Starting phenix.real_space_refine on Tue Aug 26 04:28:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y7x_39025/08_2025/8y7x_39025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y7x_39025/08_2025/8y7x_39025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y7x_39025/08_2025/8y7x_39025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y7x_39025/08_2025/8y7x_39025.map" model { file = "/net/cci-nas-00/data/ceres_data/8y7x_39025/08_2025/8y7x_39025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y7x_39025/08_2025/8y7x_39025.cif" } resolution = 3.09 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= 0.001 sd= 0.023 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 206 5.16 5 C 21179 2.51 5 N 5440 2.21 5 O 6423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33248 Number of models: 1 Model: "" Number of chains: 19 Chain: "B" Number of atoms: 9302 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1195, 9294 Classifications: {'peptide': 1195} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 1146} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 1195, 9294 Classifications: {'peptide': 1195} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 1146} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 9515 Chain: "A" Number of atoms: 9305 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1197, 9297 Classifications: {'peptide': 1197} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 1148} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 1197, 9297 Classifications: {'peptide': 1197} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 1148} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 9518 Chain: "C" Number of atoms: 9285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1195, 9277 Classifications: {'peptide': 1195} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 1146} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 1195, 9277 Classifications: {'peptide': 1195} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 1146} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 9498 Chain: "x" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1582 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 221} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 3, 'TYR:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 174 Chain: "y" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1586 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 221} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 3, 'TYR:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 174 Chain: "z" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1586 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 221} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 3, 'TYR:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 174 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 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 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASP B 366 " occ=0.46 ... (14 atoms not shown) pdb=" OD2BASP B 366 " occ=0.54 residue: pdb=" N AASP A 366 " occ=0.61 ... (14 atoms not shown) pdb=" OD2BASP A 366 " occ=0.39 residue: pdb=" N AASP C 366 " occ=0.42 ... (14 atoms not shown) pdb=" OD2BASP C 366 " occ=0.58 Time building chain proxies: 14.03, per 1000 atoms: 0.42 Number of scatterers: 33248 At special positions: 0 Unit cell: (149.24, 158.26, 238.62, 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 206 16.00 O 6423 8.00 N 5440 7.00 C 21179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 899 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B1117 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS B1167 " - pdb=" SG CYS B1212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 720 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 899 " distance=2.03 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1128 " distance=2.03 Simple disulfide: pdb=" SG CYS A1167 " - pdb=" SG CYS A1212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 569 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 720 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 899 " distance=2.04 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C1117 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS C1167 " - pdb=" SG CYS C1212 " distance=2.03 Simple disulfide: pdb=" SG CYS x 410 " - pdb=" SG CYS x 426 " distance=2.03 Simple disulfide: pdb=" SG CYS x 437 " - pdb=" SG CYS x 465 " distance=2.03 Simple disulfide: pdb=" SG CYS y 410 " - pdb=" SG CYS y 426 " distance=2.03 Simple disulfide: pdb=" SG CYS y 437 " - pdb=" SG CYS y 465 " distance=2.03 Simple disulfide: pdb=" SG CYS z 410 " - pdb=" SG CYS z 426 " distance=2.03 Simple disulfide: pdb=" SG CYS z 437 " - pdb=" SG CYS z 465 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1301 " - " ASN A 775 " " NAG A1302 " - " ASN A 780 " " NAG A1303 " - " ASN A 797 " " NAG A1304 " - " ASN A 928 " " NAG A1305 " - " ASN A 705 " " NAG A1306 " - " ASN A 686 " " NAG A1307 " - " ASN A 58 " " NAG A1308 " - " ASN A 666 " " NAG B1301 " - " ASN B 686 " " NAG B1302 " - " ASN B 780 " " NAG B1303 " - " ASN B 797 " " NAG B1304 " - " ASN B 928 " " NAG B1305 " - " ASN B 705 " " NAG B1306 " - " ASN B 58 " " NAG B1307 " - " ASN B 666 " " NAG B1308 " - " ASN B 775 " " NAG C1301 " - " ASN C 775 " " NAG C1302 " - " ASN C 780 " " NAG C1303 " - " ASN C 797 " " NAG C1304 " - " ASN C 928 " " NAG C1305 " - " ASN C 705 " " NAG C1306 " - " ASN C 686 " " NAG C1307 " - " ASN C 666 " " NAG D 1 " - " ASN B 188 " " NAG E 1 " - " ASN B 726 " " NAG F 1 " - " ASN B1215 " " NAG G 1 " - " ASN A 188 " " NAG H 1 " - " ASN A 726 " " NAG I 1 " - " ASN A1215 " " NAG J 1 " - " ASN C 188 " " NAG K 1 " - " ASN C 726 " " NAG L 1 " - " ASN C1215 " " NAG M 1 " - " ASN C 58 " Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 2.4 seconds Enol-peptide restraints added in 1.2 microseconds 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8056 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 74 sheets defined 22.4% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 285 through 295 removed outlier: 4.376A pdb=" N GLU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.723A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 removed outlier: 3.883A pdb=" N TRP B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 374 through 379 removed outlier: 4.154A pdb=" N TYR B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.509A pdb=" N ASP B 400 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 402 " --> pdb=" O SER B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 402' Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'B' and resid 478 through 484 removed outlier: 3.799A pdb=" N SER B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.569A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.574A pdb=" N VAL B 702 " --> pdb=" O LYS B 698 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 703 " --> pdb=" O CYS B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 698 through 703' Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 826 through 834 removed outlier: 3.731A pdb=" N HIS B 830 " --> pdb=" O TYR B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 865 removed outlier: 3.579A pdb=" N LEU B 865 " --> pdb=" O VAL B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 913 Processing helix chain 'B' and resid 918 through 927 Processing helix chain 'B' and resid 937 through 946 removed outlier: 4.001A pdb=" N VAL B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 969 removed outlier: 3.587A pdb=" N ILE B 959 " --> pdb=" O SER B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 993 Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.855A pdb=" N LEU B1001 " --> pdb=" O THR B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1021 removed outlier: 3.521A pdb=" N ILE B1008 " --> pdb=" O ASN B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1049 Processing helix chain 'B' and resid 1050 through 1053 removed outlier: 3.890A pdb=" N ASN B1053 " --> pdb=" O GLN B1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1050 through 1053' Processing helix chain 'B' and resid 1061 through 1069 removed outlier: 3.988A pdb=" N LEU B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1118 removed outlier: 4.812A pdb=" N VAL B1076 " --> pdb=" O PRO B1072 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B1080 " --> pdb=" O VAL B1076 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B1081 " --> pdb=" O GLN B1077 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B1109 " --> pdb=" O PHE B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1206 removed outlier: 3.725A pdb=" N ASN B1205 " --> pdb=" O SER B1202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B1206 " --> pdb=" O ASP B1203 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1202 through 1206' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.640A pdb=" N THR A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 341 through 344 removed outlier: 4.011A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.627A pdb=" N ILE A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.544A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.665A pdb=" N SER A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 698 through 705 Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 838 through 866 removed outlier: 3.547A pdb=" N LEU A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 855 " --> pdb=" O ASN A 851 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 removed outlier: 3.657A pdb=" N VAL A 892 " --> pdb=" O LYS A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 905 through 913 Processing helix chain 'A' and resid 918 through 927 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 955 through 969 removed outlier: 3.541A pdb=" N ILE A 959 " --> pdb=" O SER A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 993 Processing helix chain 'A' and resid 997 through 1004 removed outlier: 3.802A pdb=" N LEU A1001 " --> pdb=" O THR A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1022 Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 3.571A pdb=" N ALA A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A1036 " --> pdb=" O LYS A1032 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1037 " --> pdb=" O ILE A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1053 removed outlier: 4.017A pdb=" N ASN A1053 " --> pdb=" O GLN A1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1050 through 1053' Processing helix chain 'A' and resid 1061 through 1066 removed outlier: 3.562A pdb=" N ILE A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.727A pdb=" N GLN A1075 " --> pdb=" O PRO A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1118 removed outlier: 4.106A pdb=" N SER A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A1103 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.719A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.644A pdb=" N ARG C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.712A pdb=" N SER C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 698 through 705 Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 826 through 834 removed outlier: 3.682A pdb=" N HIS C 830 " --> pdb=" O TYR C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 866 removed outlier: 3.543A pdb=" N ASN C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C 866 " --> pdb=" O ALA C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 913 Processing helix chain 'C' and resid 918 through 928 removed outlier: 3.951A pdb=" N VAL C 923 " --> pdb=" O ASP C 919 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 928 " --> pdb=" O GLU C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 944 removed outlier: 3.875A pdb=" N VAL C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 969 removed outlier: 3.573A pdb=" N ILE C 959 " --> pdb=" O SER C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 993 Processing helix chain 'C' and resid 997 through 1004 removed outlier: 3.760A pdb=" N LEU C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C1003 " --> pdb=" O ASP C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1021 removed outlier: 3.683A pdb=" N ILE C1008 " --> pdb=" O ASN C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1049 removed outlier: 3.587A pdb=" N ALA C1031 " --> pdb=" O ASN C1027 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C1037 " --> pdb=" O ILE C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1053 removed outlier: 3.569A pdb=" N ASN C1053 " --> pdb=" O GLN C1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1050 through 1053' Processing helix chain 'C' and resid 1070 through 1118 removed outlier: 4.796A pdb=" N VAL C1076 " --> pdb=" O PRO C1072 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN C1077 " --> pdb=" O GLU C1073 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C1080 " --> pdb=" O VAL C1076 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C1081 " --> pdb=" O GLN C1077 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C1101 " --> pdb=" O LEU C1097 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C1102 " --> pdb=" O SER C1098 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C1103 " --> pdb=" O ASP C1099 " (cutoff:3.500A) Processing helix chain 'x' and resid 295 through 299 removed outlier: 3.668A pdb=" N GLU x 299 " --> pdb=" O HIS x 296 " (cutoff:3.500A) Processing helix chain 'x' and resid 406 through 411 Processing helix chain 'x' and resid 476 through 491 removed outlier: 4.063A pdb=" N PHE x 480 " --> pdb=" O ASN x 476 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP x 482 " --> pdb=" O MET x 478 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TRP x 483 " --> pdb=" O VAL x 479 " (cutoff:3.500A) Processing helix chain 'y' and resid 295 through 299 removed outlier: 3.687A pdb=" N GLU y 299 " --> pdb=" O HIS y 296 " (cutoff:3.500A) Processing helix chain 'y' and resid 406 through 411 Processing helix chain 'y' and resid 480 through 491 Processing helix chain 'z' and resid 295 through 299 removed outlier: 3.630A pdb=" N GLU z 299 " --> pdb=" O HIS z 296 " (cutoff:3.500A) Processing helix chain 'z' and resid 406 through 411 Processing helix chain 'z' and resid 477 through 491 removed outlier: 4.910A pdb=" N ASP z 482 " --> pdb=" O MET z 478 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TRP z 483 " --> pdb=" O VAL z 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 67 removed outlier: 3.736A pdb=" N ASN B 278 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.790A pdb=" N ARG B 75 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.963A pdb=" N GLY B 81 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.884A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AA6, first strand: chain 'B' and resid 302 through 305 removed outlier: 3.725A pdb=" N TYR B 694 " --> pdb=" O CYS B 720 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS B 720 " --> pdb=" O TYR B 694 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.688A pdb=" N GLY B 677 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 316 through 319 removed outlier: 7.410A pdb=" N VAL B 317 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB1, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.778A pdb=" N SER B 385 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 426 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 367 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER B 428 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.747A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AB5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AB6, first strand: chain 'B' and resid 649 through 651 removed outlier: 6.559A pdb=" N LEU B 650 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 667 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 725 through 732 removed outlier: 6.704A pdb=" N ASP B 725 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR B 770 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N LEU B 727 " --> pdb=" O THR B 770 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 777 through 779 removed outlier: 6.285A pdb=" N SER B 777 " --> pdb=" O LEU C 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 790 through 808 removed outlier: 6.724A pdb=" N SER B1156 " --> pdb=" O THR B 796 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE B 798 " --> pdb=" O PRO B1154 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 800 " --> pdb=" O TYR B1152 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR B1152 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 802 " --> pdb=" O PHE B1150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B1150 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU B 804 " --> pdb=" O MET B1148 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET B1148 " --> pdb=" O GLU B 804 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE B 806 " --> pdb=" O LEU B1146 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B1146 " --> pdb=" O PHE B 806 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN B 808 " --> pdb=" O GLY B1144 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY B1144 " --> pdb=" O GLN B 808 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B1135 " --> pdb=" O PHE B1150 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR B1152 " --> pdb=" O HIS B1133 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS B1133 " --> pdb=" O TYR B1152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 813 through 816 removed outlier: 4.212A pdb=" N LYS B 813 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 870 through 872 Processing sheet with id=AC3, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AC4, first strand: chain 'B' and resid 1207 through 1209 Processing sheet with id=AC5, first strand: chain 'B' and resid 1179 through 1184 Processing sheet with id=AC6, first strand: chain 'A' and resid 59 through 67 removed outlier: 3.835A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.135A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 221 through 227 removed outlier: 4.995A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 109 through 112 removed outlier: 4.082A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 120 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 187 through 190 removed outlier: 4.183A pdb=" N LYS A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 148 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.634A pdb=" N LEU A 692 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 315 through 319 removed outlier: 6.431A pdb=" N ALA A 315 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP A 625 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 317 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 667 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 662 " --> pdb=" O LYS A 667 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 660 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE A 658 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 650 " --> pdb=" O ILE A 658 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.854A pdb=" N ASN A 437 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.748A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.661A pdb=" N PHE A 354 " --> pdb=" O CYS A 605 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 604 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AD8, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AD9, first strand: chain 'A' and resid 473 through 477 removed outlier: 3.549A pdb=" N CYS A 474 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 502 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N CYS A 476 " --> pdb=" O ARG A 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 505 through 507 removed outlier: 3.977A pdb=" N TRP A 515 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AE3, first strand: chain 'A' and resid 725 through 732 removed outlier: 6.528A pdb=" N ASP A 725 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR A 770 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N LEU A 727 " --> pdb=" O THR A 770 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 790 through 808 removed outlier: 6.602A pdb=" N SER A1156 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE A 798 " --> pdb=" O PRO A1154 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 800 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A1152 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY A 802 " --> pdb=" O PHE A1150 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A1150 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU A 804 " --> pdb=" O MET A1148 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET A1148 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE A 806 " --> pdb=" O LEU A1146 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A1146 " --> pdb=" O PHE A 806 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN A 808 " --> pdb=" O GLY A1144 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A1144 " --> pdb=" O GLN A 808 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1135 " --> pdb=" O PHE A1150 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A1152 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS A1133 " --> pdb=" O TYR A1152 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.158A pdb=" N LYS A 813 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 870 through 872 removed outlier: 6.917A pdb=" N LEU A 871 " --> pdb=" O VAL C 779 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AE8, first strand: chain 'A' and resid 1206 through 1209 Processing sheet with id=AE9, first strand: chain 'A' and resid 1179 through 1183 Processing sheet with id=AF1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF2, first strand: chain 'C' and resid 60 through 67 removed outlier: 3.799A pdb=" N ASN C 278 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.592A pdb=" N ARG C 75 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 203 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 211 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.846A pdb=" N GLY C 81 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 110 through 112 Processing sheet with id=AF6, first strand: chain 'C' and resid 136 through 139 removed outlier: 4.172A pdb=" N THR C 123 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 145 through 148 removed outlier: 3.714A pdb=" N PHE C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AF9, first strand: chain 'C' and resid 316 through 319 removed outlier: 6.759A pdb=" N VAL C 317 " --> pdb=" O ASP C 625 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 667 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.994A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 345 through 349 removed outlier: 4.007A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS C 390 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER C 428 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.657A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 505 through 507 Processing sheet with id=AG6, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG7, first strand: chain 'C' and resid 725 through 732 removed outlier: 6.774A pdb=" N PHE C 768 " --> pdb=" O ASN C 726 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR C 770 " --> pdb=" O THR C 728 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR C 730 " --> pdb=" O THR C 770 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 790 through 808 removed outlier: 6.579A pdb=" N SER C1156 " --> pdb=" O THR C 796 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE C 798 " --> pdb=" O PRO C1154 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 800 " --> pdb=" O TYR C1152 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR C1152 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY C 802 " --> pdb=" O PHE C1150 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE C1150 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU C 804 " --> pdb=" O MET C1148 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET C1148 " --> pdb=" O GLU C 804 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE C 806 " --> pdb=" O LEU C1146 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU C1146 " --> pdb=" O PHE C 806 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN C 808 " --> pdb=" O GLY C1144 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY C1144 " --> pdb=" O GLN C 808 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C1135 " --> pdb=" O PHE C1150 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR C1152 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS C1133 " --> pdb=" O TYR C1152 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 813 through 816 removed outlier: 4.175A pdb=" N LYS C 813 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AH2, first strand: chain 'C' and resid 1206 through 1209 Processing sheet with id=AH3, first strand: chain 'C' and resid 1180 through 1184 Processing sheet with id=AH4, first strand: chain 'x' and resid 260 through 261 removed outlier: 7.327A pdb=" N LEU x 378 " --> pdb=" O SER x 448 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER x 448 " --> pdb=" O LEU x 378 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU x 445 " --> pdb=" O ILE x 456 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'x' and resid 260 through 261 removed outlier: 4.366A pdb=" N CYS x 426 " --> pdb=" O ILE x 405 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'x' and resid 279 through 281 Processing sheet with id=AH7, first strand: chain 'x' and resid 284 through 287 removed outlier: 3.971A pdb=" N ILE x 286 " --> pdb=" O TRP x 290 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TRP x 290 " --> pdb=" O ILE x 286 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU x 348 " --> pdb=" O VAL x 331 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL x 331 " --> pdb=" O LEU x 348 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS x 350 " --> pdb=" O GLU x 329 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'y' and resid 260 through 261 removed outlier: 4.067A pdb=" N CYS y 426 " --> pdb=" O ILE y 405 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL y 473 " --> pdb=" O SER y 460 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU y 445 " --> pdb=" O ILE y 456 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER y 382 " --> pdb=" O PRO y 444 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER y 448 " --> pdb=" O LEU y 378 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU y 378 " --> pdb=" O SER y 448 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'y' and resid 309 through 312 removed outlier: 4.097A pdb=" N ILE y 286 " --> pdb=" O TRP y 290 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP y 290 " --> pdb=" O ILE y 286 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU y 348 " --> pdb=" O VAL y 331 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL y 331 " --> pdb=" O LEU y 348 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS y 350 " --> pdb=" O GLU y 329 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'z' and resid 260 through 261 removed outlier: 4.003A pdb=" N CYS z 426 " --> pdb=" O ILE z 405 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL z 473 " --> pdb=" O SER z 460 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER z 460 " --> pdb=" O VAL z 473 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU z 445 " --> pdb=" O ILE z 456 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER z 382 " --> pdb=" O PRO z 444 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER z 448 " --> pdb=" O LEU z 378 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU z 378 " --> pdb=" O SER z 448 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'z' and resid 309 through 312 removed outlier: 4.101A pdb=" N ILE z 286 " --> pdb=" O TRP z 290 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TRP z 290 " --> pdb=" O ILE z 286 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU z 348 " --> pdb=" O VAL z 331 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL z 331 " --> pdb=" O LEU z 348 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS z 350 " --> pdb=" O GLU z 329 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2879 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: 9.48 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10555 1.34 - 1.46: 8665 1.46 - 1.58: 14609 1.58 - 1.70: 0 1.70 - 1.82: 244 Bond restraints: 34073 Sorted by residual: bond pdb=" C PRO B1071 " pdb=" N PRO B1072 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.19e-02 7.06e+03 8.28e+00 bond pdb=" N LEU A 52 " pdb=" CA LEU A 52 " ideal model delta sigma weight residual 1.453 1.475 -0.022 1.41e-02 5.03e+03 2.44e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 34068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 44737 1.20 - 2.41: 1424 2.41 - 3.61: 332 3.61 - 4.82: 22 4.82 - 6.02: 10 Bond angle restraints: 46525 Sorted by residual: angle pdb=" N GLY B 893 " pdb=" CA GLY B 893 " pdb=" C GLY B 893 " ideal model delta sigma weight residual 110.21 114.66 -4.45 9.10e-01 1.21e+00 2.40e+01 angle pdb=" N VAL B 641 " pdb=" CA VAL B 641 " pdb=" C VAL B 641 " ideal model delta sigma weight residual 113.20 109.61 3.59 9.60e-01 1.09e+00 1.40e+01 angle pdb=" N LEU C1221 " pdb=" CA LEU C1221 " pdb=" C LEU C1221 " ideal model delta sigma weight residual 114.75 110.38 4.37 1.26e+00 6.30e-01 1.20e+01 angle pdb=" N CYS C 823 " pdb=" CA CYS C 823 " pdb=" C CYS C 823 " ideal model delta sigma weight residual 108.52 114.09 -5.57 1.63e+00 3.76e-01 1.17e+01 angle pdb=" C VAL C 509 " pdb=" N LEU C 510 " pdb=" CA LEU C 510 " ideal model delta sigma weight residual 120.54 125.09 -4.55 1.35e+00 5.49e-01 1.14e+01 ... (remaining 46520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 19913 16.53 - 33.06: 576 33.06 - 49.59: 128 49.59 - 66.12: 27 66.12 - 82.65: 1 Dihedral angle restraints: 20645 sinusoidal: 8090 harmonic: 12555 Sorted by residual: dihedral pdb=" CA ILE A1168 " pdb=" C ILE A1168 " pdb=" N SER A1169 " pdb=" CA SER A1169 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB CYS A 894 " pdb=" SG CYS A 894 " pdb=" SG CYS A 899 " pdb=" CB CYS A 899 " ideal model delta sinusoidal sigma weight residual -86.00 -125.32 39.32 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CA ILE C1168 " pdb=" C ILE C1168 " pdb=" N SER C1169 " pdb=" CA SER C1169 " ideal model delta harmonic sigma weight residual -180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 20642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3770 0.035 - 0.070: 1094 0.070 - 0.106: 403 0.106 - 0.141: 136 0.141 - 0.176: 3 Chirality restraints: 5406 Sorted by residual: chirality pdb=" CA LYS A 115 " pdb=" N LYS A 115 " pdb=" C LYS A 115 " pdb=" CB LYS A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" C2 NAG B1304 " pdb=" C1 NAG B1304 " pdb=" C3 NAG B1304 " pdb=" N2 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA VAL A 113 " pdb=" N VAL A 113 " pdb=" C VAL A 113 " pdb=" CB VAL A 113 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 5403 not shown) Planarity restraints: 5958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 112 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C TYR A 112 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR A 112 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 113 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 495 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 496 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 496 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 496 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 495 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO B 496 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.021 5.00e-02 4.00e+02 ... (remaining 5955 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2306 2.74 - 3.28: 31551 3.28 - 3.82: 52040 3.82 - 4.36: 59769 4.36 - 4.90: 106276 Nonbonded interactions: 251942 Sorted by model distance: nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.201 3.040 nonbonded pdb=" O VAL C 113 " pdb=" OG1 THR C 116 " model vdw 2.211 3.040 nonbonded pdb=" OG SER B 340 " pdb=" OD1 ASN B 343 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASN B 108 " pdb=" OG SER B 119 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASN C 108 " pdb=" OG SER C 119 " model vdw 2.229 3.040 ... (remaining 251937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 154 or (resid 155 and (name N or n \ ame CA or name C or name O or name CB )) or resid 156 through 335 or (resid 336 \ and (name N or name CA or name C or name O or name CB )) or resid 337 through 36 \ 5 or resid 367 through 397 or (resid 398 and (name N or name CA or name C or nam \ e O or name CB )) or resid 399 through 602 or (resid 603 and (name N or name CA \ or name C or name O or name CB )) or resid 604 through 606 or (resid 607 through \ 610 and (name N or name CA or name C or name O or name CB )) or resid 611 throu \ gh 749 or resid 766 through 897 or (resid 898 and (name N or name CA or name C o \ r name O or name CB )) or resid 899 through 1072 or (resid 1073 through 1074 and \ (name N or name CA or name C or name O or name CB )) or resid 1075 through 1307 \ )) selection = (chain 'B' and (resid 14 through 21 or (resid 22 through 24 and (name N or name \ CA or name C or name O or name CB )) or resid 25 through 154 or (resid 155 and ( \ name N or name CA or name C or name O or name CB )) or resid 156 through 335 or \ (resid 336 and (name N or name CA or name C or name O or name CB )) or resid 337 \ through 365 or resid 367 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 602 or (resid 603 and (name N \ or name CA or name C or name O or name CB )) or resid 604 through 606 or (resid \ 607 through 610 and (name N or name CA or name C or name O or name CB )) or resi \ d 611 through 935 or (resid 936 and (name N or name CA or name C or name O or na \ me CB )) or resid 937 through 1072 or (resid 1073 through 1074 and (name N or na \ me CA or name C or name O or name CB )) or resid 1075 through 1307)) selection = (chain 'C' and (resid 14 through 21 or (resid 22 through 24 and (name N or name \ CA or name C or name O or name CB )) or resid 25 through 82 or (resid 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 365 or res \ id 367 through 607 or (resid 608 through 610 and (name N or name CA or name C or \ name O or name CB )) or resid 611 through 897 or (resid 898 and (name N or name \ CA or name C or name O or name CB )) or resid 899 through 935 or (resid 936 and \ (name N or name CA or name C or name O or name CB )) or resid 937 through 1307) \ ) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'x' selection = (chain 'y' and (resid 256 through 466 or (resid 467 through 468 and (name N or n \ ame CA or name C or name O or name CB )) or resid 469 through 491)) selection = (chain 'z' and (resid 256 through 466 or (resid 467 through 468 and (name N or n \ ame CA or name C or name O or name CB )) or resid 469 through 491)) } 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=0.15 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: 7.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 43.190 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.140 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 : 0.002 0.036 34188 Z= 0.137 Angle : 0.518 6.024 46798 Z= 0.302 Chirality : 0.041 0.176 5406 Planarity : 0.003 0.041 5925 Dihedral : 7.918 82.648 12373 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.06 % Allowed : 5.02 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.19 (0.12), residues: 4286 helix: -0.13 (0.18), residues: 802 sheet: -0.57 (0.16), residues: 911 loop : -2.35 (0.10), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.014 0.001 TYR C1152 PHE 0.007 0.001 PHE C 714 TRP 0.007 0.000 TRP C 444 HIS 0.003 0.000 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00247 (34073) covalent geometry : angle 0.51646 (46525) SS BOND : bond 0.00133 ( 72) SS BOND : angle 0.54319 ( 144) hydrogen bonds : bond 0.14940 ( 1066) hydrogen bonds : angle 5.74251 ( 2879) link_BETA1-4 : bond 0.00350 ( 10) link_BETA1-4 : angle 0.78789 ( 30) link_NAG-ASN : bond 0.00153 ( 33) link_NAG-ASN : angle 0.98687 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 682 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 MET cc_start: 0.6195 (tpp) cc_final: 0.5895 (tpp) REVERT: B 273 ARG cc_start: 0.6890 (mtm110) cc_final: 0.6654 (mtm-85) REVERT: B 320 ARG cc_start: 0.6569 (ptp90) cc_final: 0.6355 (ptp90) REVERT: B 495 CYS cc_start: 0.5925 (OUTLIER) cc_final: 0.4072 (t) REVERT: B 772 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6705 (mm-30) REVERT: B 906 PHE cc_start: 0.8367 (t80) cc_final: 0.8100 (t80) REVERT: B 1054 LYS cc_start: 0.8440 (mttp) cc_final: 0.8235 (mttm) REVERT: A 28 LEU cc_start: 0.5009 (OUTLIER) cc_final: 0.4771 (mp) REVERT: A 48 THR cc_start: 0.8387 (m) cc_final: 0.7950 (p) REVERT: A 140 GLN cc_start: 0.7423 (tt0) cc_final: 0.7129 (tt0) REVERT: A 467 PHE cc_start: 0.7188 (m-80) cc_final: 0.6793 (m-80) REVERT: A 476 CYS cc_start: 0.1698 (OUTLIER) cc_final: 0.1208 (p) REVERT: A 515 TRP cc_start: 0.7519 (t-100) cc_final: 0.6839 (t-100) REVERT: A 667 LYS cc_start: 0.7993 (mttp) cc_final: 0.7752 (mtpp) REVERT: A 685 GLN cc_start: 0.7739 (pt0) cc_final: 0.7523 (pt0) REVERT: A 747 TYR cc_start: 0.8017 (t80) cc_final: 0.7701 (t80) REVERT: A 748 ASN cc_start: 0.7126 (p0) cc_final: 0.6818 (p0) REVERT: C 160 HIS cc_start: 0.7587 (p-80) cc_final: 0.7182 (p-80) REVERT: C 638 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7580 (p) REVERT: C 685 GLN cc_start: 0.7503 (pt0) cc_final: 0.7245 (pt0) REVERT: C 826 TYR cc_start: 0.8629 (m-80) cc_final: 0.8129 (m-80) REVERT: C 879 LEU cc_start: 0.8738 (mm) cc_final: 0.8537 (mp) REVERT: C 1075 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6627 (mp10) REVERT: y 411 ASN cc_start: 0.9209 (p0) cc_final: 0.8891 (p0) REVERT: z 349 MET cc_start: 0.5316 (mpp) cc_final: 0.4749 (mpp) REVERT: z 424 MET cc_start: 0.5794 (pmm) cc_final: 0.5571 (pmm) outliers start: 73 outliers final: 20 residues processed: 734 average time/residue: 0.2266 time to fit residues: 270.5914 Evaluate side-chains 590 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 565 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1075 GLN Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain z residue 285 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN B 99 ASN B 201 HIS B 402 GLN B 589 ASN B 656 ASN ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN B 830 HIS B 878 ASN B 927 ASN ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 GLN B1126 ASN A 132 ASN A 318 HIS A 803 GLN A 880 HIS A 992 ASN A1020 GLN A1053 ASN A1075 GLN C 29 ASN C 351 ASN C 410 GLN C 711 GLN C 830 HIS C 858 GLN C 988 GLN C1075 GLN C1210 ASN ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.185222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134822 restraints weight = 55205.314| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.98 r_work: 0.3465 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 34188 Z= 0.236 Angle : 0.635 22.525 46798 Z= 0.328 Chirality : 0.047 0.643 5406 Planarity : 0.005 0.052 5925 Dihedral : 5.309 59.333 5539 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 2.31 % Allowed : 9.73 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4286 helix: 0.57 (0.19), residues: 835 sheet: -0.34 (0.16), residues: 930 loop : -2.02 (0.11), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1068 TYR 0.031 0.002 TYR C 212 PHE 0.032 0.002 PHE B 771 TRP 0.027 0.001 TRP C 577 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00558 (34073) covalent geometry : angle 0.61380 (46525) SS BOND : bond 0.00353 ( 72) SS BOND : angle 1.99323 ( 144) hydrogen bonds : bond 0.05214 ( 1066) hydrogen bonds : angle 4.83677 ( 2879) link_BETA1-4 : bond 0.00472 ( 10) link_BETA1-4 : angle 0.99481 ( 30) link_NAG-ASN : bond 0.00427 ( 33) link_NAG-ASN : angle 2.78526 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 599 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 MET cc_start: 0.6578 (tpp) cc_final: 0.6156 (tpp) REVERT: B 196 ASP cc_start: 0.7568 (p0) cc_final: 0.7267 (p0) REVERT: B 255 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7144 (mm110) REVERT: B 320 ARG cc_start: 0.7603 (ptp90) cc_final: 0.7372 (ptp90) REVERT: B 495 CYS cc_start: 0.6219 (OUTLIER) cc_final: 0.4734 (t) REVERT: B 739 MET cc_start: 0.8691 (mmm) cc_final: 0.8487 (mmp) REVERT: B 772 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 776 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8319 (m) REVERT: B 998 MET cc_start: 0.8056 (tpt) cc_final: 0.7649 (mmt) REVERT: B 1054 LYS cc_start: 0.8664 (mttp) cc_final: 0.8459 (mttm) REVERT: A 28 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4794 (mp) REVERT: A 69 LYS cc_start: 0.8214 (tttm) cc_final: 0.7811 (tttp) REVERT: A 264 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7182 (mtt90) REVERT: A 467 PHE cc_start: 0.7687 (m-80) cc_final: 0.7115 (m-80) REVERT: A 515 TRP cc_start: 0.7582 (t-100) cc_final: 0.6808 (t-100) REVERT: A 667 LYS cc_start: 0.8368 (mttp) cc_final: 0.8133 (mtpp) REVERT: A 748 ASN cc_start: 0.7324 (p0) cc_final: 0.7051 (p0) REVERT: A 825 ASN cc_start: 0.6688 (t0) cc_final: 0.6407 (t0) REVERT: A 835 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 1098 SER cc_start: 0.8753 (t) cc_final: 0.8497 (p) REVERT: C 273 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7885 (mtm-85) REVERT: C 275 VAL cc_start: 0.8706 (t) cc_final: 0.8444 (m) REVERT: C 402 GLN cc_start: 0.7085 (mp10) cc_final: 0.6779 (mp10) REVERT: C 637 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7064 (tm-30) REVERT: C 904 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7769 (mtp180) REVERT: C 937 ASP cc_start: 0.6712 (t0) cc_final: 0.6447 (t0) REVERT: C 1075 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: C 1211 THR cc_start: 0.8319 (p) cc_final: 0.8118 (p) REVERT: x 416 TYR cc_start: 0.7278 (m-10) cc_final: 0.7043 (m-10) REVERT: y 285 ILE cc_start: 0.1884 (OUTLIER) cc_final: 0.1611 (tt) REVERT: y 454 TRP cc_start: 0.8301 (m-90) cc_final: 0.8083 (m-90) REVERT: z 349 MET cc_start: 0.6235 (mpp) cc_final: 0.5553 (mpp) outliers start: 82 outliers final: 53 residues processed: 650 average time/residue: 0.1950 time to fit residues: 208.5524 Evaluate side-chains 617 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 559 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 285 ILE Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 387 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 376 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 247 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 380 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 607 ASN ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 GLN B1126 ASN B1185 ASN A 201 HIS A 318 HIS A 880 HIS A 898 HIS C 140 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN C 858 GLN C1020 GLN ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.183004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131743 restraints weight = 54896.985| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.97 r_work: 0.3463 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 34188 Z= 0.254 Angle : 0.635 16.891 46798 Z= 0.328 Chirality : 0.046 0.391 5406 Planarity : 0.005 0.066 5925 Dihedral : 5.311 59.868 5530 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.90 % Allowed : 10.83 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.43 (0.12), residues: 4286 helix: 0.90 (0.19), residues: 826 sheet: -0.31 (0.16), residues: 970 loop : -1.96 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1068 TYR 0.028 0.002 TYR C 675 PHE 0.031 0.002 PHE C1105 TRP 0.023 0.002 TRP y 453 HIS 0.010 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00600 (34073) covalent geometry : angle 0.60602 (46525) SS BOND : bond 0.00536 ( 72) SS BOND : angle 2.50464 ( 144) hydrogen bonds : bond 0.05549 ( 1066) hydrogen bonds : angle 4.83384 ( 2879) link_BETA1-4 : bond 0.00572 ( 10) link_BETA1-4 : angle 1.10062 ( 30) link_NAG-ASN : bond 0.00624 ( 33) link_NAG-ASN : angle 2.89692 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 571 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8517 (p) REVERT: B 155 MET cc_start: 0.6553 (tpp) cc_final: 0.6094 (tpp) REVERT: B 192 ASN cc_start: 0.7273 (t0) cc_final: 0.6967 (t0) REVERT: B 196 ASP cc_start: 0.7510 (p0) cc_final: 0.7240 (p0) REVERT: B 320 ARG cc_start: 0.7607 (ptp90) cc_final: 0.7141 (ptp90) REVERT: B 495 CYS cc_start: 0.5522 (OUTLIER) cc_final: 0.3875 (t) REVERT: B 772 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 804 GLU cc_start: 0.7741 (pm20) cc_final: 0.7445 (pm20) REVERT: B 998 MET cc_start: 0.8361 (tpt) cc_final: 0.8097 (mmt) REVERT: B 1054 LYS cc_start: 0.8685 (mttp) cc_final: 0.8469 (mttm) REVERT: B 1075 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7655 (mp10) REVERT: A 467 PHE cc_start: 0.7580 (m-80) cc_final: 0.7054 (m-80) REVERT: A 515 TRP cc_start: 0.7344 (t-100) cc_final: 0.6673 (t-100) REVERT: A 667 LYS cc_start: 0.8389 (mttp) cc_final: 0.8138 (mtpp) REVERT: A 748 ASN cc_start: 0.7318 (p0) cc_final: 0.7097 (p0) REVERT: A 820 LEU cc_start: 0.8861 (tp) cc_final: 0.8626 (tt) REVERT: A 876 ASN cc_start: 0.7661 (p0) cc_final: 0.7341 (p0) REVERT: A 904 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7674 (mtm110) REVERT: A 915 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8458 (p) REVERT: A 1079 ASP cc_start: 0.7919 (t0) cc_final: 0.7703 (t0) REVERT: A 1211 THR cc_start: 0.8684 (m) cc_final: 0.8056 (p) REVERT: C 275 VAL cc_start: 0.8808 (t) cc_final: 0.8480 (m) REVERT: C 402 GLN cc_start: 0.7171 (mp10) cc_final: 0.6892 (mp10) REVERT: C 637 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7188 (tm-30) REVERT: C 904 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7817 (mtp180) REVERT: C 937 ASP cc_start: 0.6661 (t0) cc_final: 0.6447 (t0) REVERT: C 1075 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: y 285 ILE cc_start: 0.1182 (OUTLIER) cc_final: 0.0942 (tt) REVERT: y 454 TRP cc_start: 0.7926 (m-90) cc_final: 0.7666 (m-90) REVERT: z 349 MET cc_start: 0.5676 (mpp) cc_final: 0.5055 (mpp) REVERT: z 406 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7438 (tm-30) outliers start: 103 outliers final: 68 residues processed: 638 average time/residue: 0.1872 time to fit residues: 198.0341 Evaluate side-chains 627 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 553 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1075 GLN Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1060 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain x residue 331 VAL Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 285 ILE Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 387 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 281 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 379 optimal weight: 40.0000 chunk 344 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 405 optimal weight: 8.9990 chunk 327 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 607 ASN ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN B1185 ASN A 880 HIS C 160 HIS C 410 GLN C1187 HIS ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.184473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133109 restraints weight = 54629.730| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.10 r_work: 0.3478 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 34188 Z= 0.141 Angle : 0.568 16.595 46798 Z= 0.292 Chirality : 0.043 0.328 5406 Planarity : 0.004 0.057 5925 Dihedral : 5.017 57.916 5526 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 2.40 % Allowed : 12.04 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.23 (0.13), residues: 4286 helix: 1.15 (0.19), residues: 832 sheet: -0.25 (0.16), residues: 956 loop : -1.83 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 206 TYR 0.025 0.001 TYR A 624 PHE 0.026 0.001 PHE C1105 TRP 0.021 0.001 TRP C 577 HIS 0.007 0.001 HIS C1187 Details of bonding type rmsd covalent geometry : bond 0.00330 (34073) covalent geometry : angle 0.54464 (46525) SS BOND : bond 0.00350 ( 72) SS BOND : angle 2.06425 ( 144) hydrogen bonds : bond 0.04555 ( 1066) hydrogen bonds : angle 4.68963 ( 2879) link_BETA1-4 : bond 0.00313 ( 10) link_BETA1-4 : angle 0.95323 ( 30) link_NAG-ASN : bond 0.00656 ( 33) link_NAG-ASN : angle 2.61451 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 554 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 155 MET cc_start: 0.6375 (tpp) cc_final: 0.5952 (tpp) REVERT: B 192 ASN cc_start: 0.7114 (t0) cc_final: 0.6835 (t0) REVERT: B 196 ASP cc_start: 0.7496 (p0) cc_final: 0.7221 (p0) REVERT: B 495 CYS cc_start: 0.5503 (OUTLIER) cc_final: 0.3866 (t) REVERT: B 772 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 804 GLU cc_start: 0.7767 (pm20) cc_final: 0.7452 (pm20) REVERT: B 998 MET cc_start: 0.8357 (tpt) cc_final: 0.8052 (mmt) REVERT: B 1054 LYS cc_start: 0.8674 (mttp) cc_final: 0.8473 (mttm) REVERT: B 1075 GLN cc_start: 0.7875 (mp10) cc_final: 0.7506 (mp10) REVERT: A 164 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8822 (mmtm) REVERT: A 201 HIS cc_start: 0.7739 (t-170) cc_final: 0.7434 (t70) REVERT: A 346 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7161 (ttt90) REVERT: A 467 PHE cc_start: 0.7682 (m-80) cc_final: 0.7085 (m-80) REVERT: A 515 TRP cc_start: 0.7459 (t-100) cc_final: 0.6693 (t-100) REVERT: A 667 LYS cc_start: 0.8370 (mttp) cc_final: 0.8129 (mtpp) REVERT: A 747 TYR cc_start: 0.8413 (t80) cc_final: 0.8175 (t80) REVERT: A 748 ASN cc_start: 0.7352 (p0) cc_final: 0.7140 (p0) REVERT: A 820 LEU cc_start: 0.8735 (tp) cc_final: 0.8509 (tt) REVERT: A 835 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 876 ASN cc_start: 0.7632 (p0) cc_final: 0.7267 (p0) REVERT: A 904 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7647 (mtm110) REVERT: A 915 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8456 (p) REVERT: A 1211 THR cc_start: 0.8660 (m) cc_final: 0.8147 (p) REVERT: C 275 VAL cc_start: 0.8770 (t) cc_final: 0.8415 (m) REVERT: C 402 GLN cc_start: 0.7272 (mp10) cc_final: 0.7008 (mp10) REVERT: C 637 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 804 GLU cc_start: 0.7784 (pm20) cc_final: 0.7535 (pm20) REVERT: C 904 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7819 (mtp180) REVERT: C 937 ASP cc_start: 0.6633 (t0) cc_final: 0.6384 (t0) REVERT: C 938 LEU cc_start: 0.8580 (mt) cc_final: 0.8368 (mt) REVERT: C 1075 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: y 285 ILE cc_start: 0.1207 (OUTLIER) cc_final: 0.0961 (tt) REVERT: y 454 TRP cc_start: 0.8093 (m-90) cc_final: 0.7843 (m-90) REVERT: z 349 MET cc_start: 0.5670 (mpp) cc_final: 0.5030 (mpp) REVERT: z 406 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7314 (tm-30) outliers start: 85 outliers final: 64 residues processed: 608 average time/residue: 0.1970 time to fit residues: 198.0821 Evaluate side-chains 615 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 546 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain x residue 285 ILE Chi-restraints excluded: chain x residue 331 VAL Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 285 ILE Chi-restraints excluded: chain y residue 379 CYS Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 387 THR Chi-restraints excluded: chain z residue 477 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 183 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 407 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 340 optimal weight: 1.9990 chunk 173 optimal weight: 0.0060 chunk 225 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1075 GLN B1185 ASN A 880 HIS C 858 GLN C 867 GLN ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.183826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132627 restraints weight = 54657.097| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.26 r_work: 0.3454 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34188 Z= 0.178 Angle : 0.578 16.938 46798 Z= 0.298 Chirality : 0.044 0.287 5406 Planarity : 0.004 0.061 5925 Dihedral : 4.983 58.663 5524 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.90 % Allowed : 11.87 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.15 (0.13), residues: 4286 helix: 1.34 (0.19), residues: 815 sheet: -0.21 (0.16), residues: 955 loop : -1.79 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 206 TYR 0.024 0.002 TYR A 624 PHE 0.027 0.002 PHE C1105 TRP 0.017 0.001 TRP C 577 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00422 (34073) covalent geometry : angle 0.55509 (46525) SS BOND : bond 0.00395 ( 72) SS BOND : angle 1.99723 ( 144) hydrogen bonds : bond 0.04799 ( 1066) hydrogen bonds : angle 4.64723 ( 2879) link_BETA1-4 : bond 0.00342 ( 10) link_BETA1-4 : angle 0.99158 ( 30) link_NAG-ASN : bond 0.00607 ( 33) link_NAG-ASN : angle 2.62625 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 561 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8528 (p) REVERT: B 155 MET cc_start: 0.6489 (tpp) cc_final: 0.6095 (tpp) REVERT: B 192 ASN cc_start: 0.7125 (t0) cc_final: 0.6841 (t0) REVERT: B 196 ASP cc_start: 0.7504 (p0) cc_final: 0.7216 (p0) REVERT: B 382 CYS cc_start: 0.6346 (m) cc_final: 0.5592 (m) REVERT: B 495 CYS cc_start: 0.5567 (OUTLIER) cc_final: 0.3947 (t) REVERT: B 772 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 998 MET cc_start: 0.8351 (tpt) cc_final: 0.7966 (mmt) REVERT: B 1072 PRO cc_start: 0.8203 (Cg_exo) cc_final: 0.7979 (Cg_endo) REVERT: B 1075 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: B 1104 LYS cc_start: 0.8590 (tttp) cc_final: 0.8236 (ttpp) REVERT: A 28 LEU cc_start: 0.5060 (OUTLIER) cc_final: 0.4766 (mp) REVERT: A 132 ASN cc_start: 0.5933 (t0) cc_final: 0.5581 (m-40) REVERT: A 164 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8815 (mmtm) REVERT: A 186 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7931 (tppt) REVERT: A 201 HIS cc_start: 0.7785 (t-170) cc_final: 0.7384 (t70) REVERT: A 467 PHE cc_start: 0.7797 (m-80) cc_final: 0.7201 (m-80) REVERT: A 515 TRP cc_start: 0.7562 (t-100) cc_final: 0.6755 (t-100) REVERT: A 667 LYS cc_start: 0.8387 (mttp) cc_final: 0.8141 (mtpp) REVERT: A 747 TYR cc_start: 0.8445 (t80) cc_final: 0.8232 (t80) REVERT: A 748 ASN cc_start: 0.7396 (p0) cc_final: 0.7189 (p0) REVERT: A 835 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 876 ASN cc_start: 0.7649 (p0) cc_final: 0.7258 (p0) REVERT: A 904 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7713 (mtm110) REVERT: A 915 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8478 (p) REVERT: A 1211 THR cc_start: 0.8676 (m) cc_final: 0.8140 (p) REVERT: C 275 VAL cc_start: 0.8797 (t) cc_final: 0.8427 (m) REVERT: C 402 GLN cc_start: 0.7290 (mp10) cc_final: 0.7041 (mp10) REVERT: C 637 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 804 GLU cc_start: 0.7866 (pm20) cc_final: 0.7623 (pm20) REVERT: C 904 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7849 (mtp180) REVERT: C 937 ASP cc_start: 0.6703 (t0) cc_final: 0.6432 (t0) REVERT: C 938 LEU cc_start: 0.8568 (mt) cc_final: 0.8358 (mt) REVERT: C 1075 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: C 1172 VAL cc_start: 0.8294 (m) cc_final: 0.7993 (p) REVERT: y 285 ILE cc_start: 0.1424 (OUTLIER) cc_final: 0.1185 (tt) REVERT: y 454 TRP cc_start: 0.8073 (m-90) cc_final: 0.7793 (m-90) REVERT: z 349 MET cc_start: 0.5703 (mpp) cc_final: 0.5059 (mpp) REVERT: z 406 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7662 (tm-30) outliers start: 103 outliers final: 81 residues processed: 627 average time/residue: 0.1868 time to fit residues: 193.5335 Evaluate side-chains 643 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 555 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1075 GLN Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1171 ASP Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain x residue 285 ILE Chi-restraints excluded: chain x residue 331 VAL Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 285 ILE Chi-restraints excluded: chain y residue 379 CYS Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain z residue 280 VAL Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 387 THR Chi-restraints excluded: chain z residue 477 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 288 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 419 optimal weight: 7.9990 chunk 330 optimal weight: 0.0770 chunk 163 optimal weight: 0.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 GLN B1185 ASN A 880 HIS C 858 GLN C1187 HIS ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.183469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132065 restraints weight = 54383.201| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.15 r_work: 0.3451 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34188 Z= 0.176 Angle : 0.579 17.069 46798 Z= 0.298 Chirality : 0.044 0.303 5406 Planarity : 0.004 0.059 5925 Dihedral : 4.977 58.605 5523 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.96 % Allowed : 12.21 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.10 (0.13), residues: 4286 helix: 1.40 (0.19), residues: 819 sheet: -0.23 (0.16), residues: 961 loop : -1.76 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 206 TYR 0.025 0.002 TYR A 624 PHE 0.028 0.002 PHE C1105 TRP 0.016 0.001 TRP C 577 HIS 0.006 0.001 HIS C1187 Details of bonding type rmsd covalent geometry : bond 0.00416 (34073) covalent geometry : angle 0.55718 (46525) SS BOND : bond 0.00382 ( 72) SS BOND : angle 1.98699 ( 144) hydrogen bonds : bond 0.04761 ( 1066) hydrogen bonds : angle 4.64280 ( 2879) link_BETA1-4 : bond 0.00405 ( 10) link_BETA1-4 : angle 1.01302 ( 30) link_NAG-ASN : bond 0.00603 ( 33) link_NAG-ASN : angle 2.59803 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 551 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 155 MET cc_start: 0.6562 (tpp) cc_final: 0.6166 (tpp) REVERT: B 192 ASN cc_start: 0.7110 (t0) cc_final: 0.6899 (t0) REVERT: B 196 ASP cc_start: 0.7501 (p0) cc_final: 0.7214 (p0) REVERT: B 255 GLN cc_start: 0.7752 (mm110) cc_final: 0.7241 (mm-40) REVERT: B 772 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 894 CYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6280 (m) REVERT: B 1072 PRO cc_start: 0.8233 (Cg_exo) cc_final: 0.7984 (Cg_endo) REVERT: B 1075 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: B 1104 LYS cc_start: 0.8584 (tttp) cc_final: 0.8254 (ttpp) REVERT: A 28 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4792 (mp) REVERT: A 132 ASN cc_start: 0.5995 (t0) cc_final: 0.5619 (m-40) REVERT: A 153 TYR cc_start: 0.7802 (m-80) cc_final: 0.7512 (m-80) REVERT: A 155 MET cc_start: 0.6581 (tpp) cc_final: 0.6114 (tpp) REVERT: A 186 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7915 (tppt) REVERT: A 201 HIS cc_start: 0.7809 (t-170) cc_final: 0.7388 (t70) REVERT: A 467 PHE cc_start: 0.7738 (m-80) cc_final: 0.7144 (m-80) REVERT: A 515 TRP cc_start: 0.7500 (t-100) cc_final: 0.6712 (t-100) REVERT: A 667 LYS cc_start: 0.8403 (mttp) cc_final: 0.8154 (mtpp) REVERT: A 748 ASN cc_start: 0.7414 (p0) cc_final: 0.7206 (p0) REVERT: A 835 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 876 ASN cc_start: 0.7657 (p0) cc_final: 0.7261 (p0) REVERT: A 904 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7743 (mtm110) REVERT: A 915 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 1064 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 1211 THR cc_start: 0.8667 (m) cc_final: 0.8107 (p) REVERT: C 123 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8545 (m) REVERT: C 204 GLN cc_start: 0.8017 (pm20) cc_final: 0.7709 (pm20) REVERT: C 275 VAL cc_start: 0.8795 (t) cc_final: 0.8443 (m) REVERT: C 346 ARG cc_start: 0.6675 (ttm-80) cc_final: 0.5485 (ttm-80) REVERT: C 402 GLN cc_start: 0.7303 (mp10) cc_final: 0.7072 (mp10) REVERT: C 637 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7259 (tm-30) REVERT: C 804 GLU cc_start: 0.7922 (pm20) cc_final: 0.7672 (pm20) REVERT: C 904 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7868 (mtp180) REVERT: C 937 ASP cc_start: 0.6717 (t0) cc_final: 0.6455 (t0) REVERT: C 938 LEU cc_start: 0.8584 (mt) cc_final: 0.8376 (mt) REVERT: C 1075 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: C 1172 VAL cc_start: 0.8333 (m) cc_final: 0.8033 (p) REVERT: y 285 ILE cc_start: 0.1246 (OUTLIER) cc_final: 0.1008 (tt) REVERT: y 454 TRP cc_start: 0.7982 (m-90) cc_final: 0.7720 (m-90) REVERT: z 406 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7668 (tm-30) outliers start: 105 outliers final: 86 residues processed: 616 average time/residue: 0.1995 time to fit residues: 202.6607 Evaluate side-chains 641 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 547 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 HIS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1075 GLN Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1098 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1171 ASP Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain x residue 285 ILE Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 285 ILE Chi-restraints excluded: chain y residue 379 CYS Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 387 THR Chi-restraints excluded: chain z residue 477 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 0.9990 chunk 403 optimal weight: 30.0000 chunk 225 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 366 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 overall best weight: 0.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 704 ASN B1049 GLN B1075 GLN B1185 ASN A 684 HIS A 880 HIS C 858 GLN C1187 HIS ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.184074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133822 restraints weight = 54683.947| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.04 r_work: 0.3463 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34188 Z= 0.136 Angle : 0.562 17.150 46798 Z= 0.289 Chirality : 0.043 0.288 5406 Planarity : 0.004 0.054 5925 Dihedral : 4.817 57.302 5519 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 2.88 % Allowed : 12.71 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.13), residues: 4286 helix: 1.51 (0.20), residues: 820 sheet: -0.14 (0.16), residues: 966 loop : -1.71 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1068 TYR 0.025 0.001 TYR A 624 PHE 0.026 0.001 PHE C1105 TRP 0.016 0.001 TRP C 577 HIS 0.006 0.001 HIS C1187 Details of bonding type rmsd covalent geometry : bond 0.00319 (34073) covalent geometry : angle 0.54108 (46525) SS BOND : bond 0.00343 ( 72) SS BOND : angle 1.83535 ( 144) hydrogen bonds : bond 0.04387 ( 1066) hydrogen bonds : angle 4.57816 ( 2879) link_BETA1-4 : bond 0.00356 ( 10) link_BETA1-4 : angle 0.99089 ( 30) link_NAG-ASN : bond 0.00568 ( 33) link_NAG-ASN : angle 2.55188 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 549 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 155 MET cc_start: 0.6458 (tpp) cc_final: 0.6057 (tpp) REVERT: B 196 ASP cc_start: 0.7477 (p0) cc_final: 0.7193 (p0) REVERT: B 424 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 772 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 1075 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: B 1104 LYS cc_start: 0.8567 (tttp) cc_final: 0.8237 (ttpp) REVERT: A 28 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4781 (mp) REVERT: A 155 MET cc_start: 0.6479 (tpp) cc_final: 0.5976 (tpp) REVERT: A 201 HIS cc_start: 0.7717 (t-170) cc_final: 0.7273 (t70) REVERT: A 467 PHE cc_start: 0.7705 (m-80) cc_final: 0.7107 (m-80) REVERT: A 515 TRP cc_start: 0.7526 (t-100) cc_final: 0.6677 (t-100) REVERT: A 748 ASN cc_start: 0.7397 (p0) cc_final: 0.7196 (p0) REVERT: A 835 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 876 ASN cc_start: 0.7624 (p0) cc_final: 0.7242 (p0) REVERT: A 904 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7702 (mtm110) REVERT: A 915 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8458 (p) REVERT: A 1064 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 1211 THR cc_start: 0.8642 (m) cc_final: 0.8105 (p) REVERT: C 123 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8566 (m) REVERT: C 275 VAL cc_start: 0.8763 (t) cc_final: 0.8417 (m) REVERT: C 346 ARG cc_start: 0.6722 (ttm-80) cc_final: 0.5502 (ttm-80) REVERT: C 402 GLN cc_start: 0.7286 (mp10) cc_final: 0.7082 (mp10) REVERT: C 637 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7181 (tm-30) REVERT: C 804 GLU cc_start: 0.7876 (pm20) cc_final: 0.7628 (pm20) REVERT: C 904 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7831 (mtp180) REVERT: C 937 ASP cc_start: 0.6648 (t0) cc_final: 0.6385 (t0) REVERT: C 938 LEU cc_start: 0.8558 (mt) cc_final: 0.8345 (mt) REVERT: C 1075 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: C 1172 VAL cc_start: 0.8319 (m) cc_final: 0.8011 (p) REVERT: y 454 TRP cc_start: 0.8011 (m-90) cc_final: 0.7742 (m-90) REVERT: z 349 MET cc_start: 0.5590 (mpp) cc_final: 0.5037 (mpp) REVERT: z 406 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7677 (tm-30) outliers start: 102 outliers final: 83 residues processed: 611 average time/residue: 0.1927 time to fit residues: 194.1369 Evaluate side-chains 632 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 543 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1075 GLN Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1098 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain x residue 285 ILE Chi-restraints excluded: chain x residue 331 VAL Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 379 CYS Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain y residue 477 VAL Chi-restraints excluded: chain z residue 280 VAL Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 477 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 39 optimal weight: 9.9990 chunk 384 optimal weight: 50.0000 chunk 287 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 412 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 333 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 290 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 192 ASN B 255 GLN B 988 GLN B 992 ASN B1185 ASN A 73 ASN A 880 HIS C 318 HIS C 410 GLN C 858 GLN z 334 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.183938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132877 restraints weight = 54476.438| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.19 r_work: 0.3453 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34188 Z= 0.151 Angle : 0.567 17.140 46798 Z= 0.291 Chirality : 0.043 0.270 5406 Planarity : 0.004 0.055 5925 Dihedral : 4.813 57.434 5519 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.54 % Favored : 94.44 % Rotamer: Outliers : 2.93 % Allowed : 12.46 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 4286 helix: 1.54 (0.20), residues: 820 sheet: -0.13 (0.16), residues: 970 loop : -1.68 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1068 TYR 0.024 0.001 TYR A 624 PHE 0.028 0.001 PHE C1105 TRP 0.020 0.001 TRP A 577 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00356 (34073) covalent geometry : angle 0.54662 (46525) SS BOND : bond 0.00348 ( 72) SS BOND : angle 1.76901 ( 144) hydrogen bonds : bond 0.04450 ( 1066) hydrogen bonds : angle 4.56603 ( 2879) link_BETA1-4 : bond 0.00370 ( 10) link_BETA1-4 : angle 1.00191 ( 30) link_NAG-ASN : bond 0.00565 ( 33) link_NAG-ASN : angle 2.55120 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 546 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8509 (p) REVERT: B 155 MET cc_start: 0.6496 (tpp) cc_final: 0.6150 (tpp) REVERT: B 196 ASP cc_start: 0.7476 (p0) cc_final: 0.7187 (p0) REVERT: B 772 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 1072 PRO cc_start: 0.8181 (Cg_exo) cc_final: 0.7940 (Cg_endo) REVERT: B 1075 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: B 1104 LYS cc_start: 0.8555 (tttp) cc_final: 0.8220 (ttpp) REVERT: A 28 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4780 (mp) REVERT: A 155 MET cc_start: 0.6555 (tpp) cc_final: 0.6046 (tpp) REVERT: A 201 HIS cc_start: 0.7733 (t-170) cc_final: 0.7281 (t70) REVERT: A 467 PHE cc_start: 0.7743 (m-80) cc_final: 0.7140 (m-80) REVERT: A 515 TRP cc_start: 0.7576 (t-100) cc_final: 0.6702 (t-100) REVERT: A 748 ASN cc_start: 0.7413 (p0) cc_final: 0.7201 (p0) REVERT: A 835 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 876 ASN cc_start: 0.7609 (p0) cc_final: 0.7220 (p0) REVERT: A 904 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7737 (mtm110) REVERT: A 915 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8461 (p) REVERT: A 1064 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7675 (mm-30) REVERT: C 275 VAL cc_start: 0.8771 (t) cc_final: 0.8418 (m) REVERT: C 346 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.5615 (ttm-80) REVERT: C 402 GLN cc_start: 0.7243 (mp10) cc_final: 0.7025 (mp10) REVERT: C 637 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7160 (tm-30) REVERT: C 804 GLU cc_start: 0.7881 (pm20) cc_final: 0.7624 (pm20) REVERT: C 904 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7875 (mtp180) REVERT: C 937 ASP cc_start: 0.6699 (t0) cc_final: 0.6432 (t0) REVERT: C 1075 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: C 1172 VAL cc_start: 0.8325 (m) cc_final: 0.8009 (p) REVERT: y 454 TRP cc_start: 0.8003 (m-90) cc_final: 0.7722 (m-90) REVERT: z 349 MET cc_start: 0.5631 (mpp) cc_final: 0.5080 (mpp) REVERT: z 406 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7697 (tm-30) outliers start: 104 outliers final: 87 residues processed: 611 average time/residue: 0.2184 time to fit residues: 220.3204 Evaluate side-chains 637 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 545 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 HIS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1075 GLN Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1098 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain x residue 285 ILE Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 379 CYS Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain y residue 477 VAL Chi-restraints excluded: chain z residue 280 VAL Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 477 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 179 optimal weight: 0.0070 chunk 257 optimal weight: 0.8980 chunk 239 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 387 optimal weight: 50.0000 chunk 84 optimal weight: 0.0970 chunk 419 optimal weight: 0.0870 chunk 266 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 255 GLN B1049 GLN B1075 GLN B1185 ASN A 73 ASN A 880 HIS C 152 GLN C 858 GLN C1187 HIS ** z 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134645 restraints weight = 54416.523| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.88 r_work: 0.3519 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34188 Z= 0.108 Angle : 0.547 17.125 46798 Z= 0.280 Chirality : 0.042 0.251 5406 Planarity : 0.004 0.050 5925 Dihedral : 4.686 56.148 5519 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.42 % Allowed : 13.05 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.13), residues: 4286 helix: 1.70 (0.20), residues: 817 sheet: 0.04 (0.17), residues: 952 loop : -1.62 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1068 TYR 0.023 0.001 TYR A 624 PHE 0.028 0.001 PHE C1105 TRP 0.015 0.001 TRP C 577 HIS 0.007 0.001 HIS C1187 Details of bonding type rmsd covalent geometry : bond 0.00249 (34073) covalent geometry : angle 0.52933 (46525) SS BOND : bond 0.00285 ( 72) SS BOND : angle 1.50299 ( 144) hydrogen bonds : bond 0.03856 ( 1066) hydrogen bonds : angle 4.46019 ( 2879) link_BETA1-4 : bond 0.00296 ( 10) link_BETA1-4 : angle 0.96676 ( 30) link_NAG-ASN : bond 0.00527 ( 33) link_NAG-ASN : angle 2.48903 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 550 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 155 MET cc_start: 0.6416 (tpp) cc_final: 0.6026 (tpp) REVERT: B 196 ASP cc_start: 0.7434 (p0) cc_final: 0.7159 (p0) REVERT: B 255 GLN cc_start: 0.7697 (mm110) cc_final: 0.7214 (mm110) REVERT: B 772 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 1104 LYS cc_start: 0.8561 (tttp) cc_final: 0.8248 (ttpp) REVERT: A 28 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4723 (mp) REVERT: A 155 MET cc_start: 0.6470 (tpp) cc_final: 0.6021 (tpp) REVERT: A 201 HIS cc_start: 0.7596 (t-170) cc_final: 0.7024 (t70) REVERT: A 467 PHE cc_start: 0.7566 (m-80) cc_final: 0.7002 (m-80) REVERT: A 515 TRP cc_start: 0.7296 (t-100) cc_final: 0.6520 (t-100) REVERT: A 717 TYR cc_start: 0.8822 (t80) cc_final: 0.8506 (t80) REVERT: A 748 ASN cc_start: 0.7406 (p0) cc_final: 0.7198 (p0) REVERT: A 835 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 876 ASN cc_start: 0.7678 (p0) cc_final: 0.7322 (p0) REVERT: A 904 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7604 (mtm110) REVERT: A 915 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 1064 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7674 (mm-30) REVERT: C 123 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8556 (m) REVERT: C 275 VAL cc_start: 0.8754 (t) cc_final: 0.8495 (m) REVERT: C 346 ARG cc_start: 0.6771 (ttm-80) cc_final: 0.5717 (ttm-80) REVERT: C 637 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7095 (tm-30) REVERT: C 804 GLU cc_start: 0.7818 (pm20) cc_final: 0.7573 (pm20) REVERT: C 826 TYR cc_start: 0.8822 (m-10) cc_final: 0.8571 (m-80) REVERT: C 904 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7875 (mtp180) REVERT: C 937 ASP cc_start: 0.6551 (t0) cc_final: 0.6322 (t0) REVERT: C 1075 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: C 1172 VAL cc_start: 0.8303 (m) cc_final: 0.7980 (p) REVERT: y 454 TRP cc_start: 0.8001 (m-90) cc_final: 0.7754 (m-90) REVERT: z 349 MET cc_start: 0.5567 (mpp) cc_final: 0.5030 (mpp) outliers start: 86 outliers final: 71 residues processed: 605 average time/residue: 0.1835 time to fit residues: 183.3563 Evaluate side-chains 617 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 541 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 HIS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1098 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1039 SER Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain x residue 285 ILE Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 379 CYS Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain y residue 477 VAL Chi-restraints excluded: chain z residue 280 VAL Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 141 optimal weight: 0.0040 chunk 354 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 420 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 230 optimal weight: 0.4980 chunk 208 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 135 optimal weight: 0.1980 chunk 235 optimal weight: 0.6980 overall best weight: 0.2910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 825 ASN B1049 GLN A 73 ASN A 880 HIS ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** z 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.185477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134297 restraints weight = 54796.613| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.17 r_work: 0.3490 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.423 34188 Z= 0.160 Angle : 0.700 59.200 46798 Z= 0.375 Chirality : 0.043 0.424 5406 Planarity : 0.004 0.049 5925 Dihedral : 4.684 56.141 5519 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.34 % Allowed : 13.34 % Favored : 84.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.13), residues: 4286 helix: 1.72 (0.20), residues: 816 sheet: 0.04 (0.17), residues: 952 loop : -1.61 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1068 TYR 0.023 0.001 TYR A 624 PHE 0.027 0.001 PHE C1105 TRP 0.015 0.001 TRP A 577 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00393 (34073) covalent geometry : angle 0.65404 (46525) SS BOND : bond 0.01457 ( 72) SS BOND : angle 4.05620 ( 144) hydrogen bonds : bond 0.03873 ( 1066) hydrogen bonds : angle 4.46085 ( 2879) link_BETA1-4 : bond 0.00213 ( 10) link_BETA1-4 : angle 0.95202 ( 30) link_NAG-ASN : bond 0.00526 ( 33) link_NAG-ASN : angle 2.48998 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8572 Ramachandran restraints generated. 4286 Oldfield, 0 Emsley, 4286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 540 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 155 MET cc_start: 0.6467 (tpp) cc_final: 0.6079 (tpp) REVERT: B 196 ASP cc_start: 0.7470 (p0) cc_final: 0.7187 (p0) REVERT: B 255 GLN cc_start: 0.7713 (mm110) cc_final: 0.7223 (mm110) REVERT: B 772 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 904 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.8006 (mtm180) REVERT: B 1104 LYS cc_start: 0.8561 (tttp) cc_final: 0.8246 (ttpp) REVERT: A 155 MET cc_start: 0.6519 (tpp) cc_final: 0.6040 (tpp) REVERT: A 201 HIS cc_start: 0.7653 (t-170) cc_final: 0.7172 (t70) REVERT: A 467 PHE cc_start: 0.7655 (m-80) cc_final: 0.7062 (m-80) REVERT: A 515 TRP cc_start: 0.7412 (t-100) cc_final: 0.6579 (t-100) REVERT: A 717 TYR cc_start: 0.8839 (t80) cc_final: 0.8515 (t80) REVERT: A 748 ASN cc_start: 0.7433 (p0) cc_final: 0.7216 (p0) REVERT: A 835 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 876 ASN cc_start: 0.7651 (p0) cc_final: 0.7298 (p0) REVERT: A 904 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7610 (mtm110) REVERT: A 915 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 1064 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 123 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8577 (m) REVERT: C 275 VAL cc_start: 0.8765 (t) cc_final: 0.8506 (m) REVERT: C 346 ARG cc_start: 0.6740 (ttm-80) cc_final: 0.5684 (ttm-80) REVERT: C 637 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7160 (tm-30) REVERT: C 804 GLU cc_start: 0.7889 (pm20) cc_final: 0.7636 (pm20) REVERT: C 904 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7882 (mtp180) REVERT: C 937 ASP cc_start: 0.6625 (t0) cc_final: 0.6375 (t0) REVERT: C 1075 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: C 1172 VAL cc_start: 0.8298 (m) cc_final: 0.7975 (p) REVERT: y 454 TRP cc_start: 0.8043 (m-90) cc_final: 0.7790 (m-90) REVERT: z 349 MET cc_start: 0.5640 (mpp) cc_final: 0.5086 (mpp) outliers start: 83 outliers final: 76 residues processed: 592 average time/residue: 0.2098 time to fit residues: 204.6015 Evaluate side-chains 621 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 541 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 318 HIS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1187 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1039 SER Chi-restraints excluded: chain C residue 1046 SER Chi-restraints excluded: chain C residue 1060 SER Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain x residue 285 ILE Chi-restraints excluded: chain x residue 387 THR Chi-restraints excluded: chain y residue 379 CYS Chi-restraints excluded: chain y residue 393 THR Chi-restraints excluded: chain y residue 477 VAL Chi-restraints excluded: chain z residue 280 VAL Chi-restraints excluded: chain z residue 285 ILE Chi-restraints excluded: chain z residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 60 optimal weight: 0.0870 chunk 143 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 380 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 ASN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1185 ASN A 73 ASN A 880 HIS C 152 GLN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** z 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134683 restraints weight = 54475.709| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.90 r_work: 0.3514 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.660 34188 Z= 0.287 Angle : 0.695 59.200 46798 Z= 0.373 Chirality : 0.043 0.424 5406 Planarity : 0.004 0.049 5925 Dihedral : 4.684 56.141 5519 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.28 % Allowed : 13.34 % Favored : 84.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.13), residues: 4286 helix: 1.72 (0.20), residues: 816 sheet: 0.04 (0.17), residues: 952 loop : -1.61 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1068 TYR 0.023 0.001 TYR A 624 PHE 0.027 0.001 PHE C1105 TRP 0.015 0.001 TRP A 577 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00393 (34073) covalent geometry : angle 0.65404 (46525) SS BOND : bond 0.10486 ( 72) SS BOND : angle 3.75488 ( 144) hydrogen bonds : bond 0.03873 ( 1066) hydrogen bonds : angle 4.46085 ( 2879) link_BETA1-4 : bond 0.00213 ( 10) link_BETA1-4 : angle 0.95202 ( 30) link_NAG-ASN : bond 0.00526 ( 33) link_NAG-ASN : angle 2.48998 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10810.42 seconds wall clock time: 184 minutes 45.92 seconds (11085.92 seconds total)