Starting phenix.real_space_refine on Sat Jun 28 18:11:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y7x_39025/06_2025/8y7x_39025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y7x_39025/06_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_39025/06_2025/8y7x_39025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y7x_39025/06_2025/8y7x_39025.map" model { file = "/net/cci-nas-00/data/ceres_data/8y7x_39025/06_2025/8y7x_39025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y7x_39025/06_2025/8y7x_39025.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} 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: 31.18, per 1000 atoms: 0.94 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: 7.96 Conformation dependent library (CDL) restraints added in 7.3 seconds 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: 4.95 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: 15.57 Time building geometry restraints manager: 9.55 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 1224 \ or resid 1301 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 1224 or resid 1301 \ 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 1224 \ or resid 1301 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: 6.850 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: 0.020 Extract box with map and model: 1.400 Check model and map are aligned: 0.230 Set scattering table: 0.330 Process input model: 94.980 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.000 TRP C 444 HIS 0.003 0.000 HIS B 201 PHE 0.007 0.001 PHE C 714 TYR 0.014 0.001 TYR C1152 ARG 0.001 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 33) link_NAG-ASN : angle 0.98687 ( 99) link_BETA1-4 : bond 0.00350 ( 10) link_BETA1-4 : angle 0.78789 ( 30) hydrogen bonds : bond 0.14940 ( 1066) hydrogen bonds : angle 5.74251 ( 2879) SS BOND : bond 0.00133 ( 72) SS BOND : angle 0.54319 ( 144) covalent geometry : bond 0.00247 (34073) covalent geometry : angle 0.51646 (46525) *********************** 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 : 3.262 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: 0.4404 time to fit residues: 523.8332 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 : 3.272 ------------------------------------------------------------------------------- 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 359 optimal weight: 20.0000 chunk 322 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 333 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 386 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 29 ASN B 99 ASN B 201 HIS ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 C1020 GLN C1075 GLN C1083 ASN C1210 ASN ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.186440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136200 restraints weight = 55200.650| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.98 r_work: 0.3502 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 34188 Z= 0.200 Angle : 0.598 23.171 46798 Z= 0.307 Chirality : 0.045 0.457 5406 Planarity : 0.004 0.047 5925 Dihedral : 5.173 58.691 5539 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 2.03 % Allowed : 10.06 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4286 helix: 0.63 (0.19), residues: 830 sheet: -0.32 (0.16), residues: 936 loop : -2.04 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 577 HIS 0.011 0.001 HIS C 201 PHE 0.025 0.002 PHE B 771 TYR 0.027 0.002 TYR C 675 ARG 0.007 0.001 ARG y 413 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 33) link_NAG-ASN : angle 2.82284 ( 99) link_BETA1-4 : bond 0.00359 ( 10) link_BETA1-4 : angle 0.97577 ( 30) hydrogen bonds : bond 0.04789 ( 1066) hydrogen bonds : angle 4.75328 ( 2879) SS BOND : bond 0.00327 ( 72) SS BOND : angle 2.16125 ( 144) covalent geometry : bond 0.00474 (34073) covalent geometry : angle 0.57263 (46525) *********************** 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 659 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 587 time to evaluate : 3.366 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: B 152 GLN cc_start: 0.7523 (mt0) cc_final: 0.7115 (mp10) REVERT: B 155 MET cc_start: 0.6544 (tpp) cc_final: 0.6102 (tpp) REVERT: B 174 TRP cc_start: 0.5030 (p-90) cc_final: 0.4186 (p-90) REVERT: B 196 ASP cc_start: 0.7560 (p0) cc_final: 0.7256 (p0) REVERT: B 320 ARG cc_start: 0.7561 (ptp90) cc_final: 0.7258 (ptp90) REVERT: B 424 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7464 (tm-30) REVERT: B 495 CYS cc_start: 0.6109 (OUTLIER) cc_final: 0.4555 (t) REVERT: B 772 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 776 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8308 (m) REVERT: B 803 GLN cc_start: 0.7677 (tp-100) cc_final: 0.7416 (tp-100) REVERT: B 998 MET cc_start: 0.8081 (tpt) cc_final: 0.7771 (mmt) REVERT: B 1054 LYS cc_start: 0.8680 (mttp) cc_final: 0.8471 (mttm) REVERT: B 1075 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: A 28 LEU cc_start: 0.5154 (OUTLIER) cc_final: 0.4861 (mp) REVERT: A 467 PHE cc_start: 0.7623 (m-80) cc_final: 0.7067 (m-80) REVERT: A 476 CYS cc_start: 0.2229 (OUTLIER) cc_final: 0.1754 (p) REVERT: A 515 TRP cc_start: 0.7501 (t-100) cc_final: 0.6770 (t-100) REVERT: A 717 TYR cc_start: 0.8840 (t80) cc_final: 0.8525 (t80) REVERT: A 747 TYR cc_start: 0.8339 (t80) cc_final: 0.8085 (t80) REVERT: A 748 ASN cc_start: 0.7302 (p0) cc_final: 0.7047 (p0) REVERT: A 825 ASN cc_start: 0.6584 (t0) cc_final: 0.6297 (t0) REVERT: A 1098 SER cc_start: 0.8755 (t) cc_final: 0.8493 (p) REVERT: C 46 LEU cc_start: 0.8258 (tt) cc_final: 0.7959 (tt) REVERT: C 263 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8331 (ttmt) REVERT: C 273 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7794 (mtm-85) REVERT: C 275 VAL cc_start: 0.8684 (t) cc_final: 0.8411 (m) REVERT: C 402 GLN cc_start: 0.6968 (mp10) cc_final: 0.6656 (mp10) REVERT: C 637 GLU cc_start: 0.7716 (tm-30) cc_final: 0.6970 (tm-30) REVERT: C 831 ASP cc_start: 0.8060 (m-30) cc_final: 0.7729 (m-30) REVERT: C 904 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7719 (mtp180) REVERT: C 937 ASP cc_start: 0.6680 (t0) cc_final: 0.6419 (t0) REVERT: C 1075 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: x 416 TYR cc_start: 0.7027 (m-10) cc_final: 0.6820 (m-10) REVERT: y 285 ILE cc_start: 0.1656 (OUTLIER) cc_final: 0.1384 (tt) REVERT: y 454 TRP cc_start: 0.8122 (m-90) cc_final: 0.7901 (m-90) REVERT: z 349 MET cc_start: 0.6127 (mpp) cc_final: 0.5451 (mpp) outliers start: 72 outliers final: 49 residues processed: 632 average time/residue: 0.4345 time to fit residues: 447.3788 Evaluate side-chains 614 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 558 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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 1075 GLN Chi-restraints excluded: chain B residue 1102 LEU 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 213 TYR 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 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 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 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 53 optimal weight: 0.0980 chunk 39 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 421 optimal weight: 40.0000 chunk 181 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 342 optimal weight: 0.7980 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 402 GLN ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 ASN A 318 HIS A 880 HIS A 898 HIS C 152 GLN C 858 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 = 0.4331 r_free = 0.4331 target = 0.186489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135637 restraints weight = 55186.955| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.12 r_work: 0.3514 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34188 Z= 0.139 Angle : 0.558 16.839 46798 Z= 0.285 Chirality : 0.043 0.375 5406 Planarity : 0.004 0.048 5925 Dihedral : 5.069 57.235 5535 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 2.45 % Allowed : 10.85 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4286 helix: 1.04 (0.19), residues: 831 sheet: -0.22 (0.16), residues: 937 loop : -1.85 (0.11), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 577 HIS 0.007 0.001 HIS B 201 PHE 0.020 0.001 PHE A 714 TYR 0.028 0.002 TYR C 675 ARG 0.010 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 33) link_NAG-ASN : angle 2.69536 ( 99) link_BETA1-4 : bond 0.00293 ( 10) link_BETA1-4 : angle 0.94710 ( 30) hydrogen bonds : bond 0.04224 ( 1066) hydrogen bonds : angle 4.61282 ( 2879) SS BOND : bond 0.00350 ( 72) SS BOND : angle 2.05285 ( 144) covalent geometry : bond 0.00324 (34073) covalent geometry : angle 0.53296 (46525) *********************** 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 650 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 563 time to evaluate : 3.380 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: B 48 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 120 GLU cc_start: 0.8150 (pt0) cc_final: 0.7905 (pm20) REVERT: B 155 MET cc_start: 0.6514 (tpp) cc_final: 0.6011 (tpp) REVERT: B 174 TRP cc_start: 0.4767 (p-90) cc_final: 0.3820 (p-90) REVERT: B 196 ASP cc_start: 0.7550 (p0) cc_final: 0.7240 (p0) REVERT: B 255 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7260 (mm-40) REVERT: B 273 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7257 (mtm-85) REVERT: B 320 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7383 (ptp90) REVERT: B 382 CYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5571 (m) REVERT: B 495 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.4094 (t) REVERT: B 772 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7404 (mm-30) REVERT: B 1054 LYS cc_start: 0.8665 (mttp) cc_final: 0.8460 (mttm) REVERT: A 346 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.7088 (ttt90) REVERT: A 467 PHE cc_start: 0.7594 (m-80) cc_final: 0.7056 (m-80) REVERT: A 515 TRP cc_start: 0.7424 (t-100) cc_final: 0.6705 (t-100) REVERT: A 658 ILE cc_start: 0.8686 (mm) cc_final: 0.8369 (mm) REVERT: A 717 TYR cc_start: 0.8833 (t80) cc_final: 0.8513 (t80) REVERT: A 748 ASN cc_start: 0.7365 (p0) cc_final: 0.7122 (p0) REVERT: A 1098 SER cc_start: 0.8726 (t) cc_final: 0.8435 (p) REVERT: A 1211 THR cc_start: 0.8622 (m) cc_final: 0.8000 (p) REVERT: C 46 LEU cc_start: 0.8291 (tt) cc_final: 0.8062 (tt) REVERT: C 94 PHE cc_start: 0.7279 (m-10) cc_final: 0.7066 (m-10) REVERT: C 273 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7850 (mtm-85) REVERT: C 275 VAL cc_start: 0.8743 (t) cc_final: 0.8429 (m) REVERT: C 402 GLN cc_start: 0.7160 (mp10) cc_final: 0.6872 (mp10) REVERT: C 637 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7072 (tm-30) REVERT: C 904 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7766 (mtp180) REVERT: C 937 ASP cc_start: 0.6628 (t0) cc_final: 0.6389 (t0) REVERT: C 1075 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: y 285 ILE cc_start: 0.1438 (OUTLIER) cc_final: 0.1190 (tt) REVERT: y 454 TRP cc_start: 0.8001 (m-90) cc_final: 0.7773 (m-90) REVERT: z 349 MET cc_start: 0.5832 (mpp) cc_final: 0.5189 (mpp) REVERT: z 406 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 87 outliers final: 56 residues processed: 619 average time/residue: 0.4418 time to fit residues: 453.9327 Evaluate side-chains 605 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 544 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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 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 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 917 LEU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1168 ILE 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 104 SER 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 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 947 ILE 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 148 ILE 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 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 1075 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1209 MET 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 214 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 293 optimal weight: 50.0000 chunk 219 optimal weight: 1.9990 chunk 346 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 316 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN B1139 GLN B1185 ASN A 318 HIS A 880 HIS C 140 GLN C 410 GLN C 858 GLN ** 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 = 0.4304 r_free = 0.4304 target = 0.184042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132701 restraints weight = 54725.373| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.20 r_work: 0.3460 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 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 = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34188 Z= 0.210 Angle : 0.598 15.547 46798 Z= 0.310 Chirality : 0.045 0.347 5406 Planarity : 0.004 0.065 5925 Dihedral : 5.062 58.932 5529 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 2.96 % Allowed : 10.85 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 4286 helix: 1.20 (0.19), residues: 826 sheet: -0.23 (0.16), residues: 929 loop : -1.82 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 577 HIS 0.008 0.001 HIS C 201 PHE 0.025 0.002 PHE B 771 TYR 0.025 0.002 TYR C 212 ARG 0.008 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00765 ( 33) link_NAG-ASN : angle 2.59966 ( 99) link_BETA1-4 : bond 0.00370 ( 10) link_BETA1-4 : angle 1.01256 ( 30) hydrogen bonds : bond 0.05115 ( 1066) hydrogen bonds : angle 4.70018 ( 2879) SS BOND : bond 0.00425 ( 72) SS BOND : angle 2.02653 ( 144) covalent geometry : bond 0.00497 (34073) covalent geometry : angle 0.57596 (46525) *********************** 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 674 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 569 time to evaluate : 3.320 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: 0.8802 (OUTLIER) cc_final: 0.8522 (p) REVERT: B 155 MET cc_start: 0.6515 (tpp) cc_final: 0.6101 (tpp) REVERT: B 192 ASN cc_start: 0.7136 (t0) cc_final: 0.6866 (t0) REVERT: B 196 ASP cc_start: 0.7528 (p0) cc_final: 0.7246 (p0) REVERT: B 320 ARG cc_start: 0.7609 (ptp90) cc_final: 0.7155 (ptp90) REVERT: B 382 CYS cc_start: 0.6290 (OUTLIER) cc_final: 0.6031 (m) REVERT: B 424 GLN cc_start: 0.7934 (pp30) cc_final: 0.7450 (tm-30) REVERT: B 495 CYS cc_start: 0.5530 (OUTLIER) cc_final: 0.3862 (t) REVERT: B 772 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 1054 LYS cc_start: 0.8684 (mttp) cc_final: 0.8482 (mttm) REVERT: B 1075 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: A 104 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8449 (p) REVERT: A 346 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7190 (ttt90) REVERT: A 467 PHE cc_start: 0.7735 (m-80) cc_final: 0.7175 (m-80) REVERT: A 515 TRP cc_start: 0.7531 (t-100) cc_final: 0.6766 (t-100) REVERT: A 658 ILE cc_start: 0.8778 (mm) cc_final: 0.8371 (mt) REVERT: A 668 THR cc_start: 0.8470 (p) cc_final: 0.8264 (p) REVERT: A 717 TYR cc_start: 0.8869 (t80) cc_final: 0.8582 (t80) REVERT: A 746 ASP cc_start: 0.7944 (t0) cc_final: 0.7616 (t0) REVERT: A 747 TYR cc_start: 0.8579 (t80) cc_final: 0.8114 (t80) REVERT: A 748 ASN cc_start: 0.7351 (p0) cc_final: 0.7119 (p0) REVERT: A 820 LEU cc_start: 0.8891 (tp) cc_final: 0.8658 (tt) REVERT: A 853 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7568 (mp) REVERT: A 876 ASN cc_start: 0.7548 (p0) cc_final: 0.7151 (p0) REVERT: A 904 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7630 (mtm110) REVERT: A 915 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 1211 THR cc_start: 0.8712 (m) cc_final: 0.8104 (p) REVERT: C 275 VAL cc_start: 0.8818 (t) cc_final: 0.8438 (m) REVERT: C 402 GLN cc_start: 0.7193 (mp10) cc_final: 0.6933 (mp10) REVERT: C 637 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7274 (tm-30) REVERT: C 904 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7834 (mtp180) REVERT: C 937 ASP cc_start: 0.6747 (t0) cc_final: 0.6487 (t0) REVERT: C 1075 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: y 285 ILE cc_start: 0.1139 (OUTLIER) cc_final: 0.0895 (tt) REVERT: z 349 MET cc_start: 0.5650 (mpp) cc_final: 0.5026 (mpp) REVERT: z 406 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7488 (tm-30) outliers start: 105 outliers final: 73 residues processed: 633 average time/residue: 0.4438 time to fit residues: 461.2861 Evaluate side-chains 635 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 553 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 190 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 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 615 GLU 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 820 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 1049 GLN 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 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 92 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 120 GLU 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 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 853 LEU 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 947 ILE 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 190 THR 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 629 ILE 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 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 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 418 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 267 optimal weight: 0.4980 chunk 410 optimal weight: 50.0000 chunk 11 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 298 optimal weight: 0.0980 chunk 398 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1185 ASN A 880 HIS C 160 HIS C 858 GLN C1187 HIS ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.183904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132386 restraints weight = 54555.074| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.28 r_work: 0.3454 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- 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: 9 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34188 Z= 0.191 Angle : 0.585 16.653 46798 Z= 0.302 Chirality : 0.044 0.288 5406 Planarity : 0.004 0.064 5925 Dihedral : 5.117 58.742 5529 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 2.73 % Allowed : 11.53 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 4286 helix: 1.24 (0.19), residues: 833 sheet: -0.27 (0.16), residues: 919 loop : -1.78 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 577 HIS 0.008 0.001 HIS C 160 PHE 0.019 0.002 PHE B 771 TYR 0.025 0.002 TYR C 624 ARG 0.010 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 33) link_NAG-ASN : angle 2.62367 ( 99) link_BETA1-4 : bond 0.00385 ( 10) link_BETA1-4 : angle 0.99553 ( 30) hydrogen bonds : bond 0.04861 ( 1066) hydrogen bonds : angle 4.68513 ( 2879) SS BOND : bond 0.00407 ( 72) SS BOND : angle 2.07710 ( 144) covalent geometry : bond 0.00451 (34073) covalent geometry : angle 0.56220 (46525) *********************** 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 657 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 560 time to evaluate : 3.225 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: B 48 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8530 (p) REVERT: B 155 MET cc_start: 0.6459 (tpp) cc_final: 0.5995 (tpp) REVERT: B 192 ASN cc_start: 0.7140 (t0) cc_final: 0.6926 (t0) REVERT: B 196 ASP cc_start: 0.7520 (p0) cc_final: 0.7226 (p0) REVERT: B 320 ARG cc_start: 0.7623 (ptp90) cc_final: 0.7395 (ptp90) REVERT: B 382 CYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5933 (m) REVERT: B 424 GLN cc_start: 0.8048 (pp30) cc_final: 0.7700 (tm-30) REVERT: B 495 CYS cc_start: 0.5684 (OUTLIER) cc_final: 0.4049 (t) REVERT: B 772 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7465 (mm-30) REVERT: B 804 GLU cc_start: 0.7770 (pm20) cc_final: 0.7462 (pm20) REVERT: B 894 CYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6236 (m) REVERT: B 1054 LYS cc_start: 0.8692 (mttp) cc_final: 0.8487 (mttm) REVERT: B 1075 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: B 1104 LYS cc_start: 0.8603 (tttm) cc_final: 0.8289 (ttpp) REVERT: A 28 LEU cc_start: 0.5027 (OUTLIER) cc_final: 0.4748 (mp) REVERT: A 104 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 346 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7056 (ttt90) REVERT: A 467 PHE cc_start: 0.7750 (m-80) cc_final: 0.7175 (m-80) REVERT: A 515 TRP cc_start: 0.7565 (t-100) cc_final: 0.6769 (t-100) REVERT: A 658 ILE cc_start: 0.8763 (mm) cc_final: 0.8360 (mt) REVERT: A 668 THR cc_start: 0.8433 (p) cc_final: 0.8215 (p) REVERT: A 717 TYR cc_start: 0.8859 (t80) cc_final: 0.8564 (t80) REVERT: A 746 ASP cc_start: 0.7950 (t0) cc_final: 0.7612 (t0) REVERT: A 747 TYR cc_start: 0.8594 (t80) cc_final: 0.8150 (t80) REVERT: A 748 ASN cc_start: 0.7376 (p0) cc_final: 0.7144 (p0) REVERT: A 853 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7565 (mp) REVERT: A 876 ASN cc_start: 0.7685 (p0) cc_final: 0.7287 (p0) REVERT: A 904 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7638 (mtm110) REVERT: A 915 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 1064 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 1211 THR cc_start: 0.8699 (m) cc_final: 0.8140 (p) REVERT: C 275 VAL cc_start: 0.8821 (t) cc_final: 0.8451 (m) REVERT: C 402 GLN cc_start: 0.7286 (mp10) cc_final: 0.7040 (mp10) REVERT: C 637 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7155 (tm-30) REVERT: C 904 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7840 (mtp180) REVERT: C 937 ASP cc_start: 0.6684 (t0) cc_final: 0.6450 (t0) REVERT: C 938 LEU cc_start: 0.8599 (mt) cc_final: 0.8398 (mt) REVERT: C 1075 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: y 285 ILE cc_start: 0.1168 (OUTLIER) cc_final: 0.0919 (tt) REVERT: z 406 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7523 (tm-30) outliers start: 97 outliers final: 73 residues processed: 621 average time/residue: 0.4545 time to fit residues: 464.0631 Evaluate side-chains 636 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 552 time to evaluate : 3.828 ------------------------------------------------------------------------------- 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 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 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 615 GLU 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 785 SER Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 820 LEU 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 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 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 99 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR 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 853 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 97 optimal weight: 0.5980 chunk 409 optimal weight: 6.9990 chunk 263 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 386 optimal weight: 8.9990 chunk 265 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 255 GLN ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1185 ASN A 73 ASN A 880 HIS C 140 GLN C 152 GLN C 858 GLN C 867 GLN ** 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 = 0.4309 r_free = 0.4309 target = 0.184417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133119 restraints weight = 54700.358| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.41 r_work: 0.3447 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34188 Z= 0.145 Angle : 0.566 16.731 46798 Z= 0.290 Chirality : 0.043 0.305 5406 Planarity : 0.004 0.060 5925 Dihedral : 5.009 57.294 5528 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 2.71 % Allowed : 11.76 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4286 helix: 1.47 (0.19), residues: 819 sheet: -0.23 (0.16), residues: 935 loop : -1.70 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 577 HIS 0.006 0.001 HIS C 201 PHE 0.017 0.001 PHE C 660 TYR 0.024 0.001 TYR A 624 ARG 0.009 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 33) link_NAG-ASN : angle 2.56398 ( 99) link_BETA1-4 : bond 0.00379 ( 10) link_BETA1-4 : angle 0.99008 ( 30) hydrogen bonds : bond 0.04448 ( 1066) hydrogen bonds : angle 4.62098 ( 2879) SS BOND : bond 0.00341 ( 72) SS BOND : angle 1.90256 ( 144) covalent geometry : bond 0.00340 (34073) covalent geometry : angle 0.54407 (46525) *********************** 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 638 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 542 time to evaluate : 3.127 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: 0.8799 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 155 MET cc_start: 0.6414 (tpp) cc_final: 0.6004 (tpp) REVERT: B 196 ASP cc_start: 0.7525 (p0) cc_final: 0.7226 (p0) REVERT: B 320 ARG cc_start: 0.7679 (ptp90) cc_final: 0.7456 (ptp90) REVERT: B 382 CYS cc_start: 0.6222 (OUTLIER) cc_final: 0.6002 (m) REVERT: B 424 GLN cc_start: 0.7985 (pp30) cc_final: 0.7629 (tm-30) REVERT: B 772 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 894 CYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6285 (m) REVERT: B 1054 LYS cc_start: 0.8668 (mttp) cc_final: 0.8464 (mttm) REVERT: B 1075 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: B 1104 LYS cc_start: 0.8583 (tttm) cc_final: 0.8273 (ttpp) REVERT: A 28 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4744 (mp) REVERT: A 132 ASN cc_start: 0.5990 (t0) cc_final: 0.5622 (m-40) REVERT: A 155 MET cc_start: 0.6405 (tpp) cc_final: 0.5998 (tpp) REVERT: A 346 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.6849 (ttt90) REVERT: A 467 PHE cc_start: 0.7773 (m-80) cc_final: 0.7166 (m-80) REVERT: A 515 TRP cc_start: 0.7560 (t-100) cc_final: 0.6747 (t-100) REVERT: A 658 ILE cc_start: 0.8746 (mm) cc_final: 0.8341 (mt) REVERT: A 717 TYR cc_start: 0.8868 (t80) cc_final: 0.8564 (t80) REVERT: A 746 ASP cc_start: 0.7974 (t0) cc_final: 0.7628 (t0) REVERT: A 747 TYR cc_start: 0.8601 (t80) cc_final: 0.8161 (t80) REVERT: A 748 ASN cc_start: 0.7407 (p0) cc_final: 0.7177 (p0) REVERT: A 876 ASN cc_start: 0.7690 (p0) cc_final: 0.7295 (p0) REVERT: A 904 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7617 (mtm110) REVERT: A 915 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 1064 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 1211 THR cc_start: 0.8694 (m) cc_final: 0.8144 (p) REVERT: C 204 GLN cc_start: 0.8026 (pm20) cc_final: 0.7731 (pm20) REVERT: C 346 ARG cc_start: 0.6688 (ttm-80) cc_final: 0.5530 (ttm-80) REVERT: C 402 GLN cc_start: 0.7295 (mp10) cc_final: 0.7070 (mp10) REVERT: C 637 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7216 (tm-30) REVERT: C 904 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7860 (mtp180) REVERT: C 937 ASP cc_start: 0.6675 (t0) cc_final: 0.6426 (t0) REVERT: C 1075 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: y 285 ILE cc_start: 0.1171 (OUTLIER) cc_final: 0.0930 (tt) REVERT: z 349 MET cc_start: 0.5760 (mpp) cc_final: 0.5153 (mpp) REVERT: z 406 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7615 (tm-30) outliers start: 96 outliers final: 76 residues processed: 603 average time/residue: 0.4295 time to fit residues: 427.4090 Evaluate side-chains 622 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 538 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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 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 605 CYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 792 ILE 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 937 ASP Chi-restraints excluded: chain B residue 1035 SER 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 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 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 804 GLU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 853 LEU 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 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 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 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 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 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 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 1 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 420 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 365 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN B1185 ASN A 73 ASN A 334 ASN A 880 HIS A1130 ASN C 318 HIS C 858 GLN C1187 HIS ** z 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 411 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 = 0.4246 r_free = 0.4246 target = 0.178989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127851 restraints weight = 54798.139| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.89 r_work: 0.3394 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.103 34188 Z= 0.458 Angle : 0.761 16.349 46798 Z= 0.395 Chirality : 0.053 0.377 5406 Planarity : 0.005 0.078 5925 Dihedral : 5.621 57.157 5526 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 3.19 % Allowed : 11.90 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.12), residues: 4286 helix: 0.98 (0.19), residues: 815 sheet: -0.38 (0.16), residues: 914 loop : -1.90 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 344 HIS 0.018 0.002 HIS B 201 PHE 0.049 0.003 PHE C 660 TYR 0.040 0.003 TYR B 49 ARG 0.009 0.001 ARG B1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 33) link_NAG-ASN : angle 2.88822 ( 99) link_BETA1-4 : bond 0.00473 ( 10) link_BETA1-4 : angle 1.20176 ( 30) hydrogen bonds : bond 0.06901 ( 1066) hydrogen bonds : angle 5.10364 ( 2879) SS BOND : bond 0.00716 ( 72) SS BOND : angle 2.65339 ( 144) covalent geometry : bond 0.01084 (34073) covalent geometry : angle 0.73605 (46525) *********************** 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 694 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 581 time to evaluate : 3.280 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: B 48 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 155 MET cc_start: 0.6682 (tpp) cc_final: 0.6326 (tpp) REVERT: B 196 ASP cc_start: 0.7514 (p0) cc_final: 0.7207 (p0) REVERT: B 255 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7201 (mm110) REVERT: B 320 ARG cc_start: 0.7616 (ptp90) cc_final: 0.7396 (ptp90) REVERT: B 424 GLN cc_start: 0.7951 (pp30) cc_final: 0.7658 (tm-30) REVERT: B 698 LYS cc_start: 0.8539 (mttp) cc_final: 0.8304 (mtpp) REVERT: B 772 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 908 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 937 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6669 (p0) REVERT: B 1054 LYS cc_start: 0.8706 (mttp) cc_final: 0.8487 (mttm) REVERT: B 1104 LYS cc_start: 0.8532 (tttm) cc_final: 0.8229 (ttpp) REVERT: A 28 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4711 (mp) REVERT: A 107 LYS cc_start: 0.8803 (tttt) cc_final: 0.8491 (tttm) REVERT: A 148 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 155 MET cc_start: 0.6685 (tpp) cc_final: 0.6312 (tpp) REVERT: A 467 PHE cc_start: 0.7793 (m-80) cc_final: 0.7180 (m-80) REVERT: A 515 TRP cc_start: 0.7575 (t-100) cc_final: 0.6755 (t-100) REVERT: A 658 ILE cc_start: 0.8779 (mm) cc_final: 0.8486 (mt) REVERT: A 746 ASP cc_start: 0.8039 (t0) cc_final: 0.7733 (t0) REVERT: A 748 ASN cc_start: 0.7362 (p0) cc_final: 0.7153 (p0) REVERT: A 853 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7734 (mp) REVERT: A 876 ASN cc_start: 0.7934 (p0) cc_final: 0.7439 (p0) REVERT: A 889 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8092 (ttpp) REVERT: A 904 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7667 (mtp180) REVERT: A 915 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 1064 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 1079 ASP cc_start: 0.8143 (t0) cc_final: 0.7928 (t0) REVERT: A 1099 ASP cc_start: 0.8014 (t0) cc_final: 0.7790 (t0) REVERT: A 1211 THR cc_start: 0.8709 (m) cc_final: 0.8075 (p) REVERT: C 123 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8534 (m) REVERT: C 220 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8404 (p) REVERT: C 346 ARG cc_start: 0.6817 (ttm-80) cc_final: 0.6422 (ttm-80) REVERT: C 402 GLN cc_start: 0.7348 (mp10) cc_final: 0.7030 (mp10) REVERT: C 637 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7358 (tm-30) REVERT: C 744 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6858 (t) REVERT: C 870 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8635 (p) REVERT: C 904 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7949 (mtp180) REVERT: C 937 ASP cc_start: 0.6805 (t0) cc_final: 0.6531 (t0) REVERT: C 1075 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: C 1103 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8064 (t) REVERT: x 416 TYR cc_start: 0.7206 (m-10) cc_final: 0.6811 (m-10) REVERT: y 285 ILE cc_start: 0.1142 (OUTLIER) cc_final: 0.0896 (tt) REVERT: z 349 MET cc_start: 0.5792 (mpp) cc_final: 0.5168 (mpp) REVERT: z 406 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7602 (tm-30) outliers start: 113 outliers final: 79 residues processed: 650 average time/residue: 0.4736 time to fit residues: 506.9865 Evaluate side-chains 652 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 560 time to evaluate : 3.656 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 TYR 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 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 620 VAL Chi-restraints excluded: chain B residue 645 SER 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 792 ILE Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1066 LEU 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 42 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 148 ILE 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 853 LEU 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 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 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 297 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 615 GLU 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 847 LEU 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 1058 ILE 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 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 387 THR 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 194 optimal weight: 0.5980 chunk 343 optimal weight: 0.7980 chunk 139 optimal weight: 0.0980 chunk 275 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 233 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 143 ASN B 255 GLN B 704 ASN B1004 ASN A 684 HIS C 876 ASN C1075 GLN C1187 HIS z 334 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.183880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133197 restraints weight = 54449.128| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.15 r_work: 0.3453 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34188 Z= 0.126 Angle : 0.595 17.264 46798 Z= 0.304 Chirality : 0.043 0.263 5406 Planarity : 0.004 0.055 5925 Dihedral : 5.150 59.084 5521 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.51 % Allowed : 13.36 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 4286 helix: 1.32 (0.19), residues: 824 sheet: -0.27 (0.16), residues: 916 loop : -1.72 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 577 HIS 0.009 0.001 HIS C1187 PHE 0.014 0.001 PHE A 714 TYR 0.030 0.001 TYR A 675 ARG 0.014 0.001 ARG y 413 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 33) link_NAG-ASN : angle 2.64073 ( 99) link_BETA1-4 : bond 0.00388 ( 10) link_BETA1-4 : angle 1.01045 ( 30) hydrogen bonds : bond 0.04341 ( 1066) hydrogen bonds : angle 4.75840 ( 2879) SS BOND : bond 0.00432 ( 72) SS BOND : angle 1.87536 ( 144) covalent geometry : bond 0.00293 (34073) covalent geometry : angle 0.57376 (46525) *********************** 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 642 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 553 time to evaluate : 3.306 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: 0.6459 (tpp) cc_final: 0.6128 (tpp) REVERT: B 196 ASP cc_start: 0.7455 (p0) cc_final: 0.7144 (p0) REVERT: B 255 GLN cc_start: 0.7705 (mm110) cc_final: 0.7226 (mm-40) REVERT: B 320 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7555 (ptp90) REVERT: B 698 LYS cc_start: 0.8384 (mttp) cc_final: 0.8171 (mtpp) REVERT: B 772 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7479 (mm-30) REVERT: B 904 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8007 (mtm180) REVERT: B 1054 LYS cc_start: 0.8703 (mttp) cc_final: 0.8484 (mttm) REVERT: B 1075 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: B 1104 LYS cc_start: 0.8523 (tttm) cc_final: 0.8233 (ttpp) REVERT: A 28 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4795 (mp) REVERT: A 132 ASN cc_start: 0.6098 (t0) cc_final: 0.5693 (m-40) REVERT: A 153 TYR cc_start: 0.7859 (m-80) cc_final: 0.7598 (m-80) REVERT: A 155 MET cc_start: 0.6515 (tpp) cc_final: 0.6081 (tpp) REVERT: A 467 PHE cc_start: 0.7746 (m-80) cc_final: 0.7088 (m-80) REVERT: A 515 TRP cc_start: 0.7442 (t-100) cc_final: 0.6615 (t-100) REVERT: A 658 ILE cc_start: 0.8749 (mm) cc_final: 0.8395 (mt) REVERT: A 746 ASP cc_start: 0.7964 (t0) cc_final: 0.7615 (t0) REVERT: A 748 ASN cc_start: 0.7423 (p0) cc_final: 0.7209 (p0) REVERT: A 876 ASN cc_start: 0.7801 (p0) cc_final: 0.7383 (p0) REVERT: A 904 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7643 (mtm110) REVERT: A 915 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 1064 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7652 (mm-30) REVERT: C 44 TYR cc_start: 0.8596 (m-80) cc_final: 0.8270 (m-80) REVERT: C 275 VAL cc_start: 0.8793 (t) cc_final: 0.8473 (m) REVERT: C 346 ARG cc_start: 0.6858 (ttm-80) cc_final: 0.6283 (ttm-80) REVERT: C 402 GLN cc_start: 0.7229 (mp10) cc_final: 0.7012 (mp10) REVERT: C 637 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7175 (tm-30) REVERT: C 675 TYR cc_start: 0.8092 (t80) cc_final: 0.7870 (t80) REVERT: C 826 TYR cc_start: 0.8884 (m-80) cc_final: 0.8608 (m-80) REVERT: C 870 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8551 (p) REVERT: C 879 LEU cc_start: 0.8910 (mm) cc_final: 0.8689 (mp) REVERT: C 904 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7894 (mtp180) REVERT: C 937 ASP cc_start: 0.6702 (t0) cc_final: 0.6441 (t0) REVERT: C 1075 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: y 285 ILE cc_start: 0.1045 (OUTLIER) cc_final: 0.0795 (tt) REVERT: z 349 MET cc_start: 0.5709 (mpp) cc_final: 0.5110 (mpp) outliers start: 89 outliers final: 69 residues processed: 615 average time/residue: 0.4465 time to fit residues: 452.5134 Evaluate side-chains 619 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 544 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL 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 384 LYS 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 645 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 1075 GLN 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 37 GLU 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 213 TYR Chi-restraints excluded: chain A residue 262 SER 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 804 GLU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 947 ILE 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 119 SER 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 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 615 GLU Chi-restraints excluded: chain C residue 629 ILE 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 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 1204 LYS 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 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 387 THR 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 378 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 357 optimal weight: 0.0040 chunk 117 optimal weight: 0.8980 chunk 282 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 339 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 140 GLN B 143 ASN B 351 ASN B1139 GLN A 73 ASN A1130 ASN C 876 ASN ** z 344 ASN ** 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 = 0.4287 r_free = 0.4287 target = 0.182547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131240 restraints weight = 54206.573| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.16 r_work: 0.3436 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 34188 Z= 0.208 Angle : 0.630 16.833 46798 Z= 0.323 Chirality : 0.045 0.282 5406 Planarity : 0.005 0.061 5925 Dihedral : 5.153 59.569 5521 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 2.26 % Allowed : 13.87 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4286 helix: 1.39 (0.20), residues: 818 sheet: -0.16 (0.16), residues: 942 loop : -1.73 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 577 HIS 0.007 0.001 HIS C1149 PHE 0.024 0.002 PHE B 888 TYR 0.026 0.002 TYR A 675 ARG 0.010 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 33) link_NAG-ASN : angle 2.71164 ( 99) link_BETA1-4 : bond 0.00371 ( 10) link_BETA1-4 : angle 1.05750 ( 30) hydrogen bonds : bond 0.05040 ( 1066) hydrogen bonds : angle 4.77680 ( 2879) SS BOND : bond 0.00508 ( 72) SS BOND : angle 2.34610 ( 144) covalent geometry : bond 0.00494 (34073) covalent geometry : angle 0.60449 (46525) *********************** 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 632 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 552 time to evaluate : 3.520 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: 0.6658 (tpp) cc_final: 0.6259 (tpp) REVERT: B 157 GLU cc_start: 0.7974 (pt0) cc_final: 0.7380 (mp0) REVERT: B 196 ASP cc_start: 0.7447 (p0) cc_final: 0.7143 (p0) REVERT: B 320 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7438 (ptp90) REVERT: B 698 LYS cc_start: 0.8416 (mttp) cc_final: 0.8213 (mtpp) REVERT: B 739 MET cc_start: 0.8741 (mmm) cc_final: 0.8290 (mmt) REVERT: B 772 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7471 (mm-30) REVERT: B 937 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6865 (p0) REVERT: B 1054 LYS cc_start: 0.8693 (mttp) cc_final: 0.8478 (mttm) REVERT: B 1075 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: B 1104 LYS cc_start: 0.8525 (tttm) cc_final: 0.8245 (ttpp) REVERT: A 28 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4765 (mp) REVERT: A 132 ASN cc_start: 0.6111 (t0) cc_final: 0.5730 (m-40) REVERT: A 153 TYR cc_start: 0.7931 (m-80) cc_final: 0.7660 (m-80) REVERT: A 155 MET cc_start: 0.6612 (tpp) cc_final: 0.6210 (tpp) REVERT: A 467 PHE cc_start: 0.7722 (m-80) cc_final: 0.7091 (m-80) REVERT: A 515 TRP cc_start: 0.7479 (t-100) cc_final: 0.6633 (t-100) REVERT: A 658 ILE cc_start: 0.8768 (mm) cc_final: 0.8428 (mt) REVERT: A 746 ASP cc_start: 0.7977 (t0) cc_final: 0.7650 (t0) REVERT: A 748 ASN cc_start: 0.7426 (p0) cc_final: 0.7213 (p0) REVERT: A 876 ASN cc_start: 0.7869 (p0) cc_final: 0.7359 (p0) REVERT: A 904 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7705 (mtm110) REVERT: A 915 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8544 (p) REVERT: A 1064 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 1079 ASP cc_start: 0.7933 (t0) cc_final: 0.7687 (t0) REVERT: C 275 VAL cc_start: 0.8816 (t) cc_final: 0.8457 (m) REVERT: C 402 GLN cc_start: 0.7249 (mp10) cc_final: 0.7046 (mp10) REVERT: C 544 GLU cc_start: 0.7775 (pm20) cc_final: 0.7568 (pm20) REVERT: C 620 VAL cc_start: 0.8540 (p) cc_final: 0.8272 (m) REVERT: C 637 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 870 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8560 (p) REVERT: C 904 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7930 (mtp180) REVERT: C 937 ASP cc_start: 0.6735 (t0) cc_final: 0.6483 (t0) REVERT: C 1075 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: y 285 ILE cc_start: 0.1042 (OUTLIER) cc_final: 0.0792 (tt) REVERT: z 349 MET cc_start: 0.5672 (mpp) cc_final: 0.5045 (mpp) outliers start: 80 outliers final: 67 residues processed: 611 average time/residue: 0.4721 time to fit residues: 476.0101 Evaluate side-chains 622 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 548 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL 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 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 645 SER Chi-restraints excluded: chain B residue 665 THR 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 792 ILE Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 937 ASP 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 99 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 SER 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 853 LEU 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 119 SER 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 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 615 GLU Chi-restraints excluded: chain C residue 629 ILE 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 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 1204 LYS 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 285 ILE 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 70 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 388 optimal weight: 30.0000 chunk 65 optimal weight: 0.9980 chunk 206 optimal weight: 0.1980 chunk 318 optimal weight: 1.9990 chunk 369 optimal weight: 9.9990 chunk 323 optimal weight: 1.9990 chunk 415 optimal weight: 10.0000 chunk 92 optimal weight: 0.0870 chunk 328 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 143 ASN A 73 ASN A1130 ASN C 858 GLN C 876 ASN C1187 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.184046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132646 restraints weight = 54481.066| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.25 r_work: 0.3456 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34188 Z= 0.128 Angle : 0.603 18.010 46798 Z= 0.305 Chirality : 0.044 0.592 5406 Planarity : 0.004 0.054 5925 Dihedral : 5.093 59.678 5520 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 2.06 % Allowed : 14.32 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4286 helix: 1.49 (0.20), residues: 824 sheet: -0.11 (0.17), residues: 912 loop : -1.66 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 577 HIS 0.008 0.001 HIS C1187 PHE 0.015 0.001 PHE C 660 TYR 0.028 0.001 TYR A 675 ARG 0.010 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 33) link_NAG-ASN : angle 3.26379 ( 99) link_BETA1-4 : bond 0.00379 ( 10) link_BETA1-4 : angle 1.03231 ( 30) hydrogen bonds : bond 0.04256 ( 1066) hydrogen bonds : angle 4.67461 ( 2879) SS BOND : bond 0.00422 ( 72) SS BOND : angle 1.93880 ( 144) covalent geometry : bond 0.00297 (34073) covalent geometry : angle 0.57493 (46525) ********************** 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 617 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 544 time to evaluate : 3.420 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: 0.6616 (tpp) cc_final: 0.6211 (tpp) REVERT: B 157 GLU cc_start: 0.7971 (pt0) cc_final: 0.7377 (mp0) REVERT: B 187 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8587 (ttmt) REVERT: B 196 ASP cc_start: 0.7442 (p0) cc_final: 0.7147 (p0) REVERT: B 320 ARG cc_start: 0.7719 (ptp90) cc_final: 0.7477 (ptp90) REVERT: B 698 LYS cc_start: 0.8391 (mttp) cc_final: 0.8171 (mtpp) REVERT: B 772 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 904 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7990 (mtm180) REVERT: B 1054 LYS cc_start: 0.8696 (mttp) cc_final: 0.8474 (mttm) REVERT: B 1075 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 1104 LYS cc_start: 0.8519 (tttm) cc_final: 0.8240 (ttpp) REVERT: A 28 LEU cc_start: 0.4987 (OUTLIER) cc_final: 0.4713 (mp) REVERT: A 132 ASN cc_start: 0.5953 (t0) cc_final: 0.5653 (m-40) REVERT: A 153 TYR cc_start: 0.7809 (m-80) cc_final: 0.7555 (m-80) REVERT: A 155 MET cc_start: 0.6569 (tpp) cc_final: 0.6169 (tpp) REVERT: A 467 PHE cc_start: 0.7713 (m-80) cc_final: 0.7082 (m-80) REVERT: A 515 TRP cc_start: 0.7429 (t-100) cc_final: 0.6576 (t-100) REVERT: A 658 ILE cc_start: 0.8743 (mm) cc_final: 0.8367 (mt) REVERT: A 746 ASP cc_start: 0.7964 (t0) cc_final: 0.7608 (t0) REVERT: A 748 ASN cc_start: 0.7415 (p0) cc_final: 0.7197 (p0) REVERT: A 904 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7719 (mtm110) REVERT: A 915 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8500 (p) REVERT: A 1064 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7658 (mm-30) REVERT: C 275 VAL cc_start: 0.8803 (t) cc_final: 0.8480 (m) REVERT: C 346 ARG cc_start: 0.6866 (ttm-80) cc_final: 0.6586 (ttm-80) REVERT: C 637 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 826 TYR cc_start: 0.8865 (m-10) cc_final: 0.8489 (m-80) REVERT: C 879 LEU cc_start: 0.8919 (mm) cc_final: 0.8713 (mp) REVERT: C 904 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7958 (mtp180) REVERT: C 937 ASP cc_start: 0.6754 (t0) cc_final: 0.6485 (t0) REVERT: C 1075 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: y 285 ILE cc_start: 0.1036 (OUTLIER) cc_final: 0.0792 (tt) REVERT: y 406 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7466 (tm-30) REVERT: z 349 MET cc_start: 0.5712 (mpp) cc_final: 0.5091 (mpp) outliers start: 73 outliers final: 65 residues processed: 596 average time/residue: 0.5886 time to fit residues: 582.9968 Evaluate side-chains 610 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 540 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL 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 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 645 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 744 CYS Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 937 ASP 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 99 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 SER 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 810 ASN Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 947 ILE 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 119 SER 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 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 615 GLU Chi-restraints excluded: chain C residue 629 ILE 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 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 1204 LYS 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 285 ILE 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 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 416 optimal weight: 0.0470 chunk 90 optimal weight: 0.0970 chunk 118 optimal weight: 0.2980 chunk 306 optimal weight: 0.0980 chunk 327 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN B 265 GLN A 73 ASN A 874 ASN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN C 876 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.186327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136095 restraints weight = 54566.196| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.79 r_work: 0.3533 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 34188 Z= 0.102 Angle : 0.565 16.791 46798 Z= 0.286 Chirality : 0.043 0.365 5406 Planarity : 0.004 0.051 5925 Dihedral : 4.887 58.578 5520 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.97 % Allowed : 14.49 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4286 helix: 1.68 (0.20), residues: 827 sheet: -0.07 (0.17), residues: 925 loop : -1.54 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 577 HIS 0.005 0.001 HIS C 234 PHE 0.027 0.001 PHE C 660 TYR 0.027 0.001 TYR A 675 ARG 0.010 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 33) link_NAG-ASN : angle 2.76047 ( 99) link_BETA1-4 : bond 0.00424 ( 10) link_BETA1-4 : angle 1.05753 ( 30) hydrogen bonds : bond 0.03519 ( 1066) hydrogen bonds : angle 4.50522 ( 2879) SS BOND : bond 0.00377 ( 72) SS BOND : angle 1.53682 ( 144) covalent geometry : bond 0.00226 (34073) covalent geometry : angle 0.54469 (46525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23236.10 seconds wall clock time: 402 minutes 9.31 seconds (24129.31 seconds total)