Starting phenix.real_space_refine on Thu Jan 16 04:18:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhn_60109/01_2025/8zhn_60109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhn_60109/01_2025/8zhn_60109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zhn_60109/01_2025/8zhn_60109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhn_60109/01_2025/8zhn_60109.map" model { file = "/net/cci-nas-00/data/ceres_data/8zhn_60109/01_2025/8zhn_60109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhn_60109/01_2025/8zhn_60109.cif" } resolution = 4.12 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= 0.031 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 53 residue(s): 0.10s 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: "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: "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: "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: "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: "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: "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: "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: "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 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 Time building chain proxies: 19.52, per 1000 atoms: 0.43 Number of scatterers: 45273 At special positions: 0 Unit cell: (238.08, 229.152, 208.32, 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 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=2.04 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=2.04 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 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 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 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=2.04 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=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 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 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 C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 4.7 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: 73 helices and 116 sheets defined 13.4% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.25 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.563A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.504A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.957A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.798A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 4.101A 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: 4.046A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.282A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 919' Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.747A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.066A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.566A 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 'C' and resid 1142 through 1146 removed outlier: 3.526A pdb=" N LEU C1145 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1142 through 1146' 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: 3.709A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.330A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.597A pdb=" N ASP D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 86 " --> pdb=" O THR D 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 82 through 86' Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.579A pdb=" N LYS E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.911A 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 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.512A 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: 3.941A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.892A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.619A 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 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.253A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.325A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.044A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (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 338 through 344 removed outlier: 3.668A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.922A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.775A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.254A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.748A 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 940 Processing helix chain 'B' and resid 946 through 966 removed outlier: 4.372A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.151A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.543A 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 '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: 3.962A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 3.983A pdb=" N LYS L 191 " --> pdb=" O PRO L 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 126 through 130 removed outlier: 3.554A pdb=" N LEU O 130 " --> pdb=" O SER O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 191 removed outlier: 4.020A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 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: 3.823A pdb=" N HIS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 66 removed outlier: 3.570A pdb=" N LYS J 66 " --> pdb=" O PRO J 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 63 through 66' Processing helix chain 'J' and resid 88 through 92 removed outlier: 4.186A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 138 removed outlier: 3.595A 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: 3.517A pdb=" N LYS K 197 " --> pdb=" O PRO K 193 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 66 removed outlier: 3.654A pdb=" N LYS M 66 " --> pdb=" O PRO M 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 63 through 66' Processing helix chain 'M' and resid 88 through 92 removed outlier: 3.930A pdb=" N THR M 92 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 138 removed outlier: 3.720A 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 'C' and resid 27 through 30 removed outlier: 8.576A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 226 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.622A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.911A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.094A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.335A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.826A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 583 through 586 removed outlier: 3.918A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.500A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.682A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.517A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.252A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.646A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.479A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.756A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 23 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU G 82 " --> pdb=" O THR G 69 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.561A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 131 through 135 removed outlier: 3.533A pdb=" N SER G 131 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 149 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.608A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AC7, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.798A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.798A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR I 88 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 119 through 123 removed outlier: 4.073A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 159 through 160 removed outlier: 4.543A pdb=" N TRP I 153 " --> pdb=" O VAL I 160 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS I 154 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS I 198 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS I 209 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.575A pdb=" N ASP D 68 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.288A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.288A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.774A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.774A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 156 through 159 removed outlier: 3.504A pdb=" N THR D 156 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 215 " --> pdb=" O CYS D 204 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.539A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.796A pdb=" N VAL E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.087A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN E 100 " --> pdb=" O PHE E 35 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.087A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN E 100 " --> pdb=" O PHE E 35 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.807A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.807A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.368A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.010A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.505A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.872A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.849A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.738A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.656A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.857A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AF3, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.548A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.688A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AF7, first strand: chain 'A' and resid 575 through 578 removed outlier: 3.554A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.377A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AG1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AG2, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.549A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.249A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.719A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.570A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.668A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.664A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.526A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.442A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.230A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.817A pdb=" N ARG B 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY N 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.518A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 575 through 578 removed outlier: 3.522A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.535A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 712 through 727 removed outlier: 6.516A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 712 through 727 removed outlier: 6.516A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.147A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AI3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.379A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.549A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.546A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 195 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.696A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 9 through 10 removed outlier: 3.550A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL L 35 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TYR L 51 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 49 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN L 39 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS L 47 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 9 through 10 removed outlier: 3.550A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER L 92 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL L 101 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 17 through 22 removed outlier: 3.512A pdb=" N SER L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.347A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AJ3, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.603A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 3 through 6 removed outlier: 4.000A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL N 20 " --> pdb=" O MET N 81 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET N 81 " --> pdb=" O VAL N 20 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.503A pdb=" N THR N 121 " --> pdb=" O GLU N 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP N 36 " --> pdb=" O GLY N 49 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'N' and resid 131 through 135 removed outlier: 3.743A pdb=" N GLY N 150 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU N 149 " --> pdb=" O VAL N 193 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER N 191 " --> pdb=" O CYS N 151 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL N 153 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU N 189 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP N 155 " --> pdb=" O TYR N 187 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR N 187 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'N' and resid 162 through 165 removed outlier: 3.685A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS N 220 " --> pdb=" O CYS N 207 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.556A pdb=" N LEU O 75 " --> pdb=" O ILE O 20 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER O 72 " --> pdb=" O SER O 69 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 47 through 51 removed outlier: 3.988A pdb=" N LYS O 47 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN O 39 " --> pdb=" O LYS O 47 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER O 92 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL O 101 " --> pdb=" O SER O 92 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'O' and resid 47 through 51 removed outlier: 3.988A pdb=" N LYS O 47 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN O 39 " --> pdb=" O LYS O 47 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR O 88 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR O 106 " --> pdb=" O TYR O 88 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 119 through 123 removed outlier: 4.041A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER O 181 " --> pdb=" O CYS O 139 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 150 through 154 removed outlier: 4.182A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR O 201 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS O 154 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER O 197 " --> pdb=" O LYS O 154 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AK5, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL F 10 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL F 10 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.604A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.604A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 164 through 166 removed outlier: 4.124A pdb=" N TRP F 159 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 215 " --> pdb=" O CYS F 204 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AL2, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.028A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER J 37 " --> pdb=" O ALA J 98 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR J 109 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.028A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER J 37 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'J' and resid 127 through 131 removed outlier: 3.935A pdb=" N GLY J 146 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 127 through 131 removed outlier: 3.935A pdb=" N GLY J 146 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.194A pdb=" N TYR J 201 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AL8, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.992A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.731A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.731A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'K' and resid 164 through 166 removed outlier: 4.161A pdb=" N TRP K 159 " --> pdb=" O VAL K 166 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.634A pdb=" N THR M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN M 79 " --> pdb=" O ASP M 74 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.880A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG M 99 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR M 109 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.880A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.692A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.692A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'M' and resid 158 through 161 removed outlier: 4.202A pdb=" N TYR M 201 " --> pdb=" O VAL M 218 " (cutoff:3.500A) 1594 hydrogen bonds defined for protein. 4161 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: 23.91 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14301 1.34 - 1.46: 11157 1.46 - 1.58: 20649 1.58 - 1.71: 0 1.71 - 1.83: 219 Bond restraints: 46326 Sorted by residual: bond pdb=" N SER C 530 " pdb=" CA SER C 530 " ideal model delta sigma weight residual 1.459 1.487 -0.028 9.10e-03 1.21e+04 9.22e+00 bond pdb=" N ILE C 326 " pdb=" CA ILE C 326 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.18e-02 7.18e+03 8.82e+00 bond pdb=" N VAL C 534 " pdb=" CA VAL C 534 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.76e+00 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.58e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.58e+00 ... (remaining 46321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 62100 2.29 - 4.58: 898 4.58 - 6.87: 108 6.87 - 9.16: 16 9.16 - 11.45: 4 Bond angle restraints: 63126 Sorted by residual: angle pdb=" CB MET A 740 " pdb=" CG MET A 740 " pdb=" SD MET A 740 " ideal model delta sigma weight residual 112.70 124.15 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA LYS B 386 " pdb=" CB LYS B 386 " pdb=" CG LYS B 386 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N GLY B 339 " pdb=" CA GLY B 339 " pdb=" C GLY B 339 " ideal model delta sigma weight residual 113.99 109.15 4.84 1.28e+00 6.10e-01 1.43e+01 angle pdb=" N ARG M 104 " pdb=" CA ARG M 104 " pdb=" C ARG M 104 " ideal model delta sigma weight residual 112.93 108.71 4.22 1.12e+00 7.97e-01 1.42e+01 angle pdb=" C GLY H 27 " pdb=" N THR H 28 " pdb=" CA THR H 28 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 ... (remaining 63121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 26120 17.99 - 35.98: 1786 35.98 - 53.96: 363 53.96 - 71.95: 71 71.95 - 89.94: 46 Dihedral angle restraints: 28386 sinusoidal: 11541 harmonic: 16845 Sorted by residual: 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 -175.94 89.94 1 1.00e+01 1.00e-02 9.59e+01 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 -175.44 89.44 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 4.45 88.55 1 1.00e+01 1.00e-02 9.36e+01 ... (remaining 28383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 7194 0.116 - 0.232: 135 0.232 - 0.348: 5 0.348 - 0.464: 3 0.464 - 0.580: 1 Chirality restraints: 7338 Sorted by residual: 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 -1.82 -0.58 2.00e-01 2.50e+01 8.40e+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 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 7335 not shown) Planarity restraints: 8106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.053 2.00e-02 2.50e+03 5.93e-02 4.40e+01 pdb=" CG ASN C 331 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.096 2.00e-02 2.50e+03 pdb=" C1 NAG C1306 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 112 " -0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C GLY O 112 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY O 112 " -0.033 2.00e-02 2.50e+03 pdb=" N GLN O 113 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 145 " -0.050 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO L 146 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 146 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 146 " -0.036 5.00e-02 4.00e+02 ... (remaining 8103 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3911 2.75 - 3.29: 42269 3.29 - 3.82: 74316 3.82 - 4.36: 83535 4.36 - 4.90: 146208 Nonbonded interactions: 350239 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.211 3.040 nonbonded pdb=" OG SER K 28 " pdb=" OG SER K 31 " model vdw 2.216 3.040 nonbonded pdb=" OG SER E 7 " pdb=" OG1 THR E 21 " model vdw 2.234 3.040 nonbonded pdb=" OG SER F 28 " pdb=" OG SER F 31 " model vdw 2.238 3.040 nonbonded pdb=" OG SER M 7 " pdb=" OG1 THR M 21 " model vdw 2.239 3.040 ... (remaining 350234 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 group one per residue 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.050 Extract box with map and model: 1.450 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 87.740 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.390 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 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 0.046 46326 Z= 0.220 Angle : 0.651 11.451 63126 Z= 0.336 Chirality : 0.048 0.580 7338 Planarity : 0.005 0.074 8061 Dihedral : 12.779 89.614 17400 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.66 % Allowed : 0.50 % Favored : 98.84 % 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: -1.31 (0.11), residues: 5763 helix: -0.22 (0.19), residues: 678 sheet: 0.25 (0.14), residues: 1569 loop : -1.61 (0.09), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 102 HIS 0.007 0.001 HIS B 146 PHE 0.037 0.001 PHE E 153 TYR 0.031 0.001 TYR B 904 ARG 0.009 0.001 ARG D 40 *********************** 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 313 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 280 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 267 VAL cc_start: 0.8770 (t) cc_final: 0.8430 (t) REVERT: C 535 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7938 (mtpp) REVERT: C 539 VAL cc_start: 0.7321 (t) cc_final: 0.6895 (t) REVERT: C 900 MET cc_start: 0.9154 (tpp) cc_final: 0.8904 (tpp) REVERT: A 774 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8281 (mm-40) REVERT: A 1051 SER cc_start: 0.9086 (m) cc_final: 0.8726 (p) REVERT: B 177 MET cc_start: -0.2792 (pmm) cc_final: -0.3088 (mmt) REVERT: B 592 PHE cc_start: 0.4717 (m-80) cc_final: 0.4383 (m-80) REVERT: B 1033 VAL cc_start: 0.9236 (t) cc_final: 0.8963 (t) REVERT: B 1051 SER cc_start: 0.9137 (m) cc_final: 0.8870 (p) REVERT: N 34 ILE cc_start: 0.5682 (mm) cc_final: 0.5450 (mm) REVERT: F 188 TYR cc_start: -0.0500 (m-80) cc_final: -0.0984 (m-80) outliers start: 33 outliers final: 13 residues processed: 311 average time/residue: 0.4623 time to fit residues: 240.2795 Evaluate side-chains 187 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 20.0000 chunk 436 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 451 optimal weight: 2.9990 chunk 174 optimal weight: 0.1980 chunk 274 optimal weight: 1.9990 chunk 336 optimal weight: 30.0000 chunk 523 optimal weight: 7.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 321 GLN C 439 ASN C 506 GLN C 580 GLN C 901 GLN C 913 GLN C 955 ASN C 957 GLN C1005 GLN C1023 ASN I 91 GLN D 35 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 146 HIS B 271 GLN B 388 ASN B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1083 HIS ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.129307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.106530 restraints weight = 259843.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.103865 restraints weight = 344721.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.100470 restraints weight = 273527.239| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 46326 Z= 0.341 Angle : 0.660 9.814 63126 Z= 0.337 Chirality : 0.046 0.499 7338 Planarity : 0.005 0.095 8061 Dihedral : 5.285 55.621 7416 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.94 % 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: -0.93 (0.11), residues: 5763 helix: 0.78 (0.20), residues: 698 sheet: 0.18 (0.12), residues: 1747 loop : -1.42 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 37 HIS 0.007 0.001 HIS C1088 PHE 0.036 0.002 PHE B 342 TYR 0.034 0.002 TYR K 50 ARG 0.007 0.001 ARG E 99 *********************** 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 236 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.2080 (mtp) cc_final: 0.0192 (ttm) REVERT: C 745 ASP cc_start: 0.8133 (m-30) cc_final: 0.7801 (p0) REVERT: I 85 GLU cc_start: 0.6650 (mp0) cc_final: 0.6426 (mp0) REVERT: D 173 THR cc_start: 0.3954 (p) cc_final: 0.3575 (p) REVERT: E 153 PHE cc_start: 0.4871 (t80) cc_final: 0.4589 (t80) REVERT: A 1029 MET cc_start: 0.8945 (tpp) cc_final: 0.8470 (tpt) REVERT: A 1034 LEU cc_start: 0.9287 (mt) cc_final: 0.9001 (mm) REVERT: B 177 MET cc_start: -0.2172 (pmm) cc_final: -0.3598 (mtt) REVERT: B 270 LEU cc_start: 0.8548 (mt) cc_final: 0.8339 (mp) REVERT: B 739 THR cc_start: 0.7949 (m) cc_final: 0.7625 (m) REVERT: H 195 VAL cc_start: 0.3326 (m) cc_final: 0.2978 (p) REVERT: F 188 TYR cc_start: -0.0602 (m-80) cc_final: -0.1117 (m-80) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.4722 time to fit residues: 186.2896 Evaluate side-chains 146 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 5 optimal weight: 8.9990 chunk 482 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 468 optimal weight: 5.9990 chunk 388 optimal weight: 0.0030 chunk 322 optimal weight: 2.9990 chunk 383 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 379 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 460 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 196 ASN B 422 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.130869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.108880 restraints weight = 258892.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.104307 restraints weight = 331539.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.101022 restraints weight = 249770.458| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 46326 Z= 0.149 Angle : 0.515 8.324 63126 Z= 0.262 Chirality : 0.044 0.464 7338 Planarity : 0.004 0.046 8061 Dihedral : 4.734 54.843 7416 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.40 % 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: -0.78 (0.11), residues: 5763 helix: 0.97 (0.21), residues: 725 sheet: 0.24 (0.13), residues: 1693 loop : -1.31 (0.10), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.013 0.001 HIS I 36 PHE 0.023 0.001 PHE C 275 TYR 0.024 0.001 TYR K 50 ARG 0.010 0.000 ARG C 237 *********************** 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 248 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.2260 (mtp) cc_final: 0.0384 (ttm) REVERT: C 189 LEU cc_start: 0.7733 (tp) cc_final: 0.7485 (pp) REVERT: D 101 PHE cc_start: 0.5141 (m-80) cc_final: 0.4395 (m-80) REVERT: D 173 THR cc_start: 0.3945 (p) cc_final: 0.3571 (p) REVERT: E 153 PHE cc_start: 0.4904 (t80) cc_final: 0.4472 (t80) REVERT: A 211 ASN cc_start: 0.7610 (m-40) cc_final: 0.7253 (p0) REVERT: A 697 MET cc_start: 0.8687 (mtm) cc_final: 0.8327 (mtt) REVERT: A 774 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8741 (mm-40) REVERT: A 1034 LEU cc_start: 0.9190 (mt) cc_final: 0.8984 (mm) REVERT: B 117 LEU cc_start: 0.8864 (tp) cc_final: 0.8210 (tp) REVERT: B 153 MET cc_start: 0.5641 (mpp) cc_final: 0.5348 (mpp) REVERT: B 177 MET cc_start: -0.1798 (pmm) cc_final: -0.3534 (mtt) REVERT: B 515 PHE cc_start: 0.5941 (m-80) cc_final: 0.5719 (m-80) REVERT: B 1051 SER cc_start: 0.8961 (m) cc_final: 0.8592 (p) REVERT: O 199 GLN cc_start: 0.3125 (mm-40) cc_final: 0.2893 (mm-40) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.4507 time to fit residues: 193.0605 Evaluate side-chains 151 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 82 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 510 optimal weight: 0.6980 chunk 495 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 492 optimal weight: 30.0000 chunk 304 optimal weight: 5.9990 chunk 473 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 155 optimal weight: 0.0040 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 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 = 0.4498 r_free = 0.4498 target = 0.129915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.107269 restraints weight = 258599.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.105598 restraints weight = 340098.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.103557 restraints weight = 269676.091| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46326 Z= 0.174 Angle : 0.520 17.389 63126 Z= 0.261 Chirality : 0.044 0.501 7338 Planarity : 0.004 0.058 8061 Dihedral : 4.332 54.670 7416 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: -0.63 (0.11), residues: 5763 helix: 1.12 (0.21), residues: 719 sheet: 0.40 (0.13), residues: 1716 loop : -1.26 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP J 102 HIS 0.004 0.001 HIS O 202 PHE 0.017 0.001 PHE M 153 TYR 0.015 0.001 TYR I 51 ARG 0.011 0.000 ARG D 40 *********************** 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 229 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.2458 (mtp) cc_final: 0.0570 (ttm) REVERT: C 189 LEU cc_start: 0.8111 (tp) cc_final: 0.7619 (pp) REVERT: C 745 ASP cc_start: 0.8426 (m-30) cc_final: 0.7915 (p0) REVERT: C 869 MET cc_start: 0.8874 (ptp) cc_final: 0.8654 (ptp) REVERT: D 173 THR cc_start: 0.3849 (p) cc_final: 0.3454 (p) REVERT: E 153 PHE cc_start: 0.5230 (t80) cc_final: 0.4728 (t80) REVERT: A 211 ASN cc_start: 0.7726 (m-40) cc_final: 0.7265 (p0) REVERT: A 697 MET cc_start: 0.8831 (mtm) cc_final: 0.8289 (mtt) REVERT: A 736 VAL cc_start: 0.8910 (t) cc_final: 0.8688 (t) REVERT: A 1034 LEU cc_start: 0.9428 (mt) cc_final: 0.9131 (mm) REVERT: B 117 LEU cc_start: 0.8967 (tp) cc_final: 0.8004 (tp) REVERT: B 153 MET cc_start: 0.5828 (mpp) cc_final: 0.5497 (mpp) REVERT: B 177 MET cc_start: -0.1745 (pmm) cc_final: -0.3291 (mtt) REVERT: H 89 GLU cc_start: 0.4515 (pm20) cc_final: 0.3875 (tp30) REVERT: H 195 VAL cc_start: 0.2773 (m) cc_final: 0.2518 (p) REVERT: F 1 ASN cc_start: 0.4480 (p0) cc_final: 0.4246 (p0) REVERT: F 95 ASP cc_start: 0.6086 (t0) cc_final: 0.5849 (t70) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.4352 time to fit residues: 173.0743 Evaluate side-chains 146 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 40.0000 chunk 149 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 475 optimal weight: 30.0000 chunk 378 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 480 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 207 HIS ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 955 ASN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.103766 restraints weight = 257616.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.100789 restraints weight = 362832.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.097963 restraints weight = 273062.261| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 46326 Z= 0.315 Angle : 0.622 28.191 63126 Z= 0.311 Chirality : 0.045 0.454 7338 Planarity : 0.005 0.072 8061 Dihedral : 4.780 57.285 7416 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 1.07 (0.20), residues: 704 sheet: 0.29 (0.12), residues: 1756 loop : -1.26 (0.10), residues: 3303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 102 HIS 0.007 0.001 HIS B1048 PHE 0.017 0.002 PHE A 906 TYR 0.041 0.002 TYR K 50 ARG 0.008 0.001 ARG M 99 *********************** 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 219 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.3413 (mtp) cc_final: 0.1758 (ttm) REVERT: C 731 MET cc_start: 0.8405 (ptm) cc_final: 0.8165 (ptm) REVERT: C 745 ASP cc_start: 0.8485 (m-30) cc_final: 0.8171 (p0) REVERT: C 869 MET cc_start: 0.8901 (ptp) cc_final: 0.8688 (ptp) REVERT: E 152 TYR cc_start: 0.3239 (p90) cc_final: 0.2692 (p90) REVERT: E 153 PHE cc_start: 0.5131 (t80) cc_final: 0.4594 (t80) REVERT: E 155 GLU cc_start: 0.4529 (mm-30) cc_final: 0.3692 (tp30) REVERT: A 145 TYR cc_start: 0.6125 (t80) cc_final: 0.5887 (t80) REVERT: A 697 MET cc_start: 0.9068 (mtm) cc_final: 0.8782 (mtt) REVERT: A 1029 MET cc_start: 0.9047 (tpp) cc_final: 0.8646 (tpp) REVERT: A 1034 LEU cc_start: 0.9497 (mt) cc_final: 0.9196 (mm) REVERT: B 117 LEU cc_start: 0.8959 (tp) cc_final: 0.8382 (tp) REVERT: B 153 MET cc_start: 0.6200 (mpp) cc_final: 0.5802 (mpp) REVERT: B 177 MET cc_start: -0.1869 (pmm) cc_final: -0.2761 (mmt) REVERT: B 515 PHE cc_start: 0.5783 (m-80) cc_final: 0.5438 (m-80) REVERT: O 199 GLN cc_start: 0.2128 (mm-40) cc_final: 0.1624 (mm-40) REVERT: J 183 TYR cc_start: 0.4121 (m-10) cc_final: 0.3913 (m-10) REVERT: M 34 TYR cc_start: 0.7671 (m-80) cc_final: 0.7427 (m-80) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.4476 time to fit residues: 171.0264 Evaluate side-chains 141 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 511 optimal weight: 2.9990 chunk 446 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 277 optimal weight: 0.8980 chunk 494 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 435 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 440 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN C 388 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1108 ASN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 HIS ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 913 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1106 GLN L 39 GLN L 175 ASN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.127528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.104394 restraints weight = 255885.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.101166 restraints weight = 319218.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.097329 restraints weight = 232673.886| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 46326 Z= 0.204 Angle : 0.544 26.027 63126 Z= 0.270 Chirality : 0.044 0.484 7338 Planarity : 0.004 0.054 8061 Dihedral : 4.501 55.676 7416 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -0.62 (0.11), residues: 5763 helix: 1.29 (0.21), residues: 695 sheet: 0.33 (0.12), residues: 1742 loop : -1.24 (0.10), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP O 153 HIS 0.010 0.001 HIS C 49 PHE 0.019 0.001 PHE C 275 TYR 0.028 0.001 TYR K 50 ARG 0.011 0.000 ARG D 40 *********************** 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 216 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.3160 (mtp) cc_final: 0.1604 (ttm) REVERT: C 329 PHE cc_start: 0.5246 (t80) cc_final: 0.4704 (t80) REVERT: E 152 TYR cc_start: 0.3017 (p90) cc_final: 0.2638 (p90) REVERT: E 153 PHE cc_start: 0.5159 (t80) cc_final: 0.4580 (t80) REVERT: E 155 GLU cc_start: 0.4831 (mm-30) cc_final: 0.3946 (tp30) REVERT: A 145 TYR cc_start: 0.6123 (t80) cc_final: 0.5849 (t80) REVERT: A 434 ILE cc_start: 0.8206 (mm) cc_final: 0.7795 (mm) REVERT: A 528 LYS cc_start: 0.7554 (tptp) cc_final: 0.7089 (pttt) REVERT: A 697 MET cc_start: 0.8826 (mtm) cc_final: 0.8567 (mtm) REVERT: A 1034 LEU cc_start: 0.9406 (mt) cc_final: 0.9038 (mm) REVERT: B 117 LEU cc_start: 0.8888 (tp) cc_final: 0.8409 (tp) REVERT: B 177 MET cc_start: -0.1754 (pmm) cc_final: -0.3012 (mtt) REVERT: B 515 PHE cc_start: 0.5882 (m-80) cc_final: 0.5597 (m-80) REVERT: H 89 GLU cc_start: 0.4831 (pm20) cc_final: 0.3984 (tp30) REVERT: L 3 VAL cc_start: 0.2437 (p) cc_final: 0.1906 (m) REVERT: O 199 GLN cc_start: 0.3013 (mm-40) cc_final: 0.2698 (mm-40) REVERT: J 183 TYR cc_start: 0.3979 (m-10) cc_final: 0.3738 (m-10) REVERT: M 34 TYR cc_start: 0.7361 (m-80) cc_final: 0.7130 (m-80) REVERT: M 173 PHE cc_start: 0.1386 (m-80) cc_final: 0.1179 (m-80) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.4400 time to fit residues: 165.1766 Evaluate side-chains 142 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 190 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 380 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 126 optimal weight: 2.9990 chunk 555 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 294 optimal weight: 0.7980 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 955 ASN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 907 ASN A 913 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.127283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093525 restraints weight = 256129.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090688 restraints weight = 178172.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.090817 restraints weight = 157939.724| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 46326 Z= 0.156 Angle : 0.522 23.880 63126 Z= 0.258 Chirality : 0.044 0.478 7338 Planarity : 0.004 0.053 8061 Dihedral : 4.273 54.708 7416 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 0.04 % Allowed : 1.22 % Favored : 98.74 % 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: -0.53 (0.11), residues: 5763 helix: 1.36 (0.21), residues: 702 sheet: 0.38 (0.12), residues: 1750 loop : -1.18 (0.11), residues: 3311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 153 HIS 0.006 0.001 HIS C 49 PHE 0.020 0.001 PHE C 275 TYR 0.022 0.001 TYR K 50 ARG 0.005 0.000 ARG D 40 *********************** 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 219 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4266 (mtp) cc_final: 0.2648 (ttm) REVERT: C 456 PHE cc_start: 0.7978 (m-80) cc_final: 0.7772 (m-80) REVERT: E 152 TYR cc_start: 0.3523 (p90) cc_final: 0.3262 (p90) REVERT: E 153 PHE cc_start: 0.4569 (t80) cc_final: 0.4233 (t80) REVERT: A 55 PHE cc_start: 0.8970 (m-80) cc_final: 0.8742 (m-80) REVERT: A 145 TYR cc_start: 0.6529 (t80) cc_final: 0.6011 (t80) REVERT: A 528 LYS cc_start: 0.8543 (tptp) cc_final: 0.7969 (ttpt) REVERT: A 529 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7621 (mmpt) REVERT: A 697 MET cc_start: 0.9120 (mtm) cc_final: 0.8779 (mtm) REVERT: A 1029 MET cc_start: 0.8849 (tpp) cc_final: 0.8611 (tpt) REVERT: B 117 LEU cc_start: 0.9409 (tp) cc_final: 0.8989 (tp) REVERT: B 153 MET cc_start: 0.7180 (mtm) cc_final: 0.6110 (mpp) REVERT: B 177 MET cc_start: -0.0766 (pmm) cc_final: -0.2533 (mtt) REVERT: B 329 PHE cc_start: 0.7880 (m-80) cc_final: 0.7457 (m-80) REVERT: B 515 PHE cc_start: 0.6154 (m-80) cc_final: 0.5871 (m-80) REVERT: H 89 GLU cc_start: 0.4865 (pm20) cc_final: 0.4195 (tp30) REVERT: L 3 VAL cc_start: 0.3958 (p) cc_final: 0.3557 (m) REVERT: L 189 GLN cc_start: -0.0502 (OUTLIER) cc_final: -0.1041 (tp40) REVERT: O 199 GLN cc_start: 0.3249 (mm-40) cc_final: 0.1653 (pt0) REVERT: J 183 TYR cc_start: 0.4013 (m-10) cc_final: 0.3809 (m-10) REVERT: M 173 PHE cc_start: 0.2080 (m-80) cc_final: 0.1679 (m-80) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.4312 time to fit residues: 163.8901 Evaluate side-chains 142 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 409 optimal weight: 9.9990 chunk 364 optimal weight: 0.9990 chunk 427 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 382 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 284 optimal weight: 3.9990 chunk 169 optimal weight: 40.0000 chunk 482 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 189 GLN ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4443 r_free = 0.4443 target = 0.125671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.092659 restraints weight = 254440.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.089004 restraints weight = 181808.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.089385 restraints weight = 162251.455| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4100 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= 0.235 Angle : 0.567 23.442 63126 Z= 0.283 Chirality : 0.044 0.343 7338 Planarity : 0.004 0.053 8061 Dihedral : 4.552 54.499 7416 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 0.02 % Allowed : 1.08 % Favored : 98.90 % 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: -0.59 (0.11), residues: 5763 helix: 1.25 (0.21), residues: 700 sheet: 0.34 (0.12), residues: 1755 loop : -1.20 (0.11), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 153 HIS 0.007 0.001 HIS C 49 PHE 0.022 0.001 PHE A 906 TYR 0.016 0.001 TYR K 50 ARG 0.008 0.001 ARG M 104 *********************** 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 208 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 3.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4339 (mtp) cc_final: 0.2807 (ttm) REVERT: C 276 LEU cc_start: 0.8729 (tt) cc_final: 0.8417 (mp) REVERT: C 858 LEU cc_start: 0.9097 (mm) cc_final: 0.8845 (mp) REVERT: D 40 ARG cc_start: 0.5556 (mmp-170) cc_final: 0.5118 (tpp-160) REVERT: E 5 GLN cc_start: 0.8417 (pm20) cc_final: 0.8176 (pm20) REVERT: E 152 TYR cc_start: 0.3551 (p90) cc_final: 0.2680 (p90) REVERT: E 153 PHE cc_start: 0.4791 (t80) cc_final: 0.4193 (t80) REVERT: E 155 GLU cc_start: 0.4723 (mm-30) cc_final: 0.4273 (tp30) REVERT: A 145 TYR cc_start: 0.6470 (t80) cc_final: 0.5796 (t80) REVERT: A 434 ILE cc_start: 0.8852 (mm) cc_final: 0.8504 (mm) REVERT: A 697 MET cc_start: 0.9038 (mtm) cc_final: 0.8785 (mtt) REVERT: A 1051 SER cc_start: 0.9259 (m) cc_final: 0.8736 (p) REVERT: B 117 LEU cc_start: 0.9273 (tp) cc_final: 0.8780 (tp) REVERT: B 140 PHE cc_start: 0.7995 (p90) cc_final: 0.7599 (p90) REVERT: B 177 MET cc_start: -0.1081 (pmm) cc_final: -0.2533 (ptt) REVERT: B 329 PHE cc_start: 0.7787 (m-80) cc_final: 0.7311 (m-10) REVERT: B 515 PHE cc_start: 0.6298 (m-80) cc_final: 0.6018 (m-80) REVERT: L 134 LYS cc_start: -0.1986 (pttt) cc_final: -0.2804 (mttp) REVERT: L 189 GLN cc_start: -0.0337 (OUTLIER) cc_final: -0.0952 (tp40) REVERT: N 81 MET cc_start: -0.6692 (ptm) cc_final: -0.7054 (ppp) REVERT: O 199 GLN cc_start: 0.3340 (mm-40) cc_final: 0.3033 (mm-40) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.4508 time to fit residues: 161.8807 Evaluate side-chains 137 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 188 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 220 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 530 optimal weight: 10.0000 chunk 428 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 553 optimal weight: 9.9990 chunk 470 optimal weight: 0.0870 chunk 364 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 overall best weight: 2.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 = 0.4441 r_free = 0.4441 target = 0.125544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.090299 restraints weight = 254473.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.088319 restraints weight = 168960.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.088148 restraints weight = 158883.706| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46326 Z= 0.225 Angle : 0.567 22.187 63126 Z= 0.280 Chirality : 0.044 0.411 7338 Planarity : 0.004 0.058 8061 Dihedral : 4.561 54.411 7416 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.56 (0.11), residues: 5763 helix: 1.35 (0.21), residues: 695 sheet: 0.35 (0.12), residues: 1739 loop : -1.19 (0.11), residues: 3329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.008 0.001 HIS N 211 PHE 0.019 0.001 PHE C 275 TYR 0.021 0.001 TYR E 34 ARG 0.007 0.001 ARG B1107 *********************** 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 202 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4540 (mtp) cc_final: 0.3307 (ttm) REVERT: C 276 LEU cc_start: 0.8739 (tt) cc_final: 0.8428 (mp) REVERT: C 858 LEU cc_start: 0.9115 (mm) cc_final: 0.8875 (mp) REVERT: D 40 ARG cc_start: 0.5857 (mmp-170) cc_final: 0.5394 (tpp-160) REVERT: E 152 TYR cc_start: 0.3580 (p90) cc_final: 0.3281 (p90) REVERT: E 153 PHE cc_start: 0.4538 (t80) cc_final: 0.4052 (t80) REVERT: A 434 ILE cc_start: 0.9075 (mm) cc_final: 0.8861 (mm) REVERT: A 697 MET cc_start: 0.9043 (mtm) cc_final: 0.8733 (mtm) REVERT: B 117 LEU cc_start: 0.9412 (tp) cc_final: 0.9126 (tp) REVERT: B 140 PHE cc_start: 0.8299 (p90) cc_final: 0.7726 (p90) REVERT: B 177 MET cc_start: -0.0491 (pmm) cc_final: -0.0716 (ptt) REVERT: B 329 PHE cc_start: 0.7831 (m-80) cc_final: 0.7232 (m-10) REVERT: B 515 PHE cc_start: 0.6342 (m-80) cc_final: 0.6095 (m-80) REVERT: L 134 LYS cc_start: -0.2117 (pttt) cc_final: -0.2898 (mttp) REVERT: O 199 GLN cc_start: 0.3783 (mm-40) cc_final: 0.3481 (mm-40) REVERT: M 101 LEU cc_start: 0.8261 (tt) cc_final: 0.8052 (tt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4603 time to fit residues: 159.9462 Evaluate side-chains 136 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 386 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 376 optimal weight: 0.0030 chunk 539 optimal weight: 30.0000 chunk 475 optimal weight: 20.0000 chunk 533 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 296 optimal weight: 0.7980 chunk 518 optimal weight: 10.0000 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 901 GLN L 39 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 GLN ** J 206 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.126011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.090926 restraints weight = 254430.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.089024 restraints weight = 170057.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.088839 restraints weight = 149539.636| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 46326 Z= 0.170 Angle : 0.540 21.363 63126 Z= 0.265 Chirality : 0.044 0.438 7338 Planarity : 0.004 0.056 8061 Dihedral : 4.399 54.119 7416 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 0.02 % Allowed : 0.32 % Favored : 99.66 % 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: -0.49 (0.11), residues: 5763 helix: 1.45 (0.21), residues: 695 sheet: 0.42 (0.13), residues: 1728 loop : -1.16 (0.11), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 436 HIS 0.006 0.001 HIS N 211 PHE 0.021 0.001 PHE A 329 TYR 0.019 0.001 TYR C 904 ARG 0.006 0.000 ARG A 328 ********************** 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 196 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 4.030 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: C 177 MET cc_start: 0.3966 (mtp) cc_final: 0.2520 (ttm) REVERT: C 456 PHE cc_start: 0.8003 (m-80) cc_final: 0.7774 (m-80) REVERT: D 40 ARG cc_start: 0.5861 (mmp-170) cc_final: 0.5577 (tpp-160) REVERT: E 152 TYR cc_start: 0.3509 (p90) cc_final: 0.3240 (p90) REVERT: E 153 PHE cc_start: 0.4775 (t80) cc_final: 0.4381 (t80) REVERT: A 145 TYR cc_start: 0.6897 (t80) cc_final: 0.6675 (t80) REVERT: A 153 MET cc_start: 0.6438 (tpp) cc_final: 0.6114 (tmm) REVERT: A 434 ILE cc_start: 0.9020 (mm) cc_final: 0.8807 (mm) REVERT: A 697 MET cc_start: 0.9051 (mtm) cc_final: 0.8728 (mtm) REVERT: A 902 MET cc_start: 0.9473 (mmp) cc_final: 0.9208 (mmp) REVERT: B 117 LEU cc_start: 0.9420 (tp) cc_final: 0.9144 (tp) REVERT: B 177 MET cc_start: -0.0679 (pmm) cc_final: -0.0911 (ptt) REVERT: B 329 PHE cc_start: 0.7839 (m-80) cc_final: 0.7220 (m-10) REVERT: H 116 ARG cc_start: 0.7450 (tmt170) cc_final: 0.7121 (ptm-80) REVERT: O 16 GLN cc_start: -0.2144 (OUTLIER) cc_final: -0.2478 (pp30) REVERT: O 199 GLN cc_start: 0.3701 (mm-40) cc_final: 0.3399 (mm-40) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.4486 time to fit residues: 152.5527 Evaluate side-chains 135 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 42 optimal weight: 8.9990 chunk 530 optimal weight: 0.9990 chunk 551 optimal weight: 40.0000 chunk 441 optimal weight: 40.0000 chunk 223 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 556 optimal weight: 4.9990 chunk 123 optimal weight: 0.0270 chunk 32 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN G 211 HIS ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 913 GLN A 992 GLN B 69 HIS B 474 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN J 162 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.124253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089711 restraints weight = 254569.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.086779 restraints weight = 187185.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.087128 restraints weight = 157591.179| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 46326 Z= 0.269 Angle : 0.597 21.228 63126 Z= 0.297 Chirality : 0.045 0.438 7338 Planarity : 0.004 0.055 8061 Dihedral : 4.718 54.826 7416 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.59 (0.11), residues: 5763 helix: 1.21 (0.20), residues: 700 sheet: 0.33 (0.12), residues: 1745 loop : -1.18 (0.11), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.006 0.001 HIS N 211 PHE 0.020 0.002 PHE C 855 TYR 0.021 0.001 TYR C 741 ARG 0.005 0.001 ARG C1000 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11953.27 seconds wall clock time: 209 minutes 33.23 seconds (12573.23 seconds total)