Starting phenix.real_space_refine on Fri Sep 19 07:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msy_48591/09_2025/9msy_48591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msy_48591/09_2025/9msy_48591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9msy_48591/09_2025/9msy_48591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msy_48591/09_2025/9msy_48591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9msy_48591/09_2025/9msy_48591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msy_48591/09_2025/9msy_48591.map" } resolution = 3.4 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= 0.019 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 153 5.16 5 C 15276 2.51 5 N 4050 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24315 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4189 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 22, 'TRANS': 508} Chain breaks: 9 Chain: "G" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "I" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 771 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4189 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 22, 'TRANS': 508} Chain breaks: 9 Chain: "J" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "N" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 771 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "K" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4189 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 22, 'TRANS': 508} Chain breaks: 9 Chain: "O" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "Q" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "R" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 771 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "P" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.65, per 1000 atoms: 0.27 Number of scatterers: 24315 At special positions: 0 Unit cell: (168.526, 162.322, 138.543, 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 153 16.00 O 4836 8.00 N 4050 7.00 C 15276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " 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 ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 6 " " MAN U 4 " - " MAN U 5 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 6 " " MAN b 4 " - " MAN b 5 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 6 " " MAN i 4 " - " MAN i 5 " ALPHA1-6 " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 4 " " BMA h 3 " - " MAN h 5 " " BMA i 3 " - " MAN i 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG 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 e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 701 " - " ASN A 241 " " NAG A 702 " - " ASN A 88 " " NAG A 703 " - " ASN A 160 " " NAG A 704 " - " ASN A 130 " " NAG A 705 " - " ASN A 197 " " NAG A 706 " - " ASN A 611 " " NAG A 707 " - " ASN A 442 " " NAG B 701 " - " ASN B 241 " " NAG B 702 " - " ASN B 88 " " NAG B 703 " - " ASN B 160 " " NAG B 704 " - " ASN B 130 " " NAG B 705 " - " ASN B 197 " " NAG B 706 " - " ASN B 611 " " NAG B 707 " - " ASN B 442 " " NAG C 701 " - " ASN C 241 " " NAG C 702 " - " ASN C 88 " " NAG C 703 " - " ASN C 160 " " NAG C 704 " - " ASN C 130 " " NAG C 705 " - " ASN C 197 " " NAG C 706 " - " ASN C 611 " " NAG C 707 " - " ASN C 442 " " NAG D 1 " - " ASN A 230 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 289 " " NAG G1301 " - " ASN G 26 " " NAG J1301 " - " ASN J 26 " " NAG O1301 " - " ASN O 26 " " NAG S 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN B 230 " " NAG X 1 " - " ASN B 234 " " NAG Y 1 " - " ASN B 289 " " NAG Z 1 " - " ASN B 448 " " NAG a 1 " - " ASN B 262 " " NAG b 1 " - " ASN B 332 " " NAG c 1 " - " ASN B 301 " " NAG d 1 " - " ASN C 230 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 289 " " NAG g 1 " - " ASN C 448 " " NAG h 1 " - " ASN C 262 " " NAG i 1 " - " ASN C 332 " " NAG j 1 " - " ASN C 301 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 54 sheets defined 15.0% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.861A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 removed outlier: 3.992A pdb=" N LYS A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.871A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.039A pdb=" N VAL A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.647A pdb=" N ARG A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 636 through 639 removed outlier: 3.715A pdb=" N THR A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 641 through 659 removed outlier: 3.950A pdb=" N LEU A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 100B through 100F Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.958A pdb=" N THR I 29 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'L' and resid 29 through 32 removed outlier: 3.609A pdb=" N SER L 32 " --> pdb=" O SER L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 32' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.642A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.786A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.861A pdb=" N GLU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 352 removed outlier: 3.992A pdb=" N LYS B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.871A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 Processing helix chain 'B' and resid 544 through 549 removed outlier: 4.039A pdb=" N VAL B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.646A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 636 through 639 removed outlier: 3.714A pdb=" N THR B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 639' Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.950A pdb=" N LEU B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 100B through 100F Processing helix chain 'M' and resid 26 through 30 removed outlier: 3.958A pdb=" N THR M 29 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 29 through 32 removed outlier: 3.610A pdb=" N SER N 32 " --> pdb=" O SER N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 32' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.642A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.786A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.860A pdb=" N GLU C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 352 removed outlier: 3.992A pdb=" N LYS C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.871A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.039A pdb=" N VAL C 549 " --> pdb=" O SER C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.646A pdb=" N ARG C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 636 through 639 removed outlier: 3.715A pdb=" N THR C 639 " --> pdb=" O GLY C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 636 through 639' Processing helix chain 'C' and resid 641 through 659 removed outlier: 3.949A pdb=" N LEU C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.958A pdb=" N THR Q 29 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'R' and resid 29 through 32 removed outlier: 3.610A pdb=" N SER R 32 " --> pdb=" O SER R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 29 through 32' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.642A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.786A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 497 through 499 removed outlier: 5.851A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.700A pdb=" N ILE A 225 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.598A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.665A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N PHE A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N LEU A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323A removed outlier: 3.615A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 7 removed outlier: 5.886A pdb=" N GLU G 16 " --> pdb=" O SER G 82B" (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER G 82B" --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 35 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS G 92 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG G 94 " --> pdb=" O MET G 100M" (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET G 100M" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA G 96 " --> pdb=" O TYR G 100K" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 35 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 88 " --> pdb=" O VAL G 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL I 11 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL I 11 " --> pdb=" O THR I 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 19 through 24 removed outlier: 4.129A pdb=" N ALA I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE I 75 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.635A pdb=" N ILE L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 497 through 499 removed outlier: 5.851A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.700A pdb=" N ILE B 225 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.598A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 92 through 94 Processing sheet with id=AC5, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'B' and resid 271 through 273 removed outlier: 10.665A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.350A pdb=" N PHE B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N LEU B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 316 through 323A removed outlier: 3.615A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 7 removed outlier: 5.886A pdb=" N GLU J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER J 82B" --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP J 35 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS J 92 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL J 102 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG J 94 " --> pdb=" O MET J 100M" (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET J 100M" --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA J 96 " --> pdb=" O TYR J 100K" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP J 35 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.129A pdb=" N ALA M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE M 75 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AD6, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.635A pdb=" N ILE N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.093A pdb=" N ALA K 78 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.093A pdb=" N ALA K 78 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 497 through 499 removed outlier: 5.851A pdb=" N VAL C 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR C 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.700A pdb=" N ILE C 225 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.598A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AE5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AE6, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.664A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N PHE C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.472A pdb=" N LEU C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 316 through 323A removed outlier: 3.615A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 3 through 7 removed outlier: 5.885A pdb=" N GLU O 16 " --> pdb=" O SER O 82B" (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER O 82B" --> pdb=" O GLU O 16 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP O 35 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS O 92 " --> pdb=" O VAL O 102 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL O 102 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG O 94 " --> pdb=" O MET O 100M" (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET O 100M" --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA O 96 " --> pdb=" O TYR O 100K" (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP O 35 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP Q 35 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 19 through 24 removed outlier: 4.129A pdb=" N ALA Q 19 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE Q 75 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'R' and resid 53 through 54 removed outlier: 3.635A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA P 78 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA P 78 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.608A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7280 1.34 - 1.47: 6685 1.47 - 1.59: 10653 1.59 - 1.72: 0 1.72 - 1.85: 216 Bond restraints: 24834 Sorted by residual: bond pdb=" N GLY C 367 " pdb=" CA GLY C 367 " ideal model delta sigma weight residual 1.448 1.477 -0.030 9.20e-03 1.18e+04 1.04e+01 bond pdb=" N GLY A 367 " pdb=" CA GLY A 367 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N ARG H 71 " pdb=" CA ARG H 71 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.62e+00 bond pdb=" N ARG K 71 " pdb=" CA ARG K 71 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.61e+00 ... (remaining 24829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 32042 2.10 - 4.19: 1371 4.19 - 6.29: 226 6.29 - 8.38: 54 8.38 - 10.48: 18 Bond angle restraints: 33711 Sorted by residual: angle pdb=" N GLY K 55 " pdb=" CA GLY K 55 " pdb=" C GLY K 55 " ideal model delta sigma weight residual 115.21 107.59 7.62 1.30e+00 5.92e-01 3.43e+01 angle pdb=" N GLY H 55 " pdb=" CA GLY H 55 " pdb=" C GLY H 55 " ideal model delta sigma weight residual 115.21 107.61 7.60 1.30e+00 5.92e-01 3.42e+01 angle pdb=" N GLY P 55 " pdb=" CA GLY P 55 " pdb=" C GLY P 55 " ideal model delta sigma weight residual 115.21 107.62 7.59 1.30e+00 5.92e-01 3.41e+01 angle pdb=" C TRP B 338 " pdb=" N SER B 339 " pdb=" CA SER B 339 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C TRP C 338 " pdb=" N SER C 339 " pdb=" CA SER C 339 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 ... (remaining 33706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.72: 14412 20.72 - 41.45: 1136 41.45 - 62.17: 262 62.17 - 82.89: 62 82.89 - 103.61: 22 Dihedral angle restraints: 15894 sinusoidal: 7443 harmonic: 8451 Sorted by residual: dihedral pdb=" CD ARG H 71 " pdb=" NE ARG H 71 " pdb=" CZ ARG H 71 " pdb=" NH1 ARG H 71 " ideal model delta sinusoidal sigma weight residual 0.00 -82.90 82.90 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CD ARG P 71 " pdb=" NE ARG P 71 " pdb=" CZ ARG P 71 " pdb=" NH1 ARG P 71 " ideal model delta sinusoidal sigma weight residual 0.00 -82.87 82.87 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CD ARG K 71 " pdb=" NE ARG K 71 " pdb=" CZ ARG K 71 " pdb=" NH1 ARG K 71 " ideal model delta sinusoidal sigma weight residual 0.00 -82.85 82.85 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 15891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3313 0.079 - 0.158: 628 0.158 - 0.236: 55 0.236 - 0.315: 9 0.315 - 0.394: 15 Chirality restraints: 4020 Sorted by residual: chirality pdb=" C1 NAG C 701 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG C 701 " pdb=" O5 NAG C 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 241 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 4017 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 71 " 1.086 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG P 71 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG P 71 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG P 71 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG P 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " -1.086 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG H 71 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 71 " 1.086 9.50e-02 1.11e+02 4.86e-01 1.43e+02 pdb=" NE ARG K 71 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG K 71 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG K 71 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG K 71 " 0.017 2.00e-02 2.50e+03 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5945 2.81 - 3.33: 20782 3.33 - 3.85: 38607 3.85 - 4.38: 43911 4.38 - 4.90: 77981 Nonbonded interactions: 187226 Sorted by model distance: nonbonded pdb=" OD1 ASP J 50 " pdb=" OG1 THR J 58 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP G 50 " pdb=" OG1 THR G 58 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP O 50 " pdb=" OG1 THR O 58 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR A 297 " pdb=" O ILE A 443 " model vdw 2.308 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" O ILE B 443 " model vdw 2.309 3.040 ... (remaining 187221 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'X' selection = chain 'e' } 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 'T' selection = chain 'a' selection = chain 'h' } ncs_group { reference = chain 'U' selection = chain 'b' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.050 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.069 24969 Z= 0.253 Angle : 1.057 12.628 34071 Z= 0.550 Chirality : 0.063 0.394 4020 Planarity : 0.016 0.487 4137 Dihedral : 15.846 103.613 10341 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.47 % Allowed : 13.16 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.15), residues: 2868 helix: -1.34 (0.27), residues: 333 sheet: -1.47 (0.17), residues: 969 loop : -1.84 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 94 TYR 0.018 0.002 TYR G 100 PHE 0.034 0.002 PHE A 647 TRP 0.033 0.002 TRP K 100D HIS 0.006 0.002 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00512 (24834) covalent geometry : angle 1.00614 (33711) SS BOND : bond 0.00640 ( 45) SS BOND : angle 2.92767 ( 90) hydrogen bonds : bond 0.21141 ( 721) hydrogen bonds : angle 8.65874 ( 2046) link_ALPHA1-3 : bond 0.01076 ( 9) link_ALPHA1-3 : angle 3.14645 ( 27) link_ALPHA1-6 : bond 0.00485 ( 6) link_ALPHA1-6 : angle 1.71717 ( 18) link_BETA1-4 : bond 0.01009 ( 30) link_BETA1-4 : angle 3.70084 ( 90) link_NAG-ASN : bond 0.00820 ( 45) link_NAG-ASN : angle 3.49599 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 561 time to evaluate : 0.851 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: A 39 TYR cc_start: 0.9206 (m-80) cc_final: 0.8929 (m-80) REVERT: A 46 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7709 (mtm-85) REVERT: A 107 ASP cc_start: 0.7887 (t0) cc_final: 0.7494 (t0) REVERT: A 111 LEU cc_start: 0.7907 (mt) cc_final: 0.7565 (mt) REVERT: A 200 VAL cc_start: 0.8975 (t) cc_final: 0.8738 (p) REVERT: A 215 ILE cc_start: 0.8686 (mm) cc_final: 0.8303 (pt) REVERT: A 354 HIS cc_start: 0.7821 (t-90) cc_final: 0.7421 (t-90) REVERT: A 474 ASN cc_start: 0.7240 (t0) cc_final: 0.6786 (p0) REVERT: A 575 GLN cc_start: 0.7449 (tm-30) cc_final: 0.6994 (tm-30) REVERT: G 13 LYS cc_start: 0.5690 (mmtp) cc_final: 0.5370 (mmmt) REVERT: G 22 CYS cc_start: 0.4457 (t) cc_final: 0.4161 (m) REVERT: G 100 TYR cc_start: 0.8690 (t80) cc_final: 0.8425 (t80) REVERT: G 100 MET cc_start: 0.8538 (mtt) cc_final: 0.8184 (mtt) REVERT: I 83 GLU cc_start: 0.7848 (tt0) cc_final: 0.7290 (tt0) REVERT: L 1 GLU cc_start: 0.7386 (pt0) cc_final: 0.7053 (tt0) REVERT: L 38 GLN cc_start: 0.5470 (tp-100) cc_final: 0.5144 (tp40) REVERT: L 90 GLN cc_start: 0.8556 (tp40) cc_final: 0.8344 (tp-100) REVERT: H 46 GLU cc_start: 0.5953 (mm-30) cc_final: 0.5688 (mm-30) REVERT: H 58 ASN cc_start: 0.8110 (t0) cc_final: 0.7900 (t0) REVERT: H 79 TYR cc_start: 0.7278 (m-80) cc_final: 0.6817 (m-10) REVERT: B 107 ASP cc_start: 0.7957 (t0) cc_final: 0.7633 (t0) REVERT: B 111 LEU cc_start: 0.7969 (mt) cc_final: 0.7555 (mt) REVERT: B 166 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8001 (mmt-90) REVERT: B 277 MET cc_start: 0.6748 (mtt) cc_final: 0.6432 (mtt) REVERT: B 354 HIS cc_start: 0.7757 (t-90) cc_final: 0.7516 (t70) REVERT: B 434 MET cc_start: 0.7853 (mtm) cc_final: 0.7588 (mtm) REVERT: B 474 ASN cc_start: 0.7269 (t0) cc_final: 0.6892 (p0) REVERT: B 575 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7074 (tm-30) REVERT: B 584 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7834 (mp0) REVERT: J 13 LYS cc_start: 0.5935 (mmtp) cc_final: 0.5638 (mmmt) REVERT: J 22 CYS cc_start: 0.4810 (t) cc_final: 0.4401 (m) REVERT: J 69 ILE cc_start: 0.7825 (mm) cc_final: 0.7591 (mm) REVERT: J 100 TYR cc_start: 0.8769 (p90) cc_final: 0.8411 (p90) REVERT: J 100 MET cc_start: 0.8563 (mtt) cc_final: 0.8123 (mtt) REVERT: M 83 GLU cc_start: 0.7685 (tt0) cc_final: 0.7352 (tt0) REVERT: N 38 GLN cc_start: 0.5641 (tp-100) cc_final: 0.5027 (tp-100) REVERT: K 46 GLU cc_start: 0.5911 (mm-30) cc_final: 0.5559 (mm-30) REVERT: K 79 TYR cc_start: 0.7418 (m-80) cc_final: 0.7196 (m-10) REVERT: K 109 VAL cc_start: 0.8180 (t) cc_final: 0.7939 (p) REVERT: C 54 CYS cc_start: 0.7501 (p) cc_final: 0.7242 (p) REVERT: C 107 ASP cc_start: 0.8008 (t0) cc_final: 0.7602 (t0) REVERT: C 111 LEU cc_start: 0.8054 (mt) cc_final: 0.7752 (mt) REVERT: C 434 MET cc_start: 0.7899 (mtm) cc_final: 0.7613 (mtm) REVERT: C 474 ASN cc_start: 0.7445 (t0) cc_final: 0.6874 (p0) REVERT: C 575 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7106 (tm-30) REVERT: C 584 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7688 (mp0) REVERT: O 13 LYS cc_start: 0.5443 (mmtp) cc_final: 0.5172 (mmmt) REVERT: O 22 CYS cc_start: 0.5072 (t) cc_final: 0.4705 (m) REVERT: O 100 MET cc_start: 0.8603 (mtt) cc_final: 0.8276 (mtt) REVERT: Q 45 VAL cc_start: 0.8694 (m) cc_final: 0.8492 (p) REVERT: Q 83 GLU cc_start: 0.7892 (tt0) cc_final: 0.7660 (tt0) REVERT: R 38 GLN cc_start: 0.5909 (tp-100) cc_final: 0.4678 (tm-30) REVERT: R 83 PHE cc_start: 0.4707 (m-80) cc_final: 0.4462 (m-80) REVERT: P 34 MET cc_start: 0.8369 (tpp) cc_final: 0.8133 (tpp) outliers start: 12 outliers final: 7 residues processed: 570 average time/residue: 0.1847 time to fit residues: 159.5978 Evaluate side-chains 456 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 449 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain R residue 97 PHE Chi-restraints excluded: chain P residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.0770 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 103 GLN A 195 ASN L 38 GLN H 105 GLN B 103 GLN B 195 ASN B 330 HIS B 620 GLN N 27 GLN N 38 GLN N 90 GLN K 102 HIS K 105 GLN C 92 ASN C 103 GLN C 330 HIS C 354 HIS C 620 GLN Q 79 GLN R 27 GLN R 38 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.156103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118876 restraints weight = 42403.309| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.19 r_work: 0.3384 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24969 Z= 0.153 Angle : 0.696 11.558 34071 Z= 0.343 Chirality : 0.049 0.426 4020 Planarity : 0.005 0.042 4137 Dihedral : 9.994 72.308 5036 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.78 % Allowed : 15.98 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.15), residues: 2868 helix: -0.74 (0.28), residues: 336 sheet: -1.15 (0.17), residues: 960 loop : -1.63 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 71 TYR 0.016 0.001 TYR B 484 PHE 0.016 0.002 PHE R 98 TRP 0.017 0.001 TRP P 100D HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00348 (24834) covalent geometry : angle 0.64905 (33711) SS BOND : bond 0.00829 ( 45) SS BOND : angle 1.89615 ( 90) hydrogen bonds : bond 0.04509 ( 721) hydrogen bonds : angle 6.52935 ( 2046) link_ALPHA1-3 : bond 0.00950 ( 9) link_ALPHA1-3 : angle 3.04076 ( 27) link_ALPHA1-6 : bond 0.00225 ( 6) link_ALPHA1-6 : angle 1.82552 ( 18) link_BETA1-4 : bond 0.00576 ( 30) link_BETA1-4 : angle 2.54864 ( 90) link_NAG-ASN : bond 0.00523 ( 45) link_NAG-ASN : angle 2.82539 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 443 time to evaluate : 0.912 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: A 39 TYR cc_start: 0.9296 (m-80) cc_final: 0.8917 (m-80) REVERT: A 46 ARG cc_start: 0.8151 (mtp-110) cc_final: 0.7807 (mtm-85) REVERT: A 111 LEU cc_start: 0.8133 (mt) cc_final: 0.7898 (mt) REVERT: A 354 HIS cc_start: 0.7617 (t-90) cc_final: 0.7291 (t-90) REVERT: A 474 ASN cc_start: 0.7294 (t0) cc_final: 0.6919 (t0) REVERT: A 575 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 632 ASP cc_start: 0.7900 (t0) cc_final: 0.7602 (t0) REVERT: G 13 LYS cc_start: 0.5533 (mmtp) cc_final: 0.5254 (mmmt) REVERT: G 100 TYR cc_start: 0.8693 (t80) cc_final: 0.8348 (t80) REVERT: G 100 MET cc_start: 0.8611 (mtt) cc_final: 0.8108 (mtt) REVERT: I 83 GLU cc_start: 0.7916 (tt0) cc_final: 0.7359 (tt0) REVERT: I 103 LYS cc_start: 0.7836 (tptt) cc_final: 0.7555 (tppt) REVERT: L 1 GLU cc_start: 0.7546 (pt0) cc_final: 0.7091 (tt0) REVERT: H 46 GLU cc_start: 0.5963 (mm-30) cc_final: 0.5508 (mm-30) REVERT: B 166 ARG cc_start: 0.8344 (mtp85) cc_final: 0.8025 (mmt-90) REVERT: B 354 HIS cc_start: 0.7425 (t-90) cc_final: 0.6983 (t-90) REVERT: B 434 MET cc_start: 0.7990 (mtm) cc_final: 0.7693 (mtm) REVERT: B 474 ASN cc_start: 0.7590 (t0) cc_final: 0.7159 (t0) REVERT: B 575 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7130 (tm-30) REVERT: J 13 LYS cc_start: 0.5791 (mmtp) cc_final: 0.5589 (mmmt) REVERT: J 69 ILE cc_start: 0.7719 (mm) cc_final: 0.7429 (mm) REVERT: J 100 TYR cc_start: 0.8765 (p90) cc_final: 0.8407 (p90) REVERT: J 100 MET cc_start: 0.8614 (mtt) cc_final: 0.7921 (mtt) REVERT: M 83 GLU cc_start: 0.7739 (tt0) cc_final: 0.7460 (tt0) REVERT: N 1 GLU cc_start: 0.7430 (pt0) cc_final: 0.6985 (tt0) REVERT: K 34 MET cc_start: 0.8313 (tpp) cc_final: 0.8026 (tpp) REVERT: K 39 GLN cc_start: 0.7081 (tp40) cc_final: 0.6841 (tp40) REVERT: K 46 GLU cc_start: 0.5867 (mm-30) cc_final: 0.5521 (mm-30) REVERT: K 58 ASN cc_start: 0.7554 (t0) cc_final: 0.6931 (t0) REVERT: K 101 GLN cc_start: 0.8649 (tt0) cc_final: 0.8444 (mm-40) REVERT: C 429 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8384 (mtmt) REVERT: C 434 MET cc_start: 0.8022 (mtm) cc_final: 0.7694 (mtm) REVERT: C 474 ASN cc_start: 0.7421 (t0) cc_final: 0.7002 (t0) REVERT: C 575 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7059 (tm-30) REVERT: C 632 ASP cc_start: 0.7633 (t0) cc_final: 0.7341 (t0) REVERT: O 100 MET cc_start: 0.8587 (mtt) cc_final: 0.8158 (mtt) REVERT: R 83 PHE cc_start: 0.4703 (m-80) cc_final: 0.4452 (m-80) REVERT: P 39 GLN cc_start: 0.6981 (tp40) cc_final: 0.6632 (tp40) REVERT: P 100 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.6673 (m-10) outliers start: 71 outliers final: 36 residues processed: 484 average time/residue: 0.1798 time to fit residues: 132.9844 Evaluate side-chains 445 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 408 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 48 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN A 620 GLN G 100JHIS H 96 ASN B 195 ASN J 39 GLN J 100JHIS N 27 GLN N 38 GLN N 90 GLN K 102 HIS K 105 GLN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 100JHIS R 27 GLN R 38 GLN P 39 GLN P 105 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.150942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109051 restraints weight = 42938.293| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.86 r_work: 0.3300 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 24969 Z= 0.252 Angle : 0.748 9.649 34071 Z= 0.361 Chirality : 0.051 0.485 4020 Planarity : 0.005 0.045 4137 Dihedral : 9.306 67.510 5022 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.00 % Allowed : 16.76 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.15), residues: 2868 helix: -0.81 (0.27), residues: 354 sheet: -1.17 (0.16), residues: 1005 loop : -1.63 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 77 TYR 0.029 0.002 TYR A 484 PHE 0.017 0.002 PHE O 78 TRP 0.017 0.002 TRP Q 66 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00601 (24834) covalent geometry : angle 0.69816 (33711) SS BOND : bond 0.00915 ( 45) SS BOND : angle 2.23295 ( 90) hydrogen bonds : bond 0.04291 ( 721) hydrogen bonds : angle 6.18418 ( 2046) link_ALPHA1-3 : bond 0.01043 ( 9) link_ALPHA1-3 : angle 3.36376 ( 27) link_ALPHA1-6 : bond 0.00449 ( 6) link_ALPHA1-6 : angle 2.34640 ( 18) link_BETA1-4 : bond 0.00654 ( 30) link_BETA1-4 : angle 2.54706 ( 90) link_NAG-ASN : bond 0.00586 ( 45) link_NAG-ASN : angle 2.98472 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 398 time to evaluate : 0.899 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: A 46 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7863 (mtm-85) REVERT: A 414 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8755 (mt) REVERT: A 542 ARG cc_start: 0.6497 (ptt180) cc_final: 0.6203 (ptm160) REVERT: A 575 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7184 (tm-30) REVERT: G 13 LYS cc_start: 0.5540 (mmtp) cc_final: 0.5250 (mmmt) REVERT: G 63 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7731 (tt) REVERT: G 100 MET cc_start: 0.8752 (mtt) cc_final: 0.8260 (mtt) REVERT: I 74 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8229 (p) REVERT: I 83 GLU cc_start: 0.7848 (tt0) cc_final: 0.7223 (tt0) REVERT: L 1 GLU cc_start: 0.7527 (pt0) cc_final: 0.7185 (pt0) REVERT: L 83 PHE cc_start: 0.4442 (m-80) cc_final: 0.4234 (m-80) REVERT: L 90 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8075 (tp40) REVERT: H 46 GLU cc_start: 0.6056 (mm-30) cc_final: 0.5537 (mm-30) REVERT: H 100 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.7133 (m-10) REVERT: B 166 ARG cc_start: 0.8439 (mtp85) cc_final: 0.8073 (mmt-90) REVERT: B 280 ASN cc_start: 0.7565 (m-40) cc_final: 0.7331 (p0) REVERT: B 434 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7907 (mtm) REVERT: B 575 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7337 (tm-30) REVERT: J 13 LYS cc_start: 0.5799 (mmtp) cc_final: 0.5572 (mmmt) REVERT: J 69 ILE cc_start: 0.7776 (mm) cc_final: 0.7427 (mm) REVERT: M 74 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8241 (p) REVERT: M 83 GLU cc_start: 0.7885 (tt0) cc_final: 0.7505 (tt0) REVERT: N 38 GLN cc_start: 0.5624 (OUTLIER) cc_final: 0.4028 (tp-100) REVERT: K 34 MET cc_start: 0.8436 (tpp) cc_final: 0.8222 (tpp) REVERT: K 39 GLN cc_start: 0.7040 (tp40) cc_final: 0.6799 (tp40) REVERT: K 46 GLU cc_start: 0.5840 (mm-30) cc_final: 0.5384 (mm-30) REVERT: K 58 ASN cc_start: 0.7845 (t0) cc_final: 0.7092 (t0) REVERT: K 100 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.6934 (m100) REVERT: K 101 GLN cc_start: 0.8767 (tt0) cc_final: 0.8545 (mm110) REVERT: C 429 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8442 (mtmt) REVERT: C 434 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7714 (mtm) REVERT: C 575 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7382 (tm-30) REVERT: O 100 MET cc_start: 0.8648 (mtt) cc_final: 0.8441 (mtt) REVERT: Q 61 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7913 (mtm110) REVERT: R 83 PHE cc_start: 0.4589 (m-80) cc_final: 0.4284 (m-80) REVERT: P 100 TRP cc_start: 0.7390 (OUTLIER) cc_final: 0.6637 (m100) outliers start: 102 outliers final: 59 residues processed: 455 average time/residue: 0.1757 time to fit residues: 121.5533 Evaluate side-chains 436 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 367 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 71 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 274 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 227 optimal weight: 0.1980 chunk 160 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 616 ASN N 27 GLN N 38 GLN N 90 GLN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN R 27 GLN R 38 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112283 restraints weight = 42170.886| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.81 r_work: 0.3338 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24969 Z= 0.145 Angle : 0.667 13.750 34071 Z= 0.321 Chirality : 0.048 0.437 4020 Planarity : 0.004 0.034 4137 Dihedral : 8.655 65.013 5022 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.03 % Allowed : 17.35 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.16), residues: 2868 helix: -0.46 (0.28), residues: 336 sheet: -1.07 (0.17), residues: 1005 loop : -1.44 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 76 TYR 0.016 0.001 TYR C 484 PHE 0.013 0.001 PHE A 317 TRP 0.016 0.001 TRP Q 66 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00339 (24834) covalent geometry : angle 0.61613 (33711) SS BOND : bond 0.00653 ( 45) SS BOND : angle 2.32556 ( 90) hydrogen bonds : bond 0.03748 ( 721) hydrogen bonds : angle 5.90475 ( 2046) link_ALPHA1-3 : bond 0.01185 ( 9) link_ALPHA1-3 : angle 3.16620 ( 27) link_ALPHA1-6 : bond 0.00224 ( 6) link_ALPHA1-6 : angle 1.79174 ( 18) link_BETA1-4 : bond 0.00539 ( 30) link_BETA1-4 : angle 2.32626 ( 90) link_NAG-ASN : bond 0.00517 ( 45) link_NAG-ASN : angle 2.80992 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 392 time to evaluate : 0.916 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: A 46 ARG cc_start: 0.8193 (mtp-110) cc_final: 0.7871 (mtm-85) REVERT: A 352 TYR cc_start: 0.7600 (m-80) cc_final: 0.7338 (m-80) REVERT: A 414 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8687 (mt) REVERT: A 542 ARG cc_start: 0.6382 (ptt180) cc_final: 0.6064 (ptm160) REVERT: A 575 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7282 (tm-30) REVERT: G 13 LYS cc_start: 0.5550 (mmtp) cc_final: 0.5268 (mmmt) REVERT: G 23 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7724 (p) REVERT: G 63 LEU cc_start: 0.7927 (tt) cc_final: 0.7710 (tt) REVERT: G 100 MET cc_start: 0.8674 (mtt) cc_final: 0.8162 (mtt) REVERT: I 74 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8116 (p) REVERT: I 83 GLU cc_start: 0.7799 (tt0) cc_final: 0.7171 (tt0) REVERT: L 1 GLU cc_start: 0.7578 (pt0) cc_final: 0.7247 (pt0) REVERT: L 27 GLN cc_start: 0.7374 (tt0) cc_final: 0.6816 (pm20) REVERT: H 46 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5532 (mm-30) REVERT: H 66 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7934 (ttt90) REVERT: H 100 TRP cc_start: 0.7535 (OUTLIER) cc_final: 0.7003 (m-10) REVERT: B 166 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8046 (mmt-90) REVERT: B 352 TYR cc_start: 0.7462 (m-80) cc_final: 0.7223 (m-80) REVERT: B 434 MET cc_start: 0.8090 (mtm) cc_final: 0.7790 (mtm) REVERT: B 575 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7386 (tm-30) REVERT: J 13 LYS cc_start: 0.5837 (mmtp) cc_final: 0.5605 (mmmt) REVERT: J 22 CYS cc_start: 0.4493 (t) cc_final: 0.4155 (m) REVERT: J 23 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7686 (p) REVERT: J 69 ILE cc_start: 0.7714 (mm) cc_final: 0.7410 (mm) REVERT: J 100 TYR cc_start: 0.8790 (p90) cc_final: 0.8449 (p90) REVERT: J 100 MET cc_start: 0.8626 (mtt) cc_final: 0.8131 (mtt) REVERT: M 74 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8167 (p) REVERT: M 83 GLU cc_start: 0.7830 (tt0) cc_final: 0.7446 (tt0) REVERT: N 38 GLN cc_start: 0.5879 (OUTLIER) cc_final: 0.4530 (tp-100) REVERT: K 34 MET cc_start: 0.8416 (tpp) cc_final: 0.8189 (tpp) REVERT: K 46 GLU cc_start: 0.5774 (mm-30) cc_final: 0.5314 (mm-30) REVERT: K 100 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.6718 (m100) REVERT: K 101 GLN cc_start: 0.8645 (tt0) cc_final: 0.8385 (mm110) REVERT: C 352 TYR cc_start: 0.7607 (m-80) cc_final: 0.7304 (m-80) REVERT: C 429 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8463 (mtmt) REVERT: C 434 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7640 (mtm) REVERT: C 575 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7032 (tm-30) REVERT: O 22 CYS cc_start: 0.4586 (t) cc_final: 0.4328 (m) REVERT: O 38 ARG cc_start: 0.7872 (tmm-80) cc_final: 0.7647 (tmm-80) REVERT: O 100 MET cc_start: 0.8634 (mtt) cc_final: 0.8376 (mtt) REVERT: R 38 GLN cc_start: 0.5614 (tp40) cc_final: 0.5344 (tt0) REVERT: R 83 PHE cc_start: 0.4460 (m-80) cc_final: 0.4172 (m-80) REVERT: P 39 GLN cc_start: 0.6706 (tp40) cc_final: 0.6463 (tp40) REVERT: P 100 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.6556 (m100) outliers start: 103 outliers final: 50 residues processed: 452 average time/residue: 0.1850 time to fit residues: 127.0844 Evaluate side-chains 429 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 369 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 177 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 199 optimal weight: 0.4980 chunk 65 optimal weight: 0.0050 chunk 265 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 616 ASN M 42 GLN N 27 GLN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN Q 79 GLN R 27 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.152000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110482 restraints weight = 42053.828| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.85 r_work: 0.3324 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 24969 Z= 0.176 Angle : 0.690 13.262 34071 Z= 0.332 Chirality : 0.048 0.438 4020 Planarity : 0.004 0.035 4137 Dihedral : 8.362 64.895 5022 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.88 % Allowed : 18.37 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.16), residues: 2868 helix: -0.44 (0.28), residues: 336 sheet: -0.97 (0.17), residues: 999 loop : -1.40 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 76 TYR 0.017 0.001 TYR C 484 PHE 0.012 0.002 PHE A 317 TRP 0.017 0.002 TRP M 66 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00421 (24834) covalent geometry : angle 0.63438 (33711) SS BOND : bond 0.00852 ( 45) SS BOND : angle 2.93814 ( 90) hydrogen bonds : bond 0.03727 ( 721) hydrogen bonds : angle 5.79492 ( 2046) link_ALPHA1-3 : bond 0.01163 ( 9) link_ALPHA1-3 : angle 3.24453 ( 27) link_ALPHA1-6 : bond 0.00222 ( 6) link_ALPHA1-6 : angle 1.96325 ( 18) link_BETA1-4 : bond 0.00547 ( 30) link_BETA1-4 : angle 2.30929 ( 90) link_NAG-ASN : bond 0.00515 ( 45) link_NAG-ASN : angle 2.80743 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 386 time to evaluate : 0.737 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: A 46 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7881 (mtm-85) REVERT: A 414 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 542 ARG cc_start: 0.6460 (ptt180) cc_final: 0.6055 (ptm160) REVERT: A 575 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 605 CYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6939 (m) REVERT: G 13 LYS cc_start: 0.5554 (mmtp) cc_final: 0.5299 (mmmt) REVERT: G 38 ARG cc_start: 0.8035 (tmm-80) cc_final: 0.7782 (tmm-80) REVERT: G 63 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7595 (tt) REVERT: G 100 MET cc_start: 0.8736 (mtt) cc_final: 0.8270 (mtt) REVERT: I 74 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8172 (p) REVERT: I 83 GLU cc_start: 0.7817 (tt0) cc_final: 0.7169 (tt0) REVERT: L 1 GLU cc_start: 0.7534 (pt0) cc_final: 0.7138 (pt0) REVERT: L 27 GLN cc_start: 0.7420 (tt0) cc_final: 0.6872 (pm20) REVERT: L 96 GLU cc_start: 0.6423 (pt0) cc_final: 0.6191 (pt0) REVERT: H 46 GLU cc_start: 0.6016 (mm-30) cc_final: 0.5587 (mm-30) REVERT: H 94 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6740 (ttt-90) REVERT: H 100 TRP cc_start: 0.7541 (OUTLIER) cc_final: 0.7010 (m-10) REVERT: B 166 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8071 (mmt-90) REVERT: B 280 ASN cc_start: 0.7394 (m-40) cc_final: 0.7048 (p0) REVERT: B 434 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7816 (mtm) REVERT: B 575 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7202 (tm-30) REVERT: J 13 LYS cc_start: 0.5812 (mmtp) cc_final: 0.5604 (mmmt) REVERT: J 23 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7846 (p) REVERT: J 38 ARG cc_start: 0.8213 (tmm-80) cc_final: 0.8005 (tmm-80) REVERT: J 69 ILE cc_start: 0.7678 (mm) cc_final: 0.7445 (mm) REVERT: J 100 MET cc_start: 0.8627 (mtt) cc_final: 0.8151 (mtt) REVERT: M 74 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8220 (p) REVERT: N 38 GLN cc_start: 0.5625 (tp40) cc_final: 0.4828 (tt0) REVERT: N 96 GLU cc_start: 0.6486 (pt0) cc_final: 0.6147 (pt0) REVERT: K 34 MET cc_start: 0.8417 (tpp) cc_final: 0.8180 (tpp) REVERT: K 39 GLN cc_start: 0.6815 (tp40) cc_final: 0.6399 (tp40) REVERT: K 46 GLU cc_start: 0.5768 (mm-30) cc_final: 0.5270 (mm-30) REVERT: K 100 TRP cc_start: 0.7284 (OUTLIER) cc_final: 0.6991 (m100) REVERT: K 101 GLN cc_start: 0.8666 (tt0) cc_final: 0.8222 (mm-40) REVERT: C 280 ASN cc_start: 0.7527 (m-40) cc_final: 0.7230 (p0) REVERT: C 352 TYR cc_start: 0.7697 (m-80) cc_final: 0.7340 (m-80) REVERT: C 429 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8527 (mtmt) REVERT: C 434 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7683 (mtm) REVERT: C 575 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7080 (tm-30) REVERT: O 23 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7550 (p) REVERT: O 38 ARG cc_start: 0.7937 (tmm-80) cc_final: 0.7727 (tmm-80) REVERT: O 100 MET cc_start: 0.8653 (mtt) cc_final: 0.8417 (mtt) REVERT: Q 74 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8427 (p) REVERT: R 83 PHE cc_start: 0.4505 (m-80) cc_final: 0.4194 (m-80) REVERT: R 96 GLU cc_start: 0.6323 (pt0) cc_final: 0.5960 (pt0) REVERT: P 94 ARG cc_start: 0.7058 (ttp80) cc_final: 0.6742 (ttp80) REVERT: P 100 TRP cc_start: 0.7198 (OUTLIER) cc_final: 0.6734 (m100) outliers start: 99 outliers final: 62 residues processed: 443 average time/residue: 0.1734 time to fit residues: 115.9172 Evaluate side-chains 446 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 371 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 30 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 287 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN L 6 GLN H 96 ASN M 42 GLN N 27 GLN N 90 GLN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN R 6 GLN R 27 GLN R 38 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.150126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108352 restraints weight = 42072.104| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.86 r_work: 0.3282 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 24969 Z= 0.237 Angle : 0.735 14.103 34071 Z= 0.352 Chirality : 0.050 0.479 4020 Planarity : 0.004 0.035 4137 Dihedral : 8.513 66.407 5022 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.35 % Allowed : 18.21 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.16), residues: 2868 helix: -0.66 (0.28), residues: 336 sheet: -0.90 (0.17), residues: 966 loop : -1.45 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 76 TYR 0.019 0.002 TYR A 484 PHE 0.017 0.002 PHE A 651 TRP 0.019 0.002 TRP I 66 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00565 (24834) covalent geometry : angle 0.68191 (33711) SS BOND : bond 0.00732 ( 45) SS BOND : angle 2.68377 ( 90) hydrogen bonds : bond 0.03906 ( 721) hydrogen bonds : angle 5.83291 ( 2046) link_ALPHA1-3 : bond 0.01191 ( 9) link_ALPHA1-3 : angle 3.38224 ( 27) link_ALPHA1-6 : bond 0.00322 ( 6) link_ALPHA1-6 : angle 2.22347 ( 18) link_BETA1-4 : bond 0.00573 ( 30) link_BETA1-4 : angle 2.34867 ( 90) link_NAG-ASN : bond 0.00584 ( 45) link_NAG-ASN : angle 2.97739 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 377 time to evaluate : 0.985 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: A 46 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7887 (mtm-85) REVERT: A 414 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8718 (mt) REVERT: A 542 ARG cc_start: 0.6519 (ptt180) cc_final: 0.6252 (ptm160) REVERT: A 575 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7287 (tm-30) REVERT: G 13 LYS cc_start: 0.5604 (mmtp) cc_final: 0.5336 (mmmt) REVERT: G 38 ARG cc_start: 0.8153 (tmm-80) cc_final: 0.7888 (tmm-80) REVERT: G 63 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7595 (tt) REVERT: G 100 MET cc_start: 0.8712 (mtt) cc_final: 0.8249 (mtt) REVERT: I 61 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7747 (mtm110) REVERT: I 83 GLU cc_start: 0.7887 (tt0) cc_final: 0.7213 (tt0) REVERT: L 1 GLU cc_start: 0.7394 (pt0) cc_final: 0.7045 (pt0) REVERT: L 27 GLN cc_start: 0.7630 (tt0) cc_final: 0.6993 (pm20) REVERT: H 46 GLU cc_start: 0.6016 (mm-30) cc_final: 0.5579 (mm-30) REVERT: H 94 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6928 (ttp80) REVERT: H 100 TRP cc_start: 0.7459 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: B 434 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7863 (mtm) REVERT: B 542 ARG cc_start: 0.6260 (ptt180) cc_final: 0.5963 (ptm160) REVERT: B 575 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7278 (tm-30) REVERT: B 610 TRP cc_start: 0.6749 (t-100) cc_final: 0.6203 (t-100) REVERT: J 13 LYS cc_start: 0.5812 (mmtp) cc_final: 0.5596 (mmmt) REVERT: J 23 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7876 (p) REVERT: J 69 ILE cc_start: 0.7666 (mm) cc_final: 0.7427 (mm) REVERT: J 100 MET cc_start: 0.8672 (mtt) cc_final: 0.8184 (mtt) REVERT: M 74 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8241 (p) REVERT: N 38 GLN cc_start: 0.5533 (tp40) cc_final: 0.4723 (tt0) REVERT: K 39 GLN cc_start: 0.6752 (tp40) cc_final: 0.6311 (tp40) REVERT: K 46 GLU cc_start: 0.5863 (mm-30) cc_final: 0.5391 (mm-30) REVERT: K 100 TRP cc_start: 0.7236 (OUTLIER) cc_final: 0.6699 (m100) REVERT: C 352 TYR cc_start: 0.7754 (m-80) cc_final: 0.7395 (m-80) REVERT: C 434 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7737 (mtm) REVERT: C 542 ARG cc_start: 0.6648 (ptt180) cc_final: 0.6131 (ptm160) REVERT: C 575 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7129 (tm-30) REVERT: O 23 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7884 (p) REVERT: Q 74 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8407 (p) REVERT: R 83 PHE cc_start: 0.4386 (m-80) cc_final: 0.4071 (m-80) REVERT: P 94 ARG cc_start: 0.7205 (ttp80) cc_final: 0.6857 (ttt-90) REVERT: P 100 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.6830 (m-10) outliers start: 111 outliers final: 74 residues processed: 443 average time/residue: 0.1852 time to fit residues: 124.1698 Evaluate side-chains 448 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 363 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN B 377 ASN M 42 GLN N 6 GLN N 27 GLN O 95 ASN Q 42 GLN R 27 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.151192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109661 restraints weight = 41930.432| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.86 r_work: 0.3305 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24969 Z= 0.172 Angle : 0.692 13.553 34071 Z= 0.332 Chirality : 0.048 0.446 4020 Planarity : 0.004 0.035 4137 Dihedral : 8.268 64.943 5022 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.80 % Allowed : 18.96 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.16), residues: 2868 helix: -0.42 (0.29), residues: 318 sheet: -0.84 (0.17), residues: 969 loop : -1.33 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 76 TYR 0.014 0.001 TYR C 484 PHE 0.013 0.002 PHE A 317 TRP 0.019 0.002 TRP I 66 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00407 (24834) covalent geometry : angle 0.64152 (33711) SS BOND : bond 0.00764 ( 45) SS BOND : angle 2.46229 ( 90) hydrogen bonds : bond 0.03644 ( 721) hydrogen bonds : angle 5.68854 ( 2046) link_ALPHA1-3 : bond 0.01208 ( 9) link_ALPHA1-3 : angle 3.26657 ( 27) link_ALPHA1-6 : bond 0.00231 ( 6) link_ALPHA1-6 : angle 1.92865 ( 18) link_BETA1-4 : bond 0.00526 ( 30) link_BETA1-4 : angle 2.23904 ( 90) link_NAG-ASN : bond 0.00517 ( 45) link_NAG-ASN : angle 2.85510 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 386 time to evaluate : 0.940 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: A 46 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7855 (mtm-85) REVERT: A 200 VAL cc_start: 0.9073 (t) cc_final: 0.8810 (m) REVERT: A 414 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8683 (mt) REVERT: A 542 ARG cc_start: 0.6415 (ptt180) cc_final: 0.6199 (ptm160) REVERT: A 575 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7210 (tm-30) REVERT: G 13 LYS cc_start: 0.5583 (mmtp) cc_final: 0.5314 (mmmt) REVERT: G 38 ARG cc_start: 0.8186 (tmm-80) cc_final: 0.7925 (tmm-80) REVERT: G 63 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7593 (tt) REVERT: G 100 MET cc_start: 0.8693 (mtt) cc_final: 0.8254 (mtt) REVERT: I 83 GLU cc_start: 0.7879 (tt0) cc_final: 0.7210 (tt0) REVERT: L 1 GLU cc_start: 0.7374 (pt0) cc_final: 0.7030 (pt0) REVERT: L 27 GLN cc_start: 0.7645 (tt0) cc_final: 0.6977 (pm20) REVERT: H 46 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5682 (mm-30) REVERT: H 100 TRP cc_start: 0.7465 (OUTLIER) cc_final: 0.6965 (m-10) REVERT: B 280 ASN cc_start: 0.7495 (m-40) cc_final: 0.7159 (p0) REVERT: B 434 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7808 (mtm) REVERT: B 542 ARG cc_start: 0.6258 (ptt180) cc_final: 0.6011 (ptm160) REVERT: B 575 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 584 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7754 (mp0) REVERT: B 610 TRP cc_start: 0.6718 (t-100) cc_final: 0.6204 (t-100) REVERT: J 5 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.7027 (mmm-85) REVERT: J 13 LYS cc_start: 0.5817 (mmtp) cc_final: 0.5561 (mmmt) REVERT: J 22 CYS cc_start: 0.4372 (t) cc_final: 0.4094 (m) REVERT: J 23 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7780 (p) REVERT: J 100 MET cc_start: 0.8610 (mtt) cc_final: 0.8147 (mtt) REVERT: M 61 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7652 (mtm110) REVERT: M 74 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8207 (p) REVERT: N 38 GLN cc_start: 0.5466 (tp40) cc_final: 0.4609 (tt0) REVERT: K 34 MET cc_start: 0.8398 (tpp) cc_final: 0.7934 (tpp) REVERT: K 39 GLN cc_start: 0.6696 (tp40) cc_final: 0.6341 (tp40) REVERT: K 46 GLU cc_start: 0.5824 (mm-30) cc_final: 0.5286 (mm-30) REVERT: K 100 TRP cc_start: 0.7205 (OUTLIER) cc_final: 0.6816 (m100) REVERT: K 101 GLN cc_start: 0.8978 (mt0) cc_final: 0.8626 (mt0) REVERT: C 110 SER cc_start: 0.9040 (m) cc_final: 0.8824 (m) REVERT: C 280 ASN cc_start: 0.7655 (m-40) cc_final: 0.7069 (p0) REVERT: C 352 TYR cc_start: 0.7753 (m-80) cc_final: 0.7427 (m-80) REVERT: C 434 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7726 (mtm) REVERT: C 542 ARG cc_start: 0.6572 (ptt180) cc_final: 0.6272 (ptm160) REVERT: C 575 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7072 (tm-30) REVERT: Q 74 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8391 (p) REVERT: R 83 PHE cc_start: 0.4391 (m-80) cc_final: 0.4103 (m-80) REVERT: R 96 GLU cc_start: 0.6403 (pt0) cc_final: 0.5881 (pt0) REVERT: P 68 THR cc_start: 0.8749 (m) cc_final: 0.8490 (p) REVERT: P 94 ARG cc_start: 0.6992 (ttp80) cc_final: 0.6702 (ttp80) REVERT: P 100 TRP cc_start: 0.7150 (OUTLIER) cc_final: 0.6925 (m-10) outliers start: 97 outliers final: 71 residues processed: 442 average time/residue: 0.1907 time to fit residues: 127.6986 Evaluate side-chains 449 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 368 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 88 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 278 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 42 GLN M 42 GLN N 27 GLN N 90 GLN C 478 ASN O 100JHIS Q 42 GLN R 27 GLN R 37 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.148411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106463 restraints weight = 41986.446| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.84 r_work: 0.3258 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 24969 Z= 0.288 Angle : 0.791 13.843 34071 Z= 0.379 Chirality : 0.051 0.500 4020 Planarity : 0.005 0.041 4137 Dihedral : 8.665 68.184 5022 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.11 % Allowed : 19.08 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.16), residues: 2868 helix: -0.85 (0.27), residues: 336 sheet: -0.92 (0.17), residues: 978 loop : -1.49 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 94 TYR 0.021 0.002 TYR C 484 PHE 0.018 0.002 PHE K 97 TRP 0.018 0.002 TRP M 66 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00687 (24834) covalent geometry : angle 0.73489 (33711) SS BOND : bond 0.00996 ( 45) SS BOND : angle 3.05026 ( 90) hydrogen bonds : bond 0.04040 ( 721) hydrogen bonds : angle 5.93036 ( 2046) link_ALPHA1-3 : bond 0.01154 ( 9) link_ALPHA1-3 : angle 3.50535 ( 27) link_ALPHA1-6 : bond 0.00457 ( 6) link_ALPHA1-6 : angle 2.39930 ( 18) link_BETA1-4 : bond 0.00613 ( 30) link_BETA1-4 : angle 2.39774 ( 90) link_NAG-ASN : bond 0.00637 ( 45) link_NAG-ASN : angle 3.10338 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 365 time to evaluate : 0.910 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: A 46 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7893 (mtm-85) REVERT: A 200 VAL cc_start: 0.9097 (t) cc_final: 0.8846 (m) REVERT: A 414 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (mt) REVERT: A 542 ARG cc_start: 0.6516 (ptt180) cc_final: 0.6271 (ptm160) REVERT: A 575 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7359 (tm-30) REVERT: G 13 LYS cc_start: 0.5616 (mmtp) cc_final: 0.5335 (mmmt) REVERT: G 38 ARG cc_start: 0.8214 (tmm-80) cc_final: 0.7945 (tmm-80) REVERT: G 63 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7628 (tt) REVERT: G 100 MET cc_start: 0.8728 (mtt) cc_final: 0.8306 (mtt) REVERT: I 83 GLU cc_start: 0.7920 (tt0) cc_final: 0.7275 (tt0) REVERT: L 1 GLU cc_start: 0.7291 (pt0) cc_final: 0.6970 (pt0) REVERT: L 27 GLN cc_start: 0.7873 (tt0) cc_final: 0.7067 (pm20) REVERT: L 96 GLU cc_start: 0.6729 (pt0) cc_final: 0.6361 (pt0) REVERT: H 46 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5581 (mm-30) REVERT: H 94 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6979 (ttt-90) REVERT: H 100 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.7009 (m-10) REVERT: B 434 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7936 (mtm) REVERT: B 542 ARG cc_start: 0.6519 (ptt180) cc_final: 0.6193 (ptm160) REVERT: B 543 GLN cc_start: 0.5495 (tp40) cc_final: 0.5110 (tp40) REVERT: B 575 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 610 TRP cc_start: 0.6776 (t-100) cc_final: 0.6216 (t-100) REVERT: J 13 LYS cc_start: 0.5893 (mmtp) cc_final: 0.5645 (mmmt) REVERT: J 23 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7858 (p) REVERT: J 100 MET cc_start: 0.8698 (mtt) cc_final: 0.8240 (mtt) REVERT: K 34 MET cc_start: 0.8493 (tpp) cc_final: 0.8031 (tpp) REVERT: K 46 GLU cc_start: 0.5855 (mm-30) cc_final: 0.5356 (mm-30) REVERT: K 100 TRP cc_start: 0.7161 (OUTLIER) cc_final: 0.6758 (m-10) REVERT: C 110 SER cc_start: 0.9124 (m) cc_final: 0.8852 (m) REVERT: C 352 TYR cc_start: 0.7903 (m-80) cc_final: 0.7552 (m-80) REVERT: C 434 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7810 (mtm) REVERT: C 542 ARG cc_start: 0.6668 (ptt180) cc_final: 0.6352 (ptm160) REVERT: C 575 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7173 (tm-30) REVERT: O 23 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7882 (p) REVERT: R 83 PHE cc_start: 0.4030 (m-80) cc_final: 0.3774 (m-80) REVERT: P 68 THR cc_start: 0.8757 (m) cc_final: 0.8476 (p) REVERT: P 94 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6798 (ttt-90) REVERT: P 100 TRP cc_start: 0.7167 (OUTLIER) cc_final: 0.6669 (m-10) outliers start: 105 outliers final: 78 residues processed: 427 average time/residue: 0.1777 time to fit residues: 116.2771 Evaluate side-chains 442 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 355 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 162 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 620 GLN A 624 ASN I 42 GLN M 42 GLN N 27 GLN C 92 ASN C 195 ASN C 354 HIS Q 42 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.148295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106180 restraints weight = 42354.170| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.84 r_work: 0.3261 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24969 Z= 0.265 Angle : 0.777 14.100 34071 Z= 0.373 Chirality : 0.051 0.498 4020 Planarity : 0.004 0.062 4137 Dihedral : 8.773 69.003 5022 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.76 % Allowed : 19.55 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.16), residues: 2868 helix: -0.91 (0.27), residues: 336 sheet: -0.94 (0.17), residues: 969 loop : -1.51 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 76 TYR 0.023 0.002 TYR R 36 PHE 0.013 0.002 PHE J 78 TRP 0.017 0.002 TRP M 66 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00636 (24834) covalent geometry : angle 0.72116 (33711) SS BOND : bond 0.00919 ( 45) SS BOND : angle 3.02109 ( 90) hydrogen bonds : bond 0.03978 ( 721) hydrogen bonds : angle 5.95301 ( 2046) link_ALPHA1-3 : bond 0.01249 ( 9) link_ALPHA1-3 : angle 3.52459 ( 27) link_ALPHA1-6 : bond 0.00363 ( 6) link_ALPHA1-6 : angle 2.18920 ( 18) link_BETA1-4 : bond 0.00567 ( 30) link_BETA1-4 : angle 2.34880 ( 90) link_NAG-ASN : bond 0.00605 ( 45) link_NAG-ASN : angle 3.11190 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 361 time to evaluate : 0.834 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: A 46 ARG cc_start: 0.8205 (mtp-110) cc_final: 0.7908 (mtm-85) REVERT: A 200 VAL cc_start: 0.9066 (t) cc_final: 0.8822 (m) REVERT: A 414 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8752 (mt) REVERT: A 575 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7342 (tm-30) REVERT: G 13 LYS cc_start: 0.5584 (mmtp) cc_final: 0.5312 (mmmt) REVERT: G 38 ARG cc_start: 0.8239 (tmm-80) cc_final: 0.7956 (tmm-80) REVERT: G 63 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7649 (tt) REVERT: G 100 MET cc_start: 0.8706 (mtt) cc_final: 0.8288 (mtt) REVERT: I 83 GLU cc_start: 0.7934 (tt0) cc_final: 0.7255 (tt0) REVERT: L 27 GLN cc_start: 0.7852 (tt0) cc_final: 0.7058 (pm20) REVERT: L 96 GLU cc_start: 0.6815 (pt0) cc_final: 0.6427 (pt0) REVERT: H 46 GLU cc_start: 0.6085 (mm-30) cc_final: 0.5660 (mm-30) REVERT: H 100 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.6926 (m-10) REVERT: B 434 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: B 542 ARG cc_start: 0.6572 (ptt180) cc_final: 0.6229 (ptm160) REVERT: B 543 GLN cc_start: 0.5621 (tp40) cc_final: 0.5218 (tp40) REVERT: B 575 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 584 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7792 (mp0) REVERT: B 610 TRP cc_start: 0.6797 (t-100) cc_final: 0.6255 (t-100) REVERT: J 5 ARG cc_start: 0.7486 (mmm-85) cc_final: 0.7140 (mmm-85) REVERT: J 13 LYS cc_start: 0.5966 (mmtp) cc_final: 0.5726 (mmmt) REVERT: J 23 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7850 (p) REVERT: J 100 MET cc_start: 0.8695 (mtt) cc_final: 0.8260 (mtt) REVERT: M 76 ARG cc_start: 0.7745 (mmt-90) cc_final: 0.7278 (mmp80) REVERT: N 38 GLN cc_start: 0.5521 (tp40) cc_final: 0.4820 (tt0) REVERT: N 61 ARG cc_start: 0.6413 (ptt-90) cc_final: 0.5970 (ptp90) REVERT: K 34 MET cc_start: 0.8526 (tpp) cc_final: 0.8262 (tpp) REVERT: K 46 GLU cc_start: 0.5882 (mm-30) cc_final: 0.5460 (mm-30) REVERT: K 100 TRP cc_start: 0.7113 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: C 110 SER cc_start: 0.9125 (m) cc_final: 0.8849 (m) REVERT: C 352 TYR cc_start: 0.7908 (m-80) cc_final: 0.7548 (m-80) REVERT: C 434 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7802 (mtm) REVERT: C 542 ARG cc_start: 0.6772 (ptt180) cc_final: 0.6384 (ptm160) REVERT: C 543 GLN cc_start: 0.5636 (tp40) cc_final: 0.5301 (tp40) REVERT: C 575 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7183 (tm-30) REVERT: O 100 MET cc_start: 0.8514 (mtt) cc_final: 0.8209 (mtt) REVERT: R 83 PHE cc_start: 0.4049 (m-80) cc_final: 0.3782 (m-80) REVERT: P 94 ARG cc_start: 0.7029 (ttp80) cc_final: 0.6689 (ttp80) REVERT: P 100 TRP cc_start: 0.7223 (OUTLIER) cc_final: 0.6345 (m100) outliers start: 96 outliers final: 77 residues processed: 419 average time/residue: 0.1898 time to fit residues: 120.0731 Evaluate side-chains 436 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 351 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 89 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 235 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN G 95 ASN I 42 GLN M 42 GLN N 27 GLN N 90 GLN C 195 ASN C 354 HIS C 478 ASN Q 42 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109170 restraints weight = 42035.535| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.82 r_work: 0.3301 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 24969 Z= 0.164 Angle : 0.713 14.551 34071 Z= 0.341 Chirality : 0.048 0.453 4020 Planarity : 0.004 0.040 4137 Dihedral : 8.407 66.291 5022 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.41 % Allowed : 20.09 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.16), residues: 2868 helix: -0.54 (0.28), residues: 318 sheet: -0.79 (0.18), residues: 936 loop : -1.33 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 61 TYR 0.013 0.001 TYR R 49 PHE 0.015 0.002 PHE L 83 TRP 0.026 0.002 TRP I 66 HIS 0.006 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00390 (24834) covalent geometry : angle 0.65781 (33711) SS BOND : bond 0.00872 ( 45) SS BOND : angle 2.89282 ( 90) hydrogen bonds : bond 0.03682 ( 721) hydrogen bonds : angle 5.75333 ( 2046) link_ALPHA1-3 : bond 0.01190 ( 9) link_ALPHA1-3 : angle 3.36849 ( 27) link_ALPHA1-6 : bond 0.00208 ( 6) link_ALPHA1-6 : angle 1.84742 ( 18) link_BETA1-4 : bond 0.00498 ( 30) link_BETA1-4 : angle 2.19475 ( 90) link_NAG-ASN : bond 0.00529 ( 45) link_NAG-ASN : angle 2.92510 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 369 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7880 (mtm-85) REVERT: A 200 VAL cc_start: 0.9065 (t) cc_final: 0.8838 (m) REVERT: A 414 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8687 (mt) REVERT: A 575 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7210 (tm-30) REVERT: G 13 LYS cc_start: 0.5594 (mmtp) cc_final: 0.5356 (mmmt) REVERT: G 38 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7952 (tmm-80) REVERT: G 100 MET cc_start: 0.8656 (mtt) cc_final: 0.8252 (mtt) REVERT: I 83 GLU cc_start: 0.7907 (tt0) cc_final: 0.7230 (tt0) REVERT: L 27 GLN cc_start: 0.7834 (tt0) cc_final: 0.7078 (pm20) REVERT: L 96 GLU cc_start: 0.6670 (pt0) cc_final: 0.6306 (pt0) REVERT: H 37 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7974 (m) REVERT: H 46 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5543 (mm-30) REVERT: H 100 TRP cc_start: 0.7384 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: B 434 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: B 543 GLN cc_start: 0.5549 (tp40) cc_final: 0.5140 (tp40) REVERT: B 575 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7181 (tm-30) REVERT: B 584 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7746 (mp0) REVERT: J 6 GLU cc_start: 0.6688 (mp0) cc_final: 0.5840 (mp0) REVERT: J 13 LYS cc_start: 0.5967 (mmtp) cc_final: 0.5759 (mmmt) REVERT: J 23 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7792 (p) REVERT: J 100 MET cc_start: 0.8605 (mtt) cc_final: 0.8172 (mtt) REVERT: M 76 ARG cc_start: 0.7722 (mmt-90) cc_final: 0.7300 (mmp80) REVERT: N 27 GLN cc_start: 0.7901 (tt0) cc_final: 0.7576 (tt0) REVERT: N 38 GLN cc_start: 0.5499 (tp40) cc_final: 0.4756 (tt0) REVERT: N 61 ARG cc_start: 0.6359 (ptt-90) cc_final: 0.5978 (ptp90) REVERT: K 34 MET cc_start: 0.8456 (tpp) cc_final: 0.8246 (tpp) REVERT: K 37 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7822 (m) REVERT: K 46 GLU cc_start: 0.5833 (mm-30) cc_final: 0.5303 (mm-30) REVERT: K 100 TRP cc_start: 0.7015 (OUTLIER) cc_final: 0.6556 (m-10) REVERT: C 110 SER cc_start: 0.9034 (m) cc_final: 0.8787 (m) REVERT: C 352 TYR cc_start: 0.7863 (m-80) cc_final: 0.7554 (m-80) REVERT: C 434 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7774 (mtm) REVERT: C 542 ARG cc_start: 0.6664 (ptt180) cc_final: 0.6288 (ptm160) REVERT: C 543 GLN cc_start: 0.5537 (tp40) cc_final: 0.5218 (tp40) REVERT: C 575 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7107 (tm-30) REVERT: C 584 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7727 (mp0) REVERT: R 83 PHE cc_start: 0.4000 (m-80) cc_final: 0.3725 (m-80) REVERT: P 37 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7643 (m) REVERT: P 94 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6642 (ttp80) REVERT: P 100 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6590 (m-10) outliers start: 87 outliers final: 71 residues processed: 420 average time/residue: 0.1803 time to fit residues: 115.2726 Evaluate side-chains 441 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 360 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 268 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 240 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN I 42 GLN B 195 ASN M 42 GLN N 90 GLN C 354 HIS C 478 ASN Q 42 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109101 restraints weight = 41804.531| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.84 r_work: 0.3298 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 24969 Z= 0.229 Angle : 0.890 59.192 34071 Z= 0.481 Chirality : 0.050 0.740 4020 Planarity : 0.005 0.224 4137 Dihedral : 8.398 66.277 5022 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.33 % Allowed : 20.37 % Favored : 76.30 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.16), residues: 2868 helix: -0.53 (0.28), residues: 318 sheet: -0.77 (0.18), residues: 936 loop : -1.33 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 633 TYR 0.013 0.001 TYR R 49 PHE 0.013 0.002 PHE A 317 TRP 0.023 0.002 TRP I 66 HIS 0.368 0.006 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00474 (24834) covalent geometry : angle 0.84489 (33711) SS BOND : bond 0.01602 ( 45) SS BOND : angle 3.29849 ( 90) hydrogen bonds : bond 0.03864 ( 721) hydrogen bonds : angle 5.75366 ( 2046) link_ALPHA1-3 : bond 0.01181 ( 9) link_ALPHA1-3 : angle 3.36697 ( 27) link_ALPHA1-6 : bond 0.00205 ( 6) link_ALPHA1-6 : angle 1.84228 ( 18) link_BETA1-4 : bond 0.00493 ( 30) link_BETA1-4 : angle 2.18959 ( 90) link_NAG-ASN : bond 0.00529 ( 45) link_NAG-ASN : angle 2.92615 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6093.13 seconds wall clock time: 105 minutes 17.97 seconds (6317.97 seconds total)