975 ( 27) link_ALPHA1-6 : bond 0.00733 ( 6) link_ALPHA1-6 : angle 1.44303 ( 18) link_BETA1-4 : bond 0.00353 ( 33) link_BETA1-4 : angle 2.27547 ( 99) link_NAG-ASN : bond 0.00528 ( 51) link_NAG-ASN : angle 4.02824 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 351 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.8877 (ttt90) cc_final: 0.8435 (ttm170) REVERT: H 43 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7535 (mm110) REVERT: H 72 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7892 (ptt-90) REVERT: H 81 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7173 (t80) REVERT: L 55 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: G 11 LEU cc_start: 0.7843 (tt) cc_final: 0.7495 (mt) REVERT: G 70 SER cc_start: 0.7670 (OUTLIER) cc_final: 0.7166 (p) REVERT: G 100 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8626 (mt-10) REVERT: A 35 TRP cc_start: 0.7071 (OUTLIER) cc_final: 0.5850 (t-100) REVERT: A 97 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8528 (mmpt) REVERT: A 117 LYS cc_start: 0.8426 (tptt) cc_final: 0.7758 (tppt) REVERT: A 125 LEU cc_start: 0.9026 (tp) cc_final: 0.8695 (mm) REVERT: A 164 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: A 346 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 396 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 626 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7758 (ttp) REVERT: B 647 GLU cc_start: 0.7777 (pt0) cc_final: 0.7492 (pt0) REVERT: K 43 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7522 (tp40) REVERT: K 72 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7509 (ptt-90) REVERT: N 55 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: J 11 LEU cc_start: 0.7938 (tt) cc_final: 0.7527 (mt) REVERT: J 100 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8661 (mt-10) REVERT: M 20 ARG cc_start: 0.7846 (mmm160) cc_final: 0.7635 (mtp85) REVERT: C 35 TRP cc_start: 0.7014 (OUTLIER) cc_final: 0.5670 (t60) REVERT: C 97 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8584 (mtpp) REVERT: C 117 LYS cc_start: 0.8490 (tptt) cc_final: 0.7807 (tppt) REVERT: C 164 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: D 626 MET cc_start: 0.7983 (ttp) cc_final: 0.7638 (ttm) REVERT: D 633 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7104 (ptpp) REVERT: D 647 GLU cc_start: 0.7178 (pt0) cc_final: 0.6940 (pt0) REVERT: P 19 ARG cc_start: 0.8813 (ttt90) cc_final: 0.8419 (ttm170) REVERT: P 43 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7548 (mm110) REVERT: P 72 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7925 (ptt-90) REVERT: O 11 LEU cc_start: 0.7901 (tt) cc_final: 0.7492 (mt) REVERT: O 100 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8817 (mt-10) REVERT: E 35 TRP cc_start: 0.7078 (OUTLIER) cc_final: 0.5846 (t60) REVERT: E 117 LYS cc_start: 0.8470 (tptt) cc_final: 0.7801 (tppt) REVERT: E 125 LEU cc_start: 0.9004 (tp) cc_final: 0.8707 (mm) REVERT: F 542 ARG cc_start: 0.8222 (ttp-170) cc_final: 0.7918 (mtm-85) REVERT: F 633 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7204 (mtmm) REVERT: F 634 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7118 (mt-10) REVERT: F 647 GLU cc_start: 0.7181 (pt0) cc_final: 0.6924 (pt0) outliers start: 111 outliers final: 66 residues processed: 428 average time/residue: 0.5766 time to fit residues: 290.2147 Evaluate side-chains 433 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 344 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 633 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 260 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 271 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN A 355 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS N 6 GLN D 616 ASN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110292 restraints weight = 31475.501| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.37 r_work: 0.3150 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.129 26115 Z= 0.370 Angle : 0.831 11.989 35694 Z= 0.399 Chirality : 0.053 0.666 4206 Planarity : 0.005 0.073 4347 Dihedral : 9.878 87.850 5431 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 4.82 % Allowed : 24.44 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.44 (0.15), residues: 2958 helix: 0.16 (0.27), residues: 399 sheet: -1.22 (0.16), residues: 969 loop : -1.00 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 30 TYR 0.022 0.002 TYR N 49 PHE 0.022 0.003 PHE H 78 TRP 0.023 0.002 TRP K 50 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00895 (25962) covalent geometry : angle 0.76408 (35283) SS BOND : bond 0.01508 ( 48) SS BOND : angle 3.23414 ( 96) hydrogen bonds : bond 0.05355 ( 828) hydrogen bonds : angle 6.25743 ( 2232) link_ALPHA1-2 : bond 0.00101 ( 6) link_ALPHA1-2 : angle 2.13332 ( 18) link_ALPHA1-3 : bond 0.01056 ( 9) link_ALPHA1-3 : angle 1.36242 ( 27) link_ALPHA1-6 : bond 0.00579 ( 6) link_ALPHA1-6 : angle 1.63676 ( 18) link_BETA1-4 : bond 0.00532 ( 33) link_BETA1-4 : angle 2.51812 ( 99) link_NAG-ASN : bond 0.00865 ( 51) link_NAG-ASN : angle 3.83816 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 330 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7461 (tp40) REVERT: H 72 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.7580 (ptt-90) REVERT: H 81 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7392 (t80) REVERT: L 55 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: G 11 LEU cc_start: 0.7849 (tt) cc_final: 0.7486 (mt) REVERT: G 70 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7374 (p) REVERT: G 100 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8624 (mt-10) REVERT: A 35 TRP cc_start: 0.7171 (OUTLIER) cc_final: 0.5991 (t-100) REVERT: A 97 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8553 (mmpt) REVERT: A 117 LYS cc_start: 0.8453 (tptt) cc_final: 0.7762 (tppt) REVERT: A 125 LEU cc_start: 0.9055 (tp) cc_final: 0.8587 (mm) REVERT: A 164 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: A 166 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8128 (ttp80) REVERT: A 396 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7918 (mt) REVERT: K 19 ARG cc_start: 0.8964 (ttt90) cc_final: 0.8608 (ttm170) REVERT: K 43 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7487 (tp40) REVERT: K 72 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.7906 (ptt-90) REVERT: K 107 TYR cc_start: 0.8853 (m-80) cc_final: 0.8632 (m-80) REVERT: N 55 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: J 11 LEU cc_start: 0.7947 (tt) cc_final: 0.7494 (mt) REVERT: J 100 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: M 20 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7724 (mtp85) REVERT: C 35 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.5850 (t-100) REVERT: C 97 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8619 (mtpp) REVERT: C 117 LYS cc_start: 0.8529 (tptt) cc_final: 0.7856 (tppt) REVERT: C 164 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: D 626 MET cc_start: 0.8063 (ttp) cc_final: 0.7688 (ttm) REVERT: D 633 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7154 (ptpp) REVERT: D 647 GLU cc_start: 0.7415 (pt0) cc_final: 0.7085 (pt0) REVERT: P 43 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7524 (mm110) REVERT: P 72 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8272 (ptt-90) REVERT: R 32 TYR cc_start: 0.7691 (m-80) cc_final: 0.7357 (m-80) REVERT: O 11 LEU cc_start: 0.7878 (tt) cc_final: 0.7435 (mt) REVERT: O 100 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8793 (mt-10) REVERT: E 35 TRP cc_start: 0.7149 (OUTLIER) cc_final: 0.6002 (t-100) REVERT: E 117 LYS cc_start: 0.8507 (tptt) cc_final: 0.7827 (tppt) REVERT: E 125 LEU cc_start: 0.9083 (tp) cc_final: 0.8689 (mm) REVERT: F 542 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7993 (mtm-85) REVERT: F 633 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7238 (mtmm) REVERT: F 647 GLU cc_start: 0.7441 (pt0) cc_final: 0.7130 (pt0) outliers start: 128 outliers final: 80 residues processed: 421 average time/residue: 0.5580 time to fit residues: 275.6695 Evaluate side-chains 421 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 320 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 633 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 155 optimal weight: 0.8980 chunk 267 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 278 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117545 restraints weight = 31488.699| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.33 r_work: 0.3238 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 26115 Z= 0.155 Angle : 0.676 11.030 35694 Z= 0.326 Chirality : 0.047 0.626 4206 Planarity : 0.004 0.079 4347 Dihedral : 9.178 80.460 5431 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 3.39 % Allowed : 25.95 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.24 (0.15), residues: 2958 helix: 0.40 (0.27), residues: 399 sheet: -1.22 (0.16), residues: 984 loop : -0.78 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 30 TYR 0.016 0.001 TYR O 91 PHE 0.011 0.001 PHE E 383 TRP 0.024 0.001 TRP K 50 HIS 0.002 0.000 HIS P 73 Details of bonding type rmsd covalent geometry : bond 0.00361 (25962) covalent geometry : angle 0.61803 (35283) SS BOND : bond 0.00786 ( 48) SS BOND : angle 2.33691 ( 96) hydrogen bonds : bond 0.04222 ( 828) hydrogen bonds : angle 5.97607 ( 2232) link_ALPHA1-2 : bond 0.00269 ( 6) link_ALPHA1-2 : angle 1.75803 ( 18) link_ALPHA1-3 : bond 0.01133 ( 9) link_ALPHA1-3 : angle 1.51329 ( 27) link_ALPHA1-6 : bond 0.00755 ( 6) link_ALPHA1-6 : angle 1.35975 ( 18) link_BETA1-4 : bond 0.00349 ( 33) link_BETA1-4 : angle 2.28020 ( 99) link_NAG-ASN : bond 0.00518 ( 51) link_NAG-ASN : angle 3.27774 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 348 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7394 (tp40) REVERT: H 72 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.7468 (ptt-90) REVERT: H 81 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7175 (t80) REVERT: L 55 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: G 11 LEU cc_start: 0.7841 (tt) cc_final: 0.7443 (mt) REVERT: G 100 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: A 35 TRP cc_start: 0.7201 (OUTLIER) cc_final: 0.6150 (t-100) REVERT: A 97 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8641 (mmpt) REVERT: A 117 LYS cc_start: 0.8569 (tptt) cc_final: 0.7919 (tppt) REVERT: A 125 LEU cc_start: 0.9049 (tp) cc_final: 0.8741 (mm) REVERT: A 164 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: A 346 VAL cc_start: 0.8659 (p) cc_final: 0.8410 (p) REVERT: B 633 LYS cc_start: 0.7588 (pttt) cc_final: 0.7266 (ptpp) REVERT: K 43 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7442 (tp40) REVERT: K 72 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7627 (ptt-90) REVERT: K 91 ARG cc_start: 0.8453 (mpp80) cc_final: 0.8145 (mpp80) REVERT: N 55 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: J 11 LEU cc_start: 0.7921 (tt) cc_final: 0.7456 (mt) REVERT: J 100 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8701 (mt-10) REVERT: C 35 TRP cc_start: 0.7105 (OUTLIER) cc_final: 0.6010 (t-100) REVERT: C 97 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8710 (mtpp) REVERT: C 117 LYS cc_start: 0.8627 (tptt) cc_final: 0.7980 (tppt) REVERT: C 164 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: D 626 MET cc_start: 0.8063 (ttp) cc_final: 0.7814 (ttm) REVERT: D 633 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7117 (ptpp) REVERT: D 647 GLU cc_start: 0.7329 (pt0) cc_final: 0.7063 (pt0) REVERT: P 43 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7583 (mm110) REVERT: P 72 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8011 (ptt-90) REVERT: R 32 TYR cc_start: 0.7562 (m-80) cc_final: 0.7271 (m-80) REVERT: O 11 LEU cc_start: 0.7886 (tt) cc_final: 0.7441 (mt) REVERT: O 100 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8801 (mt-10) REVERT: E 35 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.6171 (t-100) REVERT: E 46 LYS cc_start: 0.8736 (tttt) cc_final: 0.8061 (tppt) REVERT: E 117 LYS cc_start: 0.8613 (tptt) cc_final: 0.7967 (tppt) REVERT: E 125 LEU cc_start: 0.9031 (tp) cc_final: 0.8759 (mm) REVERT: F 542 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.8020 (mtm-85) REVERT: F 633 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7252 (mtmm) REVERT: F 634 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6988 (mt-10) REVERT: F 647 GLU cc_start: 0.7294 (pt0) cc_final: 0.7053 (pt0) outliers start: 90 outliers final: 64 residues processed: 411 average time/residue: 0.5665 time to fit residues: 273.3682 Evaluate side-chains 423 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 340 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 633 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 157 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 288 optimal weight: 0.0570 chunk 240 optimal weight: 0.4980 chunk 225 optimal weight: 4.9990 chunk 248 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.154881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119064 restraints weight = 31434.476| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.36 r_work: 0.3253 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26115 Z= 0.133 Angle : 0.656 11.221 35694 Z= 0.316 Chirality : 0.046 0.571 4206 Planarity : 0.004 0.078 4347 Dihedral : 8.959 79.593 5431 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 3.09 % Allowed : 26.52 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.13 (0.15), residues: 2958 helix: 0.56 (0.27), residues: 399 sheet: -1.10 (0.16), residues: 993 loop : -0.76 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 30 TYR 0.016 0.001 TYR O 91 PHE 0.019 0.001 PHE P 78 TRP 0.023 0.001 TRP P 50 HIS 0.001 0.000 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00303 (25962) covalent geometry : angle 0.60127 (35283) SS BOND : bond 0.00710 ( 48) SS BOND : angle 2.19465 ( 96) hydrogen bonds : bond 0.04019 ( 828) hydrogen bonds : angle 5.84684 ( 2232) link_ALPHA1-2 : bond 0.00284 ( 6) link_ALPHA1-2 : angle 1.76278 ( 18) link_ALPHA1-3 : bond 0.01149 ( 9) link_ALPHA1-3 : angle 1.52623 ( 27) link_ALPHA1-6 : bond 0.00781 ( 6) link_ALPHA1-6 : angle 1.38282 ( 18) link_BETA1-4 : bond 0.00361 ( 33) link_BETA1-4 : angle 2.21478 ( 99) link_NAG-ASN : bond 0.00513 ( 51) link_NAG-ASN : angle 3.14678 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 348 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7563 (mm110) REVERT: H 72 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7727 (ptt-90) REVERT: H 81 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7180 (t80) REVERT: L 55 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: G 11 LEU cc_start: 0.7858 (tt) cc_final: 0.7465 (mt) REVERT: G 100 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: A 35 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6148 (t-100) REVERT: A 97 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8635 (mmpt) REVERT: A 117 LYS cc_start: 0.8591 (tptt) cc_final: 0.7993 (tppt) REVERT: A 125 LEU cc_start: 0.9032 (tp) cc_final: 0.8733 (mm) REVERT: A 164 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: A 346 VAL cc_start: 0.8644 (p) cc_final: 0.8388 (p) REVERT: B 633 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7247 (ptpp) REVERT: K 43 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7454 (tp40) REVERT: K 72 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7499 (ptt-90) REVERT: K 91 ARG cc_start: 0.8472 (mpp80) cc_final: 0.8191 (mpp80) REVERT: N 55 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: J 11 LEU cc_start: 0.7889 (tt) cc_final: 0.7425 (mt) REVERT: J 100 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: C 35 TRP cc_start: 0.7101 (OUTLIER) cc_final: 0.6021 (t-100) REVERT: C 97 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8722 (mtpp) REVERT: C 117 LYS cc_start: 0.8642 (tptt) cc_final: 0.8000 (tppt) REVERT: C 125 LEU cc_start: 0.9048 (tp) cc_final: 0.8790 (mm) REVERT: C 164 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: D 626 MET cc_start: 0.8055 (ttp) cc_final: 0.7827 (ttm) REVERT: D 633 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7139 (ptpp) REVERT: D 647 GLU cc_start: 0.7247 (pt0) cc_final: 0.7002 (pt0) REVERT: P 43 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7602 (mm110) REVERT: P 72 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8021 (ptt-90) REVERT: O 11 LEU cc_start: 0.7896 (tt) cc_final: 0.7453 (mt) REVERT: O 100 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8788 (mt-10) REVERT: E 35 TRP cc_start: 0.7287 (OUTLIER) cc_final: 0.6199 (t-100) REVERT: E 46 LYS cc_start: 0.8745 (tttt) cc_final: 0.8081 (tppt) REVERT: E 117 LYS cc_start: 0.8623 (tptt) cc_final: 0.7997 (tppt) REVERT: E 125 LEU cc_start: 0.9005 (tp) cc_final: 0.8775 (mm) REVERT: E 234 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.6681 (t0) REVERT: E 346 VAL cc_start: 0.8641 (p) cc_final: 0.8326 (p) REVERT: F 626 MET cc_start: 0.7650 (ttm) cc_final: 0.7430 (ttp) REVERT: F 633 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7233 (mtmm) outliers start: 82 outliers final: 55 residues processed: 403 average time/residue: 0.5669 time to fit residues: 269.0418 Evaluate side-chains 422 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 346 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 81 TYR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 81 TYR Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 633 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 16 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 253 optimal weight: 0.0870 chunk 218 optimal weight: 0.0020 chunk 214 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120274 restraints weight = 31275.122| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.29 r_work: 0.3288 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26115 Z= 0.114 Angle : 0.627 11.523 35694 Z= 0.303 Chirality : 0.045 0.485 4206 Planarity : 0.004 0.077 4347 Dihedral : 8.575 76.857 5431 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 2.90 % Allowed : 26.82 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.97 (0.15), residues: 2958 helix: 0.81 (0.27), residues: 405 sheet: -1.01 (0.16), residues: 1017 loop : -0.68 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 30 TYR 0.016 0.001 TYR O 91 PHE 0.020 0.001 PHE P 78 TRP 0.024 0.001 TRP P 50 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00256 (25962) covalent geometry : angle 0.57959 (35283) SS BOND : bond 0.00569 ( 48) SS BOND : angle 1.89961 ( 96) hydrogen bonds : bond 0.03639 ( 828) hydrogen bonds : angle 5.63959 ( 2232) link_ALPHA1-2 : bond 0.00343 ( 6) link_ALPHA1-2 : angle 1.62703 ( 18) link_ALPHA1-3 : bond 0.01110 ( 9) link_ALPHA1-3 : angle 1.57603 ( 27) link_ALPHA1-6 : bond 0.00820 ( 6) link_ALPHA1-6 : angle 1.40681 ( 18) link_BETA1-4 : bond 0.00381 ( 33) link_BETA1-4 : angle 2.17441 ( 99) link_NAG-ASN : bond 0.00478 ( 51) link_NAG-ASN : angle 2.84076 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9467.92 seconds wall clock time: 162 minutes 40.18 seconds (9760.18 seconds total)