Starting phenix.real_space_refine on Thu Jan 16 07:51:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhm_60108/01_2025/8zhm_60108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhm_60108/01_2025/8zhm_60108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zhm_60108/01_2025/8zhm_60108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhm_60108/01_2025/8zhm_60108.map" model { file = "/net/cci-nas-00/data/ceres_data/8zhm_60108/01_2025/8zhm_60108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhm_60108/01_2025/8zhm_60108.cif" } resolution = 3.39 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9222 atoms to isotropic. 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 180 5.16 5 C 28617 2.51 5 N 7473 2.21 5 O 9003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 45273 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "H" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 19.84, per 1000 atoms: 0.44 Number of scatterers: 45273 At special positions: 0 Unit cell: (221.712, 203.856, 205.344, 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 180 16.00 O 9003 8.00 N 7473 7.00 C 28617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=66, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 207 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 91 " distance=2.03 Simple disulfide: pdb=" SG CYS K 145 " - pdb=" SG CYS K 204 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 147 " - pdb=" SG CYS M 203 " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 8.37 Conformation dependent library (CDL) restraints added in 4.6 seconds 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10788 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 122 sheets defined 13.3% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.911A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.987A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.819A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.669A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.083A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.696A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.115A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.549A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.113A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.170A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 753 removed outlier: 4.022A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.899A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.621A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.672A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.095A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 946 through 966 removed outlier: 3.854A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.013A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.209A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.506A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.918A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.784A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.726A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.068A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.664A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 removed outlier: 3.540A pdb=" N LEU C 916 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.577A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.852A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.201A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.965A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA L 132 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 3.971A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'I' and resid 129 through 133 removed outlier: 3.669A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.057A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 200 No H-bonds generated for 'chain 'N' and resid 198 through 200' Processing helix chain 'O' and resid 127 through 131 removed outlier: 3.923A pdb=" N GLN O 131 " --> pdb=" O GLU O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 191 removed outlier: 3.985A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.540A pdb=" N LYS D 197 " --> pdb=" O PRO D 193 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 4.088A pdb=" N GLY E 33 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR E 34 " --> pdb=" O SER E 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 34' Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.875A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'F' and resid 132 through 138 Processing helix chain 'F' and resid 192 through 199 removed outlier: 3.612A pdb=" N LYS F 197 " --> pdb=" O PRO F 193 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.893A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 138 removed outlier: 3.717A pdb=" N THR J 138 " --> pdb=" O SER J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 196 No H-bonds generated for 'chain 'J' and resid 194 through 196' Processing helix chain 'K' and resid 132 through 138 Processing helix chain 'K' and resid 192 through 199 removed outlier: 3.567A pdb=" N LYS K 197 " --> pdb=" O PRO K 193 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 92 removed outlier: 3.925A pdb=" N THR M 92 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 138 removed outlier: 3.768A pdb=" N THR M 138 " --> pdb=" O SER M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.335A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.732A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.802A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.942A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.716A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.757A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.632A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.695A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.381A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.500A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.216A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.605A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.701A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.622A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.050A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.206A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.780A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.516A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.387A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.152A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.838A pdb=" N ARG B 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY N 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.533A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.887A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 578 removed outlier: 3.534A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.555A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.498A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.498A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.154A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.389A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.592A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.608A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.412A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.098A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.671A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.793A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.667A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.489A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.688A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.807A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.192A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.502A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.405A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.669A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 52 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.107A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.525A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 195 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.624A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AG5, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.907A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER L 92 " --> pdb=" O VAL L 101 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.907A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.277A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AG9, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.627A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.691A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 23 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.989A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.989A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU G 113 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 131 through 135 removed outlier: 3.589A pdb=" N SER G 131 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 149 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.515A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AH7, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.834A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER I 92 " --> pdb=" O VAL I 101 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.834A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR I 88 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.990A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AI2, first strand: chain 'I' and resid 159 through 160 removed outlier: 4.554A pdb=" N TRP I 153 " --> pdb=" O VAL I 160 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS I 198 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS I 209 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 3 through 5 removed outlier: 3.969A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.516A pdb=" N TYR N 94 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 131 through 135 removed outlier: 3.755A pdb=" N GLY N 150 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU N 149 " --> pdb=" O VAL N 193 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER N 191 " --> pdb=" O CYS N 151 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL N 153 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU N 189 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP N 155 " --> pdb=" O TYR N 187 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR N 187 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 162 through 165 removed outlier: 3.747A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 220 " --> pdb=" O CYS N 207 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.558A pdb=" N LEU O 75 " --> pdb=" O ILE O 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER O 72 " --> pdb=" O SER O 69 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.852A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER O 92 " --> pdb=" O VAL O 101 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.852A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 119 through 123 removed outlier: 4.253A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 135 through 136 Processing sheet with id=AJ3, first strand: chain 'O' and resid 150 through 154 removed outlier: 4.178A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR O 201 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS O 154 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.546A pdb=" N SER D 73 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 68 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.752A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.752A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.718A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.718A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 164 through 166 removed outlier: 4.081A pdb=" N TRP D 159 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 215 " --> pdb=" O CYS D 204 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AK2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.742A pdb=" N VAL E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.070A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.070A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.638A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.638A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.240A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AK9, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.866A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 9 through 11 Processing sheet with id=AL2, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.543A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.543A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'F' and resid 164 through 166 removed outlier: 4.120A pdb=" N TRP F 159 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AL6, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AL7, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.068A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER J 37 " --> pdb=" O ALA J 98 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 98 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR J 109 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.068A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER J 37 " --> pdb=" O ALA J 98 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 98 " --> pdb=" O SER J 37 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'J' and resid 127 through 131 removed outlier: 3.853A pdb=" N GLY J 146 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'J' and resid 127 through 131 removed outlier: 3.853A pdb=" N GLY J 146 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.204A pdb=" N TYR J 201 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AM4, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.578A pdb=" N VAL K 10 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.510A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.510A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'K' and resid 164 through 166 removed outlier: 4.121A pdb=" N TRP K 159 " --> pdb=" O VAL K 166 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AM9, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.665A pdb=" N VAL M 12 " --> pdb=" O THR M 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM9 Processing sheet with id=AN1, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.927A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR M 109 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.927A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.651A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.651A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'M' and resid 158 through 161 removed outlier: 4.227A pdb=" N TYR M 201 " --> pdb=" O VAL M 218 " (cutoff:3.500A) 1647 hydrogen bonds defined for protein. 4272 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: 20.86 Time building geometry restraints manager: 9.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 14406 1.35 - 1.47: 11533 1.47 - 1.59: 20168 1.59 - 1.71: 0 1.71 - 1.83: 219 Bond restraints: 46326 Sorted by residual: bond pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.85e+00 bond pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.18e+00 bond pdb=" C LYS N 212 " pdb=" N PRO N 213 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.87e+00 bond pdb=" N ASN B 234 " pdb=" CA ASN B 234 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.21e-02 6.83e+03 6.74e+00 ... (remaining 46321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 61888 1.83 - 3.65: 1090 3.65 - 5.48: 92 5.48 - 7.31: 45 7.31 - 9.14: 11 Bond angle restraints: 63126 Sorted by residual: angle pdb=" O GLY C 526 " pdb=" C GLY C 526 " pdb=" N PRO C 527 " ideal model delta sigma weight residual 121.77 113.78 7.99 1.00e+00 1.00e+00 6.38e+01 angle pdb=" CA LYS C 558 " pdb=" CB LYS C 558 " pdb=" CG LYS C 558 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CA GLN J 3 " pdb=" CB GLN J 3 " pdb=" CG GLN J 3 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 angle pdb=" C GLY H 27 " pdb=" N THR H 28 " pdb=" CA THR H 28 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C GLY N 27 " pdb=" N THR N 28 " pdb=" CA THR N 28 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 ... (remaining 63121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 25468 18.00 - 35.99: 2207 35.99 - 53.99: 577 53.99 - 71.99: 89 71.99 - 89.98: 45 Dihedral angle restraints: 28386 sinusoidal: 11541 harmonic: 16845 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.63 87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 5.40 87.60 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -171.05 85.05 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 28383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 7331 0.239 - 0.478: 4 0.478 - 0.718: 2 0.718 - 0.957: 0 0.957 - 1.196: 1 Chirality restraints: 7338 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.58e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 7335 not shown) Planarity restraints: 8106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " 0.053 2.00e-02 2.50e+03 1.01e-01 1.02e+02 pdb=" C GLY C 526 " -0.175 2.00e-02 2.50e+03 pdb=" O GLY C 526 " 0.065 2.00e-02 2.50e+03 pdb=" N PRO C 527 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 112 " 0.033 2.00e-02 2.50e+03 6.46e-02 4.18e+01 pdb=" C GLY O 112 " -0.112 2.00e-02 2.50e+03 pdb=" O GLY O 112 " 0.042 2.00e-02 2.50e+03 pdb=" N GLN O 113 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 102 " 0.014 2.00e-02 2.50e+03 1.41e-02 4.98e+00 pdb=" CG TRP E 102 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP E 102 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 102 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 102 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 102 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 102 " 0.004 2.00e-02 2.50e+03 ... (remaining 8103 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2229 2.72 - 3.27: 41518 3.27 - 3.81: 74047 3.81 - 4.36: 85210 4.36 - 4.90: 148594 Nonbonded interactions: 351598 Sorted by model distance: nonbonded pdb=" CB SER K 13 " pdb=" CB LEU K 110 " model vdw 2.181 3.840 nonbonded pdb=" CA SER K 13 " pdb=" CB LEU K 110 " model vdw 2.196 3.870 nonbonded pdb=" OG SER M 7 " pdb=" OG1 THR M 21 " model vdw 2.248 3.040 nonbonded pdb=" OG SER K 28 " pdb=" OG SER K 31 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" OD2 ASP C 364 " model vdw 2.251 3.040 ... (remaining 351593 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.040 Extract box with map and model: 1.390 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 83.920 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.003 0.048 46326 Z= 0.199 Angle : 0.566 9.136 63126 Z= 0.292 Chirality : 0.048 1.196 7338 Planarity : 0.005 0.101 8061 Dihedral : 14.344 89.983 17400 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 0.80 % Allowed : 18.37 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -1.04 (0.11), residues: 5763 helix: 0.66 (0.20), residues: 648 sheet: 0.21 (0.13), residues: 1673 loop : -1.49 (0.10), residues: 3442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 102 HIS 0.003 0.001 HIS G 211 PHE 0.020 0.001 PHE B 133 TYR 0.027 0.001 TYR E 54 ARG 0.009 0.000 ARG M 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7825 (mmtm) REVERT: B 137 ASN cc_start: 0.5908 (m110) cc_final: 0.5401 (t0) REVERT: B 177 MET cc_start: 0.1452 (mtm) cc_final: -0.1688 (mmt) REVERT: B 523 THR cc_start: 0.5982 (OUTLIER) cc_final: 0.5686 (p) REVERT: B 524 VAL cc_start: 0.1745 (OUTLIER) cc_final: 0.1427 (p) REVERT: B 869 MET cc_start: 0.9057 (mtt) cc_final: 0.8842 (mtp) REVERT: B 1130 ILE cc_start: 0.7880 (pt) cc_final: 0.7620 (mt) REVERT: C 144 TYR cc_start: 0.6869 (t80) cc_final: 0.6089 (t80) REVERT: H 204 THR cc_start: 0.7742 (p) cc_final: 0.7371 (m) REVERT: L 71 THR cc_start: 0.5711 (OUTLIER) cc_final: 0.5447 (m) REVERT: G 207 CYS cc_start: 0.3606 (OUTLIER) cc_final: 0.3311 (t) REVERT: N 207 CYS cc_start: 0.4950 (OUTLIER) cc_final: 0.3362 (t) REVERT: O 16 GLN cc_start: 0.4630 (pp30) cc_final: 0.4282 (mt0) REVERT: O 111 LEU cc_start: 0.3849 (tp) cc_final: 0.3536 (mt) REVERT: O 165 GLU cc_start: 0.2670 (pp20) cc_final: 0.1937 (mm-30) REVERT: O 171 LYS cc_start: 0.1936 (mmtt) cc_final: 0.1447 (tttp) REVERT: F 12 GLU cc_start: 0.7877 (tp30) cc_final: 0.6500 (tt0) REVERT: J 153 PHE cc_start: 0.4754 (t80) cc_final: 0.4532 (t80) REVERT: J 180 SER cc_start: 0.4952 (p) cc_final: 0.4588 (m) REVERT: J 183 TYR cc_start: 0.6084 (m-80) cc_final: 0.5805 (m-80) REVERT: M 3 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7643 (pp30) outliers start: 40 outliers final: 8 residues processed: 283 average time/residue: 0.5063 time to fit residues: 230.4796 Evaluate side-chains 150 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 207 CYS Chi-restraints excluded: chain N residue 207 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 30.0000 chunk 436 optimal weight: 7.9990 chunk 242 optimal weight: 0.0770 chunk 149 optimal weight: 30.0000 chunk 294 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 451 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 336 optimal weight: 40.0000 chunk 523 optimal weight: 20.0000 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 613 GLN B 751 ASN B 895 GLN B 913 GLN C 66 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 506 GLN L 81 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN I 113 GLN I 202 HIS N 3 GLN ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN K 119 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.161595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.131882 restraints weight = 155383.382| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 4.06 r_work: 0.3750 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 46326 Z= 0.249 Angle : 0.563 9.640 63126 Z= 0.292 Chirality : 0.045 0.495 7338 Planarity : 0.004 0.050 8061 Dihedral : 5.401 59.850 7435 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.28 % Allowed : 17.97 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.82 (0.11), residues: 5763 helix: 0.98 (0.21), residues: 709 sheet: 0.24 (0.13), residues: 1791 loop : -1.40 (0.10), residues: 3263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 37 HIS 0.019 0.001 HIS N 175 PHE 0.020 0.001 PHE B 133 TYR 0.023 0.001 TYR A 170 ARG 0.013 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 148 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 335 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4604 (mt) REVERT: A 598 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8853 (mp) REVERT: B 137 ASN cc_start: 0.6002 (m110) cc_final: 0.5579 (p0) REVERT: B 1086 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8518 (pttp) REVERT: C 105 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7529 (pt) REVERT: C 166 CYS cc_start: 0.3906 (OUTLIER) cc_final: 0.3448 (p) REVERT: C 740 MET cc_start: 0.7564 (mmm) cc_final: 0.7356 (mmm) REVERT: C 993 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8763 (tp) REVERT: H 6 GLU cc_start: 0.2337 (OUTLIER) cc_final: 0.0859 (mt-10) REVERT: H 191 SER cc_start: 0.0381 (OUTLIER) cc_final: 0.0005 (p) REVERT: H 207 CYS cc_start: 0.0116 (OUTLIER) cc_final: -0.0474 (t) REVERT: L 71 THR cc_start: 0.5516 (OUTLIER) cc_final: 0.5308 (m) REVERT: L 107 LYS cc_start: 0.3712 (tttp) cc_final: 0.3438 (mmtt) REVERT: N 207 CYS cc_start: -0.2961 (OUTLIER) cc_final: -0.5964 (t) REVERT: N 212 LYS cc_start: 0.2911 (OUTLIER) cc_final: 0.2675 (pttm) REVERT: O 113 GLN cc_start: -0.1526 (mm-40) cc_final: -0.3160 (pm20) REVERT: O 171 LYS cc_start: 0.2943 (mmtt) cc_final: 0.1557 (tttp) REVERT: D 40 ARG cc_start: 0.4989 (mmp-170) cc_final: 0.4414 (mmp-170) REVERT: D 151 TYR cc_start: 0.6013 (t80) cc_final: 0.5503 (m-80) REVERT: D 204 CYS cc_start: 0.0202 (OUTLIER) cc_final: -0.0707 (p) REVERT: E 3 GLN cc_start: 0.7157 (mm110) cc_final: 0.6608 (mm110) REVERT: E 176 VAL cc_start: -0.1421 (OUTLIER) cc_final: -0.1908 (t) REVERT: F 136 LEU cc_start: 0.3673 (tt) cc_final: 0.3254 (mt) REVERT: J 183 TYR cc_start: 0.4184 (m-80) cc_final: 0.3715 (m-80) outliers start: 114 outliers final: 33 residues processed: 254 average time/residue: 0.4272 time to fit residues: 188.8084 Evaluate side-chains 165 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain N residue 207 CYS Chi-restraints excluded: chain N residue 212 LYS Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 5 optimal weight: 10.0000 chunk 482 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 468 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 322 optimal weight: 50.0000 chunk 383 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 379 optimal weight: 0.0670 chunk 126 optimal weight: 0.4980 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 895 GLN H 208 ASN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 112 GLN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.175422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.145040 restraints weight = 158103.773| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 5.11 r_work: 0.3504 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 46326 Z= 0.256 Angle : 0.543 11.036 63126 Z= 0.278 Chirality : 0.045 0.477 7338 Planarity : 0.004 0.101 8061 Dihedral : 5.569 111.121 7422 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 2.42 % Allowed : 18.19 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.75 (0.11), residues: 5763 helix: 1.06 (0.20), residues: 712 sheet: 0.25 (0.12), residues: 1885 loop : -1.37 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 165 HIS 0.009 0.001 HIS B1064 PHE 0.018 0.001 PHE C 342 TYR 0.019 0.001 TYR A 170 ARG 0.006 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 134 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 238 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.6730 (p90) REVERT: A 323 THR cc_start: 0.7185 (p) cc_final: 0.6775 (t) REVERT: B 508 TYR cc_start: 0.7035 (m-80) cc_final: 0.6572 (m-80) REVERT: B 1086 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8701 (pttp) REVERT: C 105 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7822 (pt) REVERT: C 993 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8861 (tp) REVERT: C 1063 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8904 (mp) REVERT: H 6 GLU cc_start: 0.4878 (OUTLIER) cc_final: 0.3319 (mt-10) REVERT: H 157 PHE cc_start: 0.1933 (OUTLIER) cc_final: 0.1632 (t80) REVERT: H 207 CYS cc_start: 0.0537 (OUTLIER) cc_final: -0.0108 (t) REVERT: L 71 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5447 (m) REVERT: L 107 LYS cc_start: 0.4329 (tttp) cc_final: 0.3700 (mmtt) REVERT: L 186 THR cc_start: -0.0251 (OUTLIER) cc_final: -0.0537 (m) REVERT: I 85 GLU cc_start: 0.5313 (tm-30) cc_final: 0.5097 (tm-30) REVERT: N 181 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4608 (mm) REVERT: O 113 GLN cc_start: -0.1403 (mm-40) cc_final: -0.3196 (pm20) REVERT: D 83 THR cc_start: 0.5372 (m) cc_final: 0.4874 (t) REVERT: D 151 TYR cc_start: 0.6025 (t80) cc_final: 0.5419 (m-80) REVERT: E 3 GLN cc_start: 0.7486 (mm110) cc_final: 0.7138 (mm110) REVERT: E 24 VAL cc_start: -0.2495 (OUTLIER) cc_final: -0.2911 (t) REVERT: E 176 VAL cc_start: -0.0594 (OUTLIER) cc_final: -0.1157 (t) REVERT: F 61 ASP cc_start: 0.8148 (t0) cc_final: 0.6677 (t0) REVERT: F 136 LEU cc_start: 0.3878 (tt) cc_final: 0.3443 (mt) REVERT: F 165 PRO cc_start: 0.6251 (Cg_endo) cc_final: 0.6022 (Cg_exo) REVERT: J 183 TYR cc_start: 0.5524 (m-80) cc_final: 0.5303 (m-80) REVERT: K 110 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6468 (mt) outliers start: 121 outliers final: 48 residues processed: 247 average time/residue: 0.4332 time to fit residues: 188.0018 Evaluate side-chains 182 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 34 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain M residue 145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 82 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 510 optimal weight: 9.9990 chunk 495 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 492 optimal weight: 50.0000 chunk 304 optimal weight: 1.9990 chunk 473 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.175362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.144613 restraints weight = 157024.434| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 4.88 r_work: 0.3500 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46326 Z= 0.213 Angle : 0.508 10.353 63126 Z= 0.260 Chirality : 0.043 0.448 7338 Planarity : 0.004 0.057 8061 Dihedral : 5.107 102.802 7419 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 2.12 % Allowed : 19.00 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.68 (0.11), residues: 5763 helix: 1.24 (0.21), residues: 704 sheet: 0.24 (0.12), residues: 1801 loop : -1.28 (0.10), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 36 HIS 0.005 0.001 HIS N 175 PHE 0.013 0.001 PHE H 157 TYR 0.030 0.001 TYR A 380 ARG 0.007 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 125 time to evaluate : 3.951 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: A 238 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6598 (p90) REVERT: A 767 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8902 (mm) REVERT: B 242 LEU cc_start: 0.7970 (mp) cc_final: 0.7664 (tp) REVERT: B 969 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8825 (p0) REVERT: B 1086 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8730 (pttp) REVERT: C 105 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7784 (pt) REVERT: C 993 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8808 (tp) REVERT: H 6 GLU cc_start: 0.4936 (OUTLIER) cc_final: 0.3460 (mt-10) REVERT: H 20 VAL cc_start: -0.4017 (OUTLIER) cc_final: -0.4447 (t) REVERT: L 16 GLN cc_start: 0.6133 (pt0) cc_final: 0.5680 (pp30) REVERT: L 71 THR cc_start: 0.5517 (OUTLIER) cc_final: 0.5315 (m) REVERT: L 107 LYS cc_start: 0.4364 (tttp) cc_final: 0.3964 (mmtt) REVERT: O 16 GLN cc_start: 0.6855 (mt0) cc_final: 0.6575 (pp30) REVERT: O 113 GLN cc_start: -0.1393 (mm-40) cc_final: -0.3198 (pm20) REVERT: D 12 GLU cc_start: 0.1723 (OUTLIER) cc_final: 0.0503 (tt0) REVERT: D 204 CYS cc_start: -0.0466 (OUTLIER) cc_final: -0.1625 (p) REVERT: E 3 GLN cc_start: 0.7484 (mm110) cc_final: 0.7146 (mm110) REVERT: E 24 VAL cc_start: -0.2217 (OUTLIER) cc_final: -0.2590 (t) REVERT: E 176 VAL cc_start: -0.0555 (OUTLIER) cc_final: -0.1116 (t) REVERT: F 136 LEU cc_start: 0.3844 (tt) cc_final: 0.3433 (mt) REVERT: F 165 PRO cc_start: 0.6917 (Cg_endo) cc_final: 0.6699 (Cg_exo) REVERT: K 178 GLN cc_start: -0.0185 (mm-40) cc_final: -0.0448 (mm-40) outliers start: 106 outliers final: 59 residues processed: 224 average time/residue: 0.4184 time to fit residues: 165.6994 Evaluate side-chains 184 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 112 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 102 TRP Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 50.0000 chunk 149 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 475 optimal weight: 20.0000 chunk 378 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 334 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 253 optimal weight: 8.9990 chunk 480 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 580 GLN L 189 GLN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN E 5 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS ** M 3 GLN ** 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 = 0.4765 r_free = 0.4765 target = 0.158723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.126450 restraints weight = 151960.917| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 4.23 r_work: 0.3598 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 46326 Z= 0.310 Angle : 0.552 10.350 63126 Z= 0.282 Chirality : 0.045 0.454 7338 Planarity : 0.004 0.064 8061 Dihedral : 5.031 94.943 7419 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.74 % Allowed : 18.86 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.70 (0.11), residues: 5763 helix: 1.26 (0.21), residues: 684 sheet: 0.20 (0.12), residues: 1779 loop : -1.26 (0.10), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 110 HIS 0.007 0.001 HIS B1064 PHE 0.021 0.002 PHE B 238 TYR 0.014 0.001 TYR C 279 ARG 0.007 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 116 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6977 (p90) REVERT: A 767 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9076 (mm) REVERT: B 329 PHE cc_start: 0.6659 (m-10) cc_final: 0.6418 (m-10) REVERT: B 745 ASP cc_start: 0.7225 (m-30) cc_final: 0.6757 (t0) REVERT: B 959 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9058 (mt) REVERT: B 969 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8896 (p0) REVERT: B 1086 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (mtmt) REVERT: C 105 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (pt) REVERT: C 592 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.4571 (m-80) REVERT: C 993 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8930 (tp) REVERT: H 6 GLU cc_start: 0.3696 (OUTLIER) cc_final: 0.2947 (mt-10) REVERT: H 157 PHE cc_start: 0.2267 (OUTLIER) cc_final: 0.1765 (t80) REVERT: H 207 CYS cc_start: 0.1415 (OUTLIER) cc_final: 0.0734 (t) REVERT: L 107 LYS cc_start: 0.4409 (tttp) cc_final: 0.3978 (mmtt) REVERT: O 113 GLN cc_start: -0.1347 (mm-40) cc_final: -0.3189 (pm20) REVERT: D 12 GLU cc_start: 0.1056 (OUTLIER) cc_final: -0.0042 (tt0) REVERT: D 204 CYS cc_start: 0.0182 (OUTLIER) cc_final: -0.1274 (p) REVERT: E 3 GLN cc_start: 0.7147 (mm110) cc_final: 0.6870 (mm110) REVERT: E 5 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6613 (pp30) REVERT: E 24 VAL cc_start: -0.2057 (OUTLIER) cc_final: -0.2537 (t) REVERT: E 176 VAL cc_start: -0.1343 (OUTLIER) cc_final: -0.1851 (t) REVERT: F 136 LEU cc_start: 0.3823 (tt) cc_final: 0.3401 (mt) REVERT: F 165 PRO cc_start: 0.6974 (Cg_endo) cc_final: 0.6758 (Cg_exo) REVERT: J 183 TYR cc_start: 0.3042 (OUTLIER) cc_final: 0.1892 (m-80) outliers start: 137 outliers final: 80 residues processed: 246 average time/residue: 0.4249 time to fit residues: 184.9321 Evaluate side-chains 203 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 106 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 183 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 511 optimal weight: 6.9990 chunk 446 optimal weight: 50.0000 chunk 205 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 chunk 494 optimal weight: 0.0980 chunk 248 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 435 optimal weight: 40.0000 chunk 129 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 440 optimal weight: 50.0000 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN L 189 GLN I 189 GLN I 193 HIS ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.174674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.143724 restraints weight = 156298.778| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 4.90 r_work: 0.3466 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46326 Z= 0.168 Angle : 0.492 10.079 63126 Z= 0.251 Chirality : 0.043 0.436 7338 Planarity : 0.004 0.060 8061 Dihedral : 4.718 89.020 7417 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 2.26 % Allowed : 19.54 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.58 (0.11), residues: 5763 helix: 1.55 (0.21), residues: 678 sheet: 0.22 (0.12), residues: 1779 loop : -1.18 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 110 HIS 0.008 0.001 HIS M 171 PHE 0.020 0.001 PHE H 157 TYR 0.024 0.001 TYR A 144 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 112 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7542 (m-80) cc_final: 0.7277 (m-80) REVERT: A 238 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6569 (p90) REVERT: B 969 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8878 (p0) REVERT: B 1086 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8649 (pttp) REVERT: C 105 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7658 (pt) REVERT: C 592 PHE cc_start: 0.5621 (OUTLIER) cc_final: 0.4587 (m-80) REVERT: C 993 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8804 (tp) REVERT: H 6 GLU cc_start: 0.5144 (OUTLIER) cc_final: 0.4200 (mt-10) REVERT: H 20 VAL cc_start: -0.4934 (OUTLIER) cc_final: -0.5341 (t) REVERT: H 157 PHE cc_start: 0.1743 (OUTLIER) cc_final: 0.1435 (t80) REVERT: H 207 CYS cc_start: 0.1309 (OUTLIER) cc_final: 0.0752 (t) REVERT: L 16 GLN cc_start: 0.5547 (pt0) cc_final: 0.5139 (pp30) REVERT: L 71 THR cc_start: 0.5284 (OUTLIER) cc_final: 0.5060 (m) REVERT: L 107 LYS cc_start: 0.4593 (tttp) cc_final: 0.4262 (mmtt) REVERT: L 186 THR cc_start: -0.0174 (OUTLIER) cc_final: -0.0460 (m) REVERT: L 189 GLN cc_start: 0.2481 (OUTLIER) cc_final: 0.2199 (pm20) REVERT: O 113 GLN cc_start: -0.1379 (mm-40) cc_final: -0.3084 (pm20) REVERT: O 165 GLU cc_start: 0.0652 (pp20) cc_final: -0.1630 (mm-30) REVERT: D 12 GLU cc_start: 0.1451 (OUTLIER) cc_final: 0.0175 (tt0) REVERT: E 3 GLN cc_start: 0.7596 (mm110) cc_final: 0.7343 (mm110) REVERT: E 5 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: E 24 VAL cc_start: -0.1202 (OUTLIER) cc_final: -0.1764 (t) REVERT: F 136 LEU cc_start: 0.3923 (tt) cc_final: 0.3506 (mt) REVERT: F 165 PRO cc_start: 0.6869 (Cg_endo) cc_final: 0.6662 (Cg_exo) REVERT: J 183 TYR cc_start: 0.5111 (OUTLIER) cc_final: 0.3875 (m-80) outliers start: 113 outliers final: 56 residues processed: 218 average time/residue: 0.4057 time to fit residues: 158.2426 Evaluate side-chains 176 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 103 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 183 TYR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 190 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 380 optimal weight: 40.0000 chunk 65 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 555 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 294 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN E 5 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** 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 = 0.4771 r_free = 0.4771 target = 0.159182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.127255 restraints weight = 152670.119| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 4.18 r_work: 0.3467 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46326 Z= 0.228 Angle : 0.511 10.905 63126 Z= 0.259 Chirality : 0.043 0.428 7338 Planarity : 0.004 0.060 8061 Dihedral : 4.622 82.164 7417 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 2.24 % Allowed : 19.54 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.57 (0.11), residues: 5763 helix: 1.56 (0.21), residues: 678 sheet: 0.27 (0.12), residues: 1748 loop : -1.19 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 110 HIS 0.005 0.001 HIS C 49 PHE 0.020 0.001 PHE H 157 TYR 0.024 0.001 TYR A 144 ARG 0.004 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 109 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7328 (m-80) cc_final: 0.7100 (m-80) REVERT: A 153 MET cc_start: 0.7844 (pmm) cc_final: 0.7513 (pmm) REVERT: B 242 LEU cc_start: 0.8134 (mp) cc_final: 0.7750 (tp) REVERT: B 745 ASP cc_start: 0.7096 (m-30) cc_final: 0.6701 (t0) REVERT: B 969 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8875 (p0) REVERT: B 1086 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8636 (pttp) REVERT: C 105 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7832 (pt) REVERT: C 592 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4663 (m-80) REVERT: C 993 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8842 (tp) REVERT: H 6 GLU cc_start: 0.4994 (OUTLIER) cc_final: 0.4057 (mt-10) REVERT: H 20 VAL cc_start: -0.4923 (OUTLIER) cc_final: -0.5273 (t) REVERT: H 157 PHE cc_start: 0.1785 (OUTLIER) cc_final: 0.1530 (t80) REVERT: H 207 CYS cc_start: 0.1592 (OUTLIER) cc_final: 0.1009 (t) REVERT: L 71 THR cc_start: 0.5198 (OUTLIER) cc_final: 0.4974 (m) REVERT: L 107 LYS cc_start: 0.4488 (tttp) cc_final: 0.4164 (mmtt) REVERT: O 113 GLN cc_start: -0.1451 (mm-40) cc_final: -0.3135 (pm20) REVERT: D 12 GLU cc_start: 0.1370 (OUTLIER) cc_final: 0.0126 (tt0) REVERT: D 151 TYR cc_start: 0.6072 (t80) cc_final: 0.5391 (m-80) REVERT: D 204 CYS cc_start: -0.0666 (OUTLIER) cc_final: -0.1908 (p) REVERT: E 3 GLN cc_start: 0.7611 (mm110) cc_final: 0.7368 (mm110) REVERT: E 5 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6974 (pp30) REVERT: E 24 VAL cc_start: -0.1232 (OUTLIER) cc_final: -0.1820 (t) REVERT: J 183 TYR cc_start: 0.4615 (OUTLIER) cc_final: 0.3316 (m-80) outliers start: 112 outliers final: 79 residues processed: 213 average time/residue: 0.4104 time to fit residues: 155.7759 Evaluate side-chains 194 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 100 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 189 GLN Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 183 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 409 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 427 optimal weight: 0.3980 chunk 183 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 382 optimal weight: 20.0000 chunk 211 optimal weight: 0.9990 chunk 122 optimal weight: 0.0050 chunk 284 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 482 optimal weight: 50.0000 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.169956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.128740 restraints weight = 153657.839| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 6.78 r_work: 0.3195 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 46326 Z= 0.220 Angle : 0.504 9.093 63126 Z= 0.256 Chirality : 0.043 0.416 7338 Planarity : 0.004 0.062 8061 Dihedral : 4.531 74.493 7417 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.36 % Allowed : 19.40 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.57 (0.11), residues: 5763 helix: 1.39 (0.21), residues: 696 sheet: 0.28 (0.12), residues: 1761 loop : -1.18 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 110 HIS 0.005 0.001 HIS B1064 PHE 0.020 0.001 PHE H 157 TYR 0.025 0.001 TYR A 144 ARG 0.007 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 102 time to evaluate : 4.056 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: A 135 PHE cc_start: 0.7586 (m-80) cc_final: 0.7327 (m-80) REVERT: A 153 MET cc_start: 0.7864 (pmm) cc_final: 0.7631 (pmm) REVERT: A 238 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6325 (p90) REVERT: B 200 TYR cc_start: 0.8069 (m-80) cc_final: 0.7658 (t80) REVERT: B 242 LEU cc_start: 0.8378 (mp) cc_final: 0.7883 (tp) REVERT: B 745 ASP cc_start: 0.7763 (m-30) cc_final: 0.7125 (t0) REVERT: B 969 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8700 (p0) REVERT: B 1086 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8625 (pttp) REVERT: C 105 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7492 (pt) REVERT: C 136 CYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7508 (p) REVERT: C 592 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.4907 (m-80) REVERT: C 993 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8664 (tp) REVERT: H 6 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: H 20 VAL cc_start: -0.4269 (OUTLIER) cc_final: -0.4787 (t) REVERT: H 157 PHE cc_start: 0.1178 (OUTLIER) cc_final: 0.0942 (t80) REVERT: H 207 CYS cc_start: 0.1468 (OUTLIER) cc_final: 0.1041 (t) REVERT: L 71 THR cc_start: 0.5044 (OUTLIER) cc_final: 0.4809 (m) REVERT: L 107 LYS cc_start: 0.4771 (tttp) cc_final: 0.4504 (mmtt) REVERT: G 189 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4991 (pp) REVERT: O 165 GLU cc_start: 0.1361 (pp20) cc_final: -0.1469 (mm-30) REVERT: D 12 GLU cc_start: 0.1805 (OUTLIER) cc_final: 0.0535 (tt0) REVERT: D 151 TYR cc_start: 0.5673 (t80) cc_final: 0.5229 (m-80) REVERT: D 204 CYS cc_start: -0.2191 (OUTLIER) cc_final: -0.3074 (p) REVERT: E 5 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: E 24 VAL cc_start: 0.0900 (OUTLIER) cc_final: 0.0330 (t) REVERT: J 183 TYR cc_start: 0.5481 (OUTLIER) cc_final: 0.4656 (m-80) outliers start: 118 outliers final: 83 residues processed: 213 average time/residue: 0.4197 time to fit residues: 157.9679 Evaluate side-chains 199 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 98 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 183 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 188 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 530 optimal weight: 5.9990 chunk 428 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 553 optimal weight: 6.9990 chunk 470 optimal weight: 30.0000 chunk 364 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 189 GLN I 189 GLN I 193 HIS N 166 ASN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.158419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.126240 restraints weight = 152155.682| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 4.22 r_work: 0.3464 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 46326 Z= 0.271 Angle : 0.526 9.117 63126 Z= 0.267 Chirality : 0.044 0.413 7338 Planarity : 0.004 0.063 8061 Dihedral : 4.535 63.638 7417 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 2.36 % Allowed : 19.46 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.57 (0.11), residues: 5763 helix: 1.35 (0.21), residues: 696 sheet: 0.24 (0.12), residues: 1830 loop : -1.16 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 36 HIS 0.007 0.001 HIS B1064 PHE 0.020 0.001 PHE H 157 TYR 0.014 0.001 TYR G 187 ARG 0.006 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 102 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7425 (m-80) cc_final: 0.7196 (m-80) REVERT: A 153 MET cc_start: 0.7760 (pmm) cc_final: 0.7508 (pmm) REVERT: B 200 TYR cc_start: 0.7985 (m-80) cc_final: 0.7707 (t80) REVERT: B 242 LEU cc_start: 0.8318 (mp) cc_final: 0.7986 (tp) REVERT: B 745 ASP cc_start: 0.7404 (m-30) cc_final: 0.7115 (t0) REVERT: B 1086 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8624 (pttp) REVERT: C 105 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7764 (pt) REVERT: C 136 CYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7893 (p) REVERT: C 200 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: C 592 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.4870 (m-80) REVERT: C 993 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8901 (tp) REVERT: H 6 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5193 (mt-10) REVERT: H 20 VAL cc_start: -0.4544 (OUTLIER) cc_final: -0.5000 (t) REVERT: H 157 PHE cc_start: 0.1944 (OUTLIER) cc_final: 0.1680 (t80) REVERT: H 207 CYS cc_start: 0.2248 (OUTLIER) cc_final: 0.1561 (t) REVERT: L 16 GLN cc_start: 0.5149 (pt0) cc_final: 0.4788 (pp30) REVERT: L 71 THR cc_start: 0.5045 (OUTLIER) cc_final: 0.4809 (m) REVERT: L 107 LYS cc_start: 0.4377 (tttp) cc_final: 0.4076 (mmtt) REVERT: G 189 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5405 (pp) REVERT: O 165 GLU cc_start: 0.1095 (pp20) cc_final: -0.1166 (mm-30) REVERT: D 12 GLU cc_start: 0.1751 (OUTLIER) cc_final: 0.0413 (tt0) REVERT: D 151 TYR cc_start: 0.6158 (t80) cc_final: 0.5472 (m-80) REVERT: D 204 CYS cc_start: -0.0288 (OUTLIER) cc_final: -0.1585 (p) REVERT: E 5 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6929 (pp30) REVERT: E 24 VAL cc_start: -0.0326 (OUTLIER) cc_final: -0.0880 (t) REVERT: J 109 TYR cc_start: 0.7866 (m-80) cc_final: 0.7605 (m-80) REVERT: J 183 TYR cc_start: 0.4159 (OUTLIER) cc_final: 0.3010 (m-80) outliers start: 118 outliers final: 81 residues processed: 213 average time/residue: 0.4344 time to fit residues: 165.8358 Evaluate side-chains 197 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 99 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 183 TYR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 386 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 376 optimal weight: 10.0000 chunk 539 optimal weight: 30.0000 chunk 475 optimal weight: 3.9990 chunk 533 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 20 optimal weight: 0.0770 chunk 296 optimal weight: 0.5980 chunk 518 optimal weight: 8.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN L 189 GLN I 189 GLN I 193 HIS O 81 GLN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.173954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.142077 restraints weight = 156146.335| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 4.79 r_work: 0.3473 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 46326 Z= 0.183 Angle : 0.499 13.401 63126 Z= 0.253 Chirality : 0.043 0.400 7338 Planarity : 0.004 0.062 8061 Dihedral : 4.391 57.026 7417 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 1.94 % Allowed : 19.86 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.51 (0.11), residues: 5763 helix: 1.47 (0.21), residues: 696 sheet: 0.27 (0.12), residues: 1830 loop : -1.14 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 36 HIS 0.004 0.001 HIS C 49 PHE 0.019 0.001 PHE H 157 TYR 0.024 0.001 TYR A 380 ARG 0.006 0.000 ARG B 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 103 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7537 (m-80) cc_final: 0.7230 (m-80) REVERT: A 153 MET cc_start: 0.7700 (pmm) cc_final: 0.7469 (pmm) REVERT: B 164 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6852 (p0) REVERT: B 242 LEU cc_start: 0.8239 (mp) cc_final: 0.7958 (tp) REVERT: B 745 ASP cc_start: 0.7225 (m-30) cc_final: 0.6983 (t0) REVERT: B 1086 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8626 (pttp) REVERT: C 105 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7785 (pt) REVERT: C 136 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7885 (p) REVERT: C 200 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: C 592 PHE cc_start: 0.5674 (OUTLIER) cc_final: 0.4660 (m-80) REVERT: C 993 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8829 (tp) REVERT: H 6 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.5158 (mt-10) REVERT: H 81 MET cc_start: -0.6037 (tpp) cc_final: -0.6299 (mmt) REVERT: H 157 PHE cc_start: 0.1813 (OUTLIER) cc_final: 0.1542 (t80) REVERT: H 207 CYS cc_start: 0.2249 (OUTLIER) cc_final: 0.1571 (t) REVERT: L 16 GLN cc_start: 0.5133 (pt0) cc_final: 0.4845 (pp30) REVERT: L 107 LYS cc_start: 0.4716 (tttp) cc_final: 0.4058 (mppt) REVERT: G 189 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5331 (pp) REVERT: O 165 GLU cc_start: 0.1021 (pp20) cc_final: -0.1166 (mm-30) REVERT: D 12 GLU cc_start: 0.1685 (OUTLIER) cc_final: 0.0359 (tt0) REVERT: D 86 GLU cc_start: 0.5251 (mm-30) cc_final: 0.4894 (mm-30) REVERT: D 151 TYR cc_start: 0.6234 (t80) cc_final: 0.5577 (m-80) REVERT: D 204 CYS cc_start: -0.0712 (OUTLIER) cc_final: -0.1727 (p) REVERT: E 5 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: E 24 VAL cc_start: -0.0251 (OUTLIER) cc_final: -0.0781 (t) REVERT: J 109 TYR cc_start: 0.8158 (m-80) cc_final: 0.7877 (m-80) outliers start: 97 outliers final: 69 residues processed: 196 average time/residue: 0.4536 time to fit residues: 155.9999 Evaluate side-chains 179 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 95 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain H residue 207 CYS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 42 optimal weight: 0.4980 chunk 530 optimal weight: 0.9980 chunk 551 optimal weight: 6.9990 chunk 441 optimal weight: 40.0000 chunk 223 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 556 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 404 optimal weight: 30.0000 chunk 144 optimal weight: 50.0000 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 66 HIS ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN I 91 GLN I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.171502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.133810 restraints weight = 154373.215| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 5.03 r_work: 0.3258 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 46326 Z= 0.533 Angle : 0.673 13.688 63126 Z= 0.344 Chirality : 0.048 0.405 7338 Planarity : 0.005 0.072 8061 Dihedral : 4.981 55.396 7417 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 2.04 % Allowed : 19.68 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.79 (0.11), residues: 5763 helix: 0.83 (0.20), residues: 691 sheet: 0.13 (0.12), residues: 1810 loop : -1.23 (0.11), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 36 HIS 0.017 0.001 HIS B1064 PHE 0.030 0.002 PHE C 92 TYR 0.020 0.002 TYR F 188 ARG 0.008 0.001 ARG B 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21391.55 seconds wall clock time: 368 minutes 9.68 seconds (22089.68 seconds total)