Starting phenix.real_space_refine on Sun Dec 29 00:08:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yeg_33772/12_2024/7yeg_33772.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yeg_33772/12_2024/7yeg_33772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yeg_33772/12_2024/7yeg_33772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yeg_33772/12_2024/7yeg_33772.map" model { file = "/net/cci-nas-00/data/ceres_data/7yeg_33772/12_2024/7yeg_33772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yeg_33772/12_2024/7yeg_33772.cif" } resolution = 3.73 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= 0.000 sd= 0.005 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 4497 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 240 5.16 5 C 31752 2.51 5 N 8259 2.21 5 O 9720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 403 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 49974 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "E" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4865 Classifications: {'peptide': 596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 1690 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: "J" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4865 Classifications: {'peptide': 596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "M" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4865 Classifications: {'peptide': 596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "N" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 1690 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 22.77, per 1000 atoms: 0.46 Number of scatterers: 49974 At special positions: 0 Unit cell: (240.768, 228.096, 216.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 240 16.00 O 9720 8.00 N 8259 7.00 C 31752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=66, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 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=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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 E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS G 151 " - pdb=" SG ACYS G 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS G 151 " - pdb=" SG BCYS 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 J 133 " - pdb=" SG CYS J 141 " distance=2.04 Simple disulfide: pdb=" SG CYS J 344 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 530 " - pdb=" SG CYS J 542 " distance=2.04 Simple disulfide: pdb=" SG CYS M 133 " - pdb=" SG CYS M 141 " distance=2.04 Simple disulfide: pdb=" SG CYS M 344 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 530 " - pdb=" SG CYS M 542 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS N 151 " - pdb=" SG ACYS N 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS N 151 " - pdb=" SG BCYS 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 902 " - " ASN E 53 " " NAG E 903 " - " ASN E 90 " " NAG E 904 " - " ASN E 322 " " NAG E 905 " - " ASN E 546 " " NAG F 1 " - " ASN A 801 " " NAG J 902 " - " ASN J 53 " " NAG J 903 " - " ASN J 90 " " NAG J 904 " - " ASN J 322 " " NAG J 905 " - " ASN J 546 " " NAG K 1 " - " ASN B 717 " " NAG M 902 " - " ASN M 53 " " NAG M 903 " - " ASN M 90 " " NAG M 904 " - " ASN M 322 " " NAG M 905 " - " ASN M 546 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 8.94 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 378 " pdb=" ZN J 901 " pdb="ZN ZN J 901 " - pdb=" NE2 HIS J 374 " pdb="ZN ZN J 901 " - pdb=" NE2 HIS J 378 " pdb=" ZN M 901 " pdb="ZN ZN M 901 " - pdb=" NE2 HIS M 374 " pdb="ZN ZN M 901 " - pdb=" NE2 HIS M 378 " 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11772 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 94 sheets defined 26.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.551A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.928A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.528A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.625A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.671A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 777 removed outlier: 3.545A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 3.592A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.647A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.238A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 857 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.555A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.828A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.181A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.579A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.544A pdb=" N GLU A1144 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.527A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.758A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.576A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.702A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 777 removed outlier: 3.572A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.583A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.653A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 removed outlier: 4.191A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 857 " --> pdb=" O LYS B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.533A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 949 through 966 removed outlier: 3.812A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.175A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1032 removed outlier: 3.651A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.549A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.600A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.681A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 777 removed outlier: 3.586A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.630A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.647A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 removed outlier: 4.193A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 857 " --> pdb=" O LYS C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.558A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 949 through 966 removed outlier: 3.816A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.164A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.671A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.616A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 52 " --> pdb=" O TRP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 81 removed outlier: 3.695A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.829A pdb=" N LYS E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.576A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 127 removed outlier: 3.764A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 3.970A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 152' Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.699A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 removed outlier: 4.377A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.858A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.839A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 252 removed outlier: 3.787A pdb=" N VAL E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.618A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.784A pdb=" N LEU E 278 " --> pdb=" O TRP E 275 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 275 through 280' Processing helix chain 'E' and resid 293 through 298 removed outlier: 3.665A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.578A pdb=" N SER E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 383 removed outlier: 4.102A pdb=" N LEU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.579A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.779A pdb=" N LEU E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN E 442 " --> pdb=" O PHE E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 464 removed outlier: 3.585A pdb=" N TYR E 454 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 464 " --> pdb=" O ARG E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 473 removed outlier: 4.023A pdb=" N TRP E 473 " --> pdb=" O LYS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 480 removed outlier: 3.732A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 529 removed outlier: 4.256A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 529 " --> pdb=" O PHE E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.580A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 542' Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.937A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 removed outlier: 3.565A pdb=" N LEU E 570 " --> pdb=" O TRP E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.923A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 removed outlier: 3.793A pdb=" N LYS E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 615 removed outlier: 3.517A pdb=" N ALA E 614 " --> pdb=" O SER E 611 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP E 615 " --> pdb=" O PRO E 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 611 through 615' 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 129 through 133 removed outlier: 3.817A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.050A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'I' and resid 129 through 133 removed outlier: 3.749A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.054A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 53 removed outlier: 3.660A pdb=" N THR J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE J 32 " --> pdb=" O PHE J 28 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP J 38 " --> pdb=" O HIS J 34 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 49 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN J 51 " --> pdb=" O SER J 47 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR J 52 " --> pdb=" O TRP J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 77 removed outlier: 3.648A pdb=" N LEU J 73 " --> pdb=" O TRP J 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS J 74 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.682A pdb=" N MET J 82 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 101 removed outlier: 3.721A pdb=" N LYS J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 129 removed outlier: 3.742A pdb=" N LYS J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN J 121 " --> pdb=" O ASN J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 152 Processing helix chain 'J' and resid 158 through 169 removed outlier: 3.917A pdb=" N ARG J 169 " --> pdb=" O TRP J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 194 removed outlier: 4.127A pdb=" N GLN J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) Proline residue: J 178 - end of helix removed outlier: 3.586A pdb=" N GLU J 182 " --> pdb=" O PRO J 178 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL J 185 " --> pdb=" O GLU J 181 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS J 187 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 205 removed outlier: 3.675A pdb=" N TYR J 202 " --> pdb=" O ASP J 198 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP J 203 " --> pdb=" O TYR J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 229 removed outlier: 3.572A pdb=" N VAL J 226 " --> pdb=" O LEU J 222 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU J 227 " --> pdb=" O ILE J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 248 Proline residue: J 235 - end of helix removed outlier: 3.506A pdb=" N LEU J 240 " --> pdb=" O LEU J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 279 removed outlier: 3.752A pdb=" N LEU J 278 " --> pdb=" O TRP J 275 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR J 279 " --> pdb=" O THR J 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 275 through 279' Processing helix chain 'J' and resid 293 through 297 Processing helix chain 'J' and resid 303 through 317 removed outlier: 3.805A pdb=" N SER J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 330 removed outlier: 3.563A pdb=" N GLU J 329 " --> pdb=" O GLN J 325 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN J 330 " --> pdb=" O GLY J 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 325 through 330' Processing helix chain 'J' and resid 366 through 371 removed outlier: 3.898A pdb=" N LEU J 370 " --> pdb=" O MET J 366 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR J 371 " --> pdb=" O ASP J 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 366 through 371' Processing helix chain 'J' and resid 371 through 385 removed outlier: 3.793A pdb=" N MET J 376 " --> pdb=" O ALA J 372 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA J 384 " --> pdb=" O GLN J 380 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR J 385 " --> pdb=" O TYR J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 413 removed outlier: 3.847A pdb=" N VAL J 404 " --> pdb=" O PHE J 400 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY J 405 " --> pdb=" O HIS J 401 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET J 408 " --> pdb=" O VAL J 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER J 409 " --> pdb=" O GLY J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 421 removed outlier: 3.594A pdb=" N SER J 420 " --> pdb=" O LYS J 416 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE J 421 " --> pdb=" O HIS J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 444 removed outlier: 3.517A pdb=" N LEU J 439 " --> pdb=" O GLU J 435 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN J 442 " --> pdb=" O PHE J 438 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 444 " --> pdb=" O LEU J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 464 removed outlier: 3.873A pdb=" N ARG J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL J 463 " --> pdb=" O TRP J 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE J 464 " --> pdb=" O ARG J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 484 removed outlier: 3.565A pdb=" N LYS J 476 " --> pdb=" O GLN J 472 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 479 " --> pdb=" O LYS J 475 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET J 480 " --> pdb=" O LYS J 476 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS J 481 " --> pdb=" O TRP J 477 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG J 482 " --> pdb=" O TRP J 478 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 528 removed outlier: 4.143A pdb=" N TYR J 516 " --> pdb=" O PHE J 512 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR J 517 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 520 " --> pdb=" O TYR J 516 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN J 522 " --> pdb=" O ARG J 518 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE J 523 " --> pdb=" O THR J 519 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN J 526 " --> pdb=" O GLN J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 542 removed outlier: 3.585A pdb=" N LYS J 541 " --> pdb=" O PRO J 538 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS J 542 " --> pdb=" O LEU J 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 538 through 542' Processing helix chain 'J' and resid 548 through 559 removed outlier: 3.516A pdb=" N GLN J 552 " --> pdb=" O THR J 548 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS J 553 " --> pdb=" O GLU J 549 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU J 554 " --> pdb=" O ALA J 550 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN J 556 " --> pdb=" O GLN J 552 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET J 557 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 558 " --> pdb=" O LEU J 554 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG J 559 " --> pdb=" O PHE J 555 " (cutoff:3.500A) Processing helix chain 'J' and resid 565 through 570 Processing helix chain 'J' and resid 570 through 575 removed outlier: 3.526A pdb=" N VAL J 574 " --> pdb=" O LEU J 570 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 588 Processing helix chain 'J' and resid 588 through 593 Processing helix chain 'J' and resid 611 through 615 removed outlier: 3.852A pdb=" N ASP J 615 " --> pdb=" O PRO J 612 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 53 removed outlier: 3.610A pdb=" N THR M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS M 31 " --> pdb=" O THR M 27 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE M 32 " --> pdb=" O PHE M 28 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP M 38 " --> pdb=" O HIS M 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN M 49 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN M 51 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR M 52 " --> pdb=" O TRP M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 78 removed outlier: 3.650A pdb=" N LEU M 73 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR M 78 " --> pdb=" O LYS M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.723A pdb=" N MET M 82 " --> pdb=" O LEU M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 101 removed outlier: 3.760A pdb=" N LYS M 94 " --> pdb=" O ASN M 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU M 95 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN M 96 " --> pdb=" O THR M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 129 removed outlier: 3.686A pdb=" N LYS M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG M 115 " --> pdb=" O ASP M 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN M 117 " --> pdb=" O SER M 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN M 121 " --> pdb=" O ASN M 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 152 Processing helix chain 'M' and resid 158 through 167 Processing helix chain 'M' and resid 175 through 194 removed outlier: 4.082A pdb=" N LEU M 179 " --> pdb=" O GLN M 175 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU M 182 " --> pdb=" O PRO M 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL M 185 " --> pdb=" O GLU M 181 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU M 186 " --> pdb=" O GLU M 182 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS M 187 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 193 " --> pdb=" O GLU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 205 removed outlier: 3.678A pdb=" N TYR M 202 " --> pdb=" O ASP M 198 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP M 203 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 229 removed outlier: 3.591A pdb=" N VAL M 226 " --> pdb=" O LEU M 222 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU M 227 " --> pdb=" O ILE M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix removed outlier: 3.541A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 279 removed outlier: 3.752A pdb=" N LEU M 278 " --> pdb=" O TRP M 275 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 279 " --> pdb=" O THR M 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 275 through 279' Processing helix chain 'M' and resid 293 through 297 Processing helix chain 'M' and resid 303 through 317 removed outlier: 3.805A pdb=" N SER M 317 " --> pdb=" O LYS M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 330 removed outlier: 3.563A pdb=" N GLU M 329 " --> pdb=" O GLN M 325 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN M 330 " --> pdb=" O GLY M 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 325 through 330' Processing helix chain 'M' and resid 366 through 371 removed outlier: 3.903A pdb=" N LEU M 370 " --> pdb=" O MET M 366 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 366 through 371' Processing helix chain 'M' and resid 371 through 385 removed outlier: 3.790A pdb=" N MET M 376 " --> pdb=" O ALA M 372 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 384 " --> pdb=" O GLN M 380 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR M 385 " --> pdb=" O TYR M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 413 removed outlier: 3.847A pdb=" N VAL M 404 " --> pdb=" O PHE M 400 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY M 405 " --> pdb=" O HIS M 401 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET M 408 " --> pdb=" O VAL M 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER M 409 " --> pdb=" O GLY M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 421 removed outlier: 3.593A pdb=" N SER M 420 " --> pdb=" O LYS M 416 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE M 421 " --> pdb=" O HIS M 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 444 removed outlier: 3.505A pdb=" N LEU M 439 " --> pdb=" O GLU M 435 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN M 442 " --> pdb=" O PHE M 438 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU M 444 " --> pdb=" O LEU M 440 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 464 removed outlier: 3.874A pdb=" N ARG M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET M 462 " --> pdb=" O LYS M 458 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 463 " --> pdb=" O TRP M 459 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE M 464 " --> pdb=" O ARG M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 484 removed outlier: 3.614A pdb=" N LYS M 476 " --> pdb=" O GLN M 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU M 479 " --> pdb=" O LYS M 475 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET M 480 " --> pdb=" O LYS M 476 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS M 481 " --> pdb=" O TRP M 477 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG M 482 " --> pdb=" O TRP M 478 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU M 483 " --> pdb=" O GLU M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 512 through 528 removed outlier: 4.143A pdb=" N TYR M 516 " --> pdb=" O PHE M 512 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR M 517 " --> pdb=" O ILE M 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU M 520 " --> pdb=" O TYR M 516 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN M 522 " --> pdb=" O ARG M 518 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N PHE M 523 " --> pdb=" O THR M 519 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN M 526 " --> pdb=" O GLN M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 538 through 542 removed outlier: 3.599A pdb=" N LYS M 541 " --> pdb=" O PRO M 538 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS M 542 " --> pdb=" O LEU M 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 538 through 542' Processing helix chain 'M' and resid 548 through 553 removed outlier: 3.504A pdb=" N GLN M 552 " --> pdb=" O THR M 548 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS M 553 " --> pdb=" O GLU M 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 548 through 553' Processing helix chain 'M' and resid 554 through 559 removed outlier: 3.564A pdb=" N LEU M 558 " --> pdb=" O LEU M 554 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG M 559 " --> pdb=" O PHE M 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 554 through 559' Processing helix chain 'M' and resid 565 through 570 Processing helix chain 'M' and resid 570 through 575 removed outlier: 3.521A pdb=" N VAL M 574 " --> pdb=" O LEU M 570 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 588 Processing helix chain 'M' and resid 588 through 593 Processing helix chain 'M' and resid 611 through 615 removed outlier: 3.851A pdb=" N ASP M 615 " --> pdb=" O PRO M 612 " (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 129 through 133 removed outlier: 3.517A pdb=" N ALA O 132 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN O 133 " --> pdb=" O LEU O 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 129 through 133' Processing helix chain 'O' and resid 186 through 191 removed outlier: 4.257A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.796A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.796A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.688A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.666A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.358A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.065A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.668A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.520A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.652A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.568A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.464A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.491A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 removed outlier: 3.709A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.591A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.709A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.531A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.359A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.168A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.698A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.826A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.673A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.720A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.115A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.660A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.097A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.775A pdb=" N ARG B 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY N 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.567A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.433A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.458A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.617A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.612A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.662A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 724 through 727 removed outlier: 3.513A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 735 removed outlier: 4.350A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.819A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.652A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE7, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.725A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 313 removed outlier: 4.100A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.547A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.756A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.589A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.426A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.603A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.733A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.733A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.454A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AG3, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.997A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'E' and resid 348 through 352 removed outlier: 6.198A pdb=" N ASP E 350 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ARG E 357 " --> pdb=" O ASP E 350 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY E 352 " --> pdb=" O ASP E 355 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.206A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.507A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.507A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.608A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.753A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN H 210 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 17 through 22 Processing sheet with id=AH2, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.879A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.879A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.717A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AH6, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.973A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.947A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.776A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA G 33 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 131 through 134 removed outlier: 3.664A pdb=" N LEU G 149 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS G 151 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL G 192 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS G 175 " --> pdb=" O VAL G 192 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.872A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AI3, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.877A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.877A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.810A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AI7, first strand: chain 'I' and resid 150 through 154 removed outlier: 4.033A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS I 198 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS I 209 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 131 through 132 removed outlier: 4.065A pdb=" N VAL J 132 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU J 142 " --> pdb=" O VAL J 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'J' and resid 347 through 350 removed outlier: 3.671A pdb=" N THR J 347 " --> pdb=" O LEU J 359 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU J 359 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP J 349 " --> pdb=" O ARG J 357 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 357 " --> pdb=" O TRP J 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'M' and resid 131 through 132 removed outlier: 3.907A pdb=" N VAL M 132 " --> pdb=" O LEU M 142 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU M 142 " --> pdb=" O VAL M 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'M' and resid 347 through 350 removed outlier: 3.577A pdb=" N THR M 347 " --> pdb=" O LEU M 359 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU M 359 " --> pdb=" O THR M 347 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP M 349 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG M 357 " --> pdb=" O TRP M 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'N' and resid 3 through 6 removed outlier: 4.398A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.364A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'N' and resid 98 through 99 removed outlier: 4.478A pdb=" N LEU N 113 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'N' and resid 131 through 134 removed outlier: 3.610A pdb=" N SER N 191 " --> pdb=" O CYS N 151 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL N 153 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU N 189 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP N 155 " --> pdb=" O TYR N 187 " (cutoff:3.500A) removed outlier: 7.944A 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: 3.735A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN N 210 " --> pdb=" O THR N 162 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.519A 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: 6.880A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.880A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR O 88 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 119 through 123 removed outlier: 3.707A pdb=" N PHE O 123 " --> pdb=" O VAL O 138 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA O 178 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER O 170 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 135 through 136 Processing sheet with id=AK4, first strand: chain 'O' and resid 150 through 154 removed outlier: 3.964A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR O 201 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) 1463 hydrogen bonds defined for protein. 3969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.93 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16025 1.34 - 1.46: 12459 1.46 - 1.58: 22378 1.58 - 1.70: 0 1.70 - 1.82: 339 Bond restraints: 51201 Sorted by residual: bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.329 1.362 -0.032 1.25e-02 6.40e+03 6.65e+00 bond pdb=" CA LYS B 528 " pdb=" C LYS B 528 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.28e-02 6.10e+03 6.22e+00 bond pdb=" C GLN I 113 " pdb=" O GLN I 113 " ideal model delta sigma weight residual 1.249 1.230 0.018 8.50e-03 1.38e+04 4.67e+00 bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.25e-02 6.40e+03 4.12e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 ... (remaining 51196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 67775 1.35 - 2.69: 1586 2.69 - 4.04: 270 4.04 - 5.38: 48 5.38 - 6.73: 17 Bond angle restraints: 69696 Sorted by residual: angle pdb=" O GLY B 526 " pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 121.77 128.50 -6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" N HIS M 378 " pdb=" CA HIS M 378 " pdb=" C HIS M 378 " ideal model delta sigma weight residual 111.07 106.12 4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" CA GLY B 526 " pdb=" C GLY B 526 " pdb=" O GLY B 526 " ideal model delta sigma weight residual 121.52 115.16 6.36 1.43e+00 4.89e-01 1.98e+01 angle pdb=" N HIS M 378 " pdb=" CA HIS M 378 " pdb=" CB HIS M 378 " ideal model delta sigma weight residual 110.01 115.99 -5.98 1.45e+00 4.76e-01 1.70e+01 angle pdb=" N LYS B 529 " pdb=" CA LYS B 529 " pdb=" C LYS B 529 " ideal model delta sigma weight residual 110.35 115.57 -5.22 1.36e+00 5.41e-01 1.47e+01 ... (remaining 69691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 28430 17.95 - 35.91: 2122 35.91 - 53.86: 432 53.86 - 71.81: 70 71.81 - 89.77: 59 Dihedral angle restraints: 31113 sinusoidal: 12765 harmonic: 18348 Sorted by residual: dihedral pdb=" CB CYS M 344 " pdb=" SG CYS M 344 " pdb=" SG CYS M 361 " pdb=" CB CYS M 361 " ideal model delta sinusoidal sigma weight residual -86.00 -169.51 83.51 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 10.17 82.83 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 174.21 -81.21 1 1.00e+01 1.00e-02 8.13e+01 ... (remaining 31110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 7836 0.131 - 0.263: 16 0.263 - 0.394: 4 0.394 - 0.526: 0 0.526 - 0.657: 1 Chirality restraints: 7857 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 7854 not shown) Planarity restraints: 9003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 376 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C MET M 376 " -0.054 2.00e-02 2.50e+03 pdb=" O MET M 376 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY M 377 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO C 987 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.038 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO A 987 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.032 5.00e-02 4.00e+02 ... (remaining 9000 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2706 2.73 - 3.27: 45850 3.27 - 3.82: 78178 3.82 - 4.36: 90843 4.36 - 4.90: 157152 Nonbonded interactions: 374729 Sorted by model distance: nonbonded pdb=" OD1 ASN A 331 " pdb=" N ILE A 332 " model vdw 2.191 3.120 nonbonded pdb=" OD1 ASN C 501 " pdb=" OH TYR J 41 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU M 402 " pdb="ZN ZN M 901 " model vdw 2.223 2.230 nonbonded pdb=" O GLU J 166 " pdb=" OG SER J 170 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.237 3.040 ... (remaining 374724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'M' } ncs_group { reference = (chain 'G' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) selection = (chain 'H' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) selection = (chain 'N' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 1.300 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: 0.060 Extract box with map and model: 1.440 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 96.540 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.280 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 51201 Z= 0.156 Angle : 0.484 6.728 69696 Z= 0.260 Chirality : 0.042 0.657 7857 Planarity : 0.004 0.057 8961 Dihedral : 13.187 89.766 19143 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 0.37 % Allowed : 2.60 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -4.62 (0.08), residues: 6258 helix: -4.70 (0.05), residues: 1464 sheet: -1.22 (0.15), residues: 1101 loop : -3.08 (0.08), residues: 3693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP J 473 HIS 0.008 0.000 HIS M 374 PHE 0.008 0.000 PHE M 603 TYR 0.007 0.000 TYR C 351 ARG 0.002 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 941 time to evaluate : 3.917 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: A 188 ASN cc_start: 0.5964 (m-40) cc_final: 0.5400 (m-40) REVERT: A 369 TYR cc_start: 0.4436 (t80) cc_final: 0.3344 (t80) REVERT: A 572 THR cc_start: 0.3595 (m) cc_final: 0.3049 (p) REVERT: A 734 THR cc_start: 0.8391 (p) cc_final: 0.7960 (t) REVERT: A 898 PHE cc_start: 0.6871 (t80) cc_final: 0.5479 (t80) REVERT: A 1073 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6557 (ttpp) REVERT: B 38 TYR cc_start: 0.7287 (m-80) cc_final: 0.6981 (m-80) REVERT: B 177 MET cc_start: -0.0426 (mmt) cc_final: -0.0911 (ttt) REVERT: B 188 ASN cc_start: 0.6338 (m-40) cc_final: 0.5756 (m110) REVERT: B 197 ILE cc_start: 0.7316 (pt) cc_final: 0.6988 (tt) REVERT: B 528 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6291 (mmmt) REVERT: B 572 THR cc_start: 0.4935 (m) cc_final: 0.4526 (p) REVERT: B 583 GLU cc_start: 0.7497 (tt0) cc_final: 0.7249 (pm20) REVERT: B 734 THR cc_start: 0.7853 (p) cc_final: 0.7600 (t) REVERT: B 748 GLU cc_start: 0.6046 (mp0) cc_final: 0.5803 (tp30) REVERT: B 859 THR cc_start: 0.5375 (p) cc_final: 0.4872 (t) REVERT: B 898 PHE cc_start: 0.6394 (t80) cc_final: 0.5599 (t80) REVERT: B 979 ASP cc_start: 0.7562 (t70) cc_final: 0.7221 (t0) REVERT: B 1101 HIS cc_start: 0.6816 (m90) cc_final: 0.6073 (m170) REVERT: B 1114 ILE cc_start: 0.7821 (mm) cc_final: 0.7564 (mm) REVERT: C 130 VAL cc_start: 0.6708 (t) cc_final: 0.6490 (m) REVERT: C 188 ASN cc_start: 0.6658 (m-40) cc_final: 0.6028 (m110) REVERT: C 197 ILE cc_start: 0.7609 (pt) cc_final: 0.7216 (tt) REVERT: C 572 THR cc_start: 0.4774 (m) cc_final: 0.4203 (p) REVERT: C 607 GLN cc_start: 0.7535 (pt0) cc_final: 0.7271 (pm20) REVERT: C 734 THR cc_start: 0.7892 (p) cc_final: 0.7597 (t) REVERT: C 950 ASP cc_start: 0.7819 (m-30) cc_final: 0.7585 (m-30) REVERT: C 969 ASN cc_start: 0.8176 (m-40) cc_final: 0.7957 (m110) REVERT: C 979 ASP cc_start: 0.7729 (t70) cc_final: 0.7197 (t0) REVERT: C 1101 HIS cc_start: 0.6257 (m90) cc_final: 0.5658 (m170) REVERT: C 1102 TRP cc_start: 0.4894 (m100) cc_final: 0.2142 (m100) REVERT: C 1122 VAL cc_start: 0.7851 (m) cc_final: 0.7638 (t) REVERT: E 26 LYS cc_start: 0.3123 (tptt) cc_final: 0.2918 (mmtt) REVERT: E 148 LEU cc_start: 0.2747 (mt) cc_final: 0.2415 (mm) REVERT: E 152 MET cc_start: 0.5066 (mmm) cc_final: 0.4316 (tpt) REVERT: E 241 HIS cc_start: 0.2573 (t-90) cc_final: 0.2157 (t-170) REVERT: E 293 VAL cc_start: 0.2097 (p) cc_final: 0.1212 (t) REVERT: E 302 TRP cc_start: 0.0208 (t60) cc_final: -0.0657 (t-100) REVERT: E 313 LYS cc_start: 0.1176 (mmmt) cc_final: 0.0949 (ptmm) REVERT: E 332 MET cc_start: 0.4425 (ttt) cc_final: 0.3308 (mtp) REVERT: E 346 PRO cc_start: 0.2649 (Cg_endo) cc_final: 0.2398 (Cg_exo) REVERT: E 366 MET cc_start: -0.0372 (mtm) cc_final: -0.0651 (tpt) REVERT: E 462 MET cc_start: 0.2480 (ptt) cc_final: 0.2153 (ptt) REVERT: E 474 MET cc_start: 0.0818 (tpp) cc_final: -0.0180 (mmp) REVERT: E 480 MET cc_start: 0.2590 (mtp) cc_final: 0.2266 (ptp) REVERT: E 518 ARG cc_start: 0.0704 (ptm160) cc_final: 0.0258 (tmt170) REVERT: E 522 GLN cc_start: 0.1046 (pt0) cc_final: 0.0343 (pp30) REVERT: E 579 MET cc_start: -0.0036 (pmm) cc_final: -0.0774 (mtm) REVERT: H 110 ASN cc_start: 0.2502 (p0) cc_final: 0.2281 (t0) REVERT: H 162 THR cc_start: 0.3947 (t) cc_final: 0.3709 (p) REVERT: L 64 PHE cc_start: -0.0146 (m-80) cc_final: -0.0955 (m-80) REVERT: G 111 PHE cc_start: 0.2482 (m-80) cc_final: 0.2274 (m-80) REVERT: G 175 HIS cc_start: 0.1273 (t-90) cc_final: 0.0744 (m-70) REVERT: J 73 LEU cc_start: 0.1365 (tt) cc_final: 0.1107 (mt) REVERT: J 75 GLU cc_start: 0.3325 (pt0) cc_final: 0.3093 (tm-30) REVERT: J 180 TYR cc_start: 0.0917 (t80) cc_final: 0.0615 (t80) REVERT: J 217 TYR cc_start: 0.2612 (t80) cc_final: 0.1571 (m-80) REVERT: J 225 ASP cc_start: 0.2948 (p0) cc_final: 0.2499 (p0) REVERT: J 241 HIS cc_start: 0.1375 (t-90) cc_final: 0.1071 (t-90) REVERT: J 270 MET cc_start: 0.0110 (tpp) cc_final: -0.1572 (tpp) REVERT: J 271 TRP cc_start: 0.1588 (m-90) cc_final: 0.0433 (t-100) REVERT: J 281 LEU cc_start: 0.3104 (tp) cc_final: 0.2768 (mp) REVERT: J 332 MET cc_start: 0.2069 (ttt) cc_final: 0.0552 (mtt) REVERT: J 356 PHE cc_start: 0.1333 (m-80) cc_final: -0.0136 (m-80) REVERT: J 374 HIS cc_start: -0.0928 (OUTLIER) cc_final: -0.1879 (t-170) REVERT: J 497 TYR cc_start: 0.3417 (m-80) cc_final: 0.3084 (m-80) REVERT: J 505 HIS cc_start: 0.1710 (m170) cc_final: 0.0791 (p-80) REVERT: J 515 TYR cc_start: 0.3138 (t80) cc_final: 0.2533 (t80) REVERT: M 26 LYS cc_start: 0.4510 (mtmm) cc_final: 0.4281 (mmpt) REVERT: M 42 GLN cc_start: 0.6722 (mt0) cc_final: 0.6209 (tp40) REVERT: M 145 GLU cc_start: 0.5324 (pp20) cc_final: 0.5102 (mm-30) REVERT: M 195 HIS cc_start: 0.5965 (t-170) cc_final: 0.5730 (m170) REVERT: M 217 TYR cc_start: 0.4061 (t80) cc_final: 0.2936 (m-80) REVERT: M 270 MET cc_start: 0.0025 (tpp) cc_final: -0.0949 (tpp) REVERT: M 271 TRP cc_start: 0.0946 (m-90) cc_final: 0.0527 (t-100) REVERT: M 297 MET cc_start: 0.0660 (mtt) cc_final: 0.0271 (ppp) REVERT: M 356 PHE cc_start: 0.1393 (m-80) cc_final: 0.0130 (m-80) REVERT: M 366 MET cc_start: -0.0817 (mtp) cc_final: -0.1292 (tpp) REVERT: M 482 ARG cc_start: 0.4140 (mtt180) cc_final: 0.3874 (ttm-80) REVERT: M 515 TYR cc_start: 0.2803 (t80) cc_final: 0.2033 (t80) REVERT: M 566 TRP cc_start: 0.2755 (p-90) cc_final: 0.2122 (p-90) REVERT: M 579 MET cc_start: 0.2391 (ptp) cc_final: 0.1511 (mtm) REVERT: N 4 LEU cc_start: 0.3343 (mp) cc_final: 0.2776 (mt) REVERT: N 81 MET cc_start: -0.0800 (ttt) cc_final: -0.1086 (ttt) REVERT: N 122 VAL cc_start: 0.0868 (p) cc_final: 0.0605 (m) REVERT: O 48 LEU cc_start: 0.5431 (tp) cc_final: 0.4892 (tp) REVERT: O 64 PHE cc_start: -0.0573 (m-80) cc_final: -0.1153 (m-10) outliers start: 18 outliers final: 5 residues processed: 954 average time/residue: 0.5035 time to fit residues: 788.7967 Evaluate side-chains 492 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 485 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain J residue 374 HIS Chi-restraints excluded: chain O residue 109 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 10.0000 chunk 472 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 489 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 364 optimal weight: 10.0000 chunk 566 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 165 ASN A 183 GLN A 196 ASN A 218 GLN A 271 GLN A 409 GLN A 474 GLN A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 703 ASN A 751 ASN A 762 GLN A 926 GLN A1101 HIS A1142 GLN B 66 HIS B 137 ASN B 165 ASN B 183 GLN B 196 ASN B 218 GLN B 271 GLN B 460 ASN B 498 GLN B 532 ASN B 580 GLN B 762 GLN B 901 GLN B 926 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 165 ASN C 183 GLN C 196 ASN C 218 GLN C 271 GLN C 314 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 493 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 580 GLN C 675 GLN C 762 GLN C 920 GLN C 926 GLN C1058 HIS C1142 GLN E 33 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 101 GLN E 134 ASN E 188 ASN E 325 GLN E 378 HIS E 397 ASN E 442 GLN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 HIS H 208 ASN H 210 ASN ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 208 ASN G 210 ASN I 55 ASN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 63 ASN J 188 ASN J 265 HIS J 432 ASN J 522 GLN J 599 ASN ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN M 63 ASN M 98 GLN M 101 GLN M 188 ASN ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 325 GLN M 505 HIS M 522 GLN M 556 ASN M 599 ASN ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 ASN N 208 ASN O 16 GLN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 51201 Z= 0.267 Angle : 0.616 11.740 69696 Z= 0.316 Chirality : 0.046 0.357 7857 Planarity : 0.005 0.082 8961 Dihedral : 5.329 59.379 7793 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.34 % Allowed : 10.73 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -3.27 (0.09), residues: 6258 helix: -2.43 (0.10), residues: 1581 sheet: -0.71 (0.15), residues: 1176 loop : -2.66 (0.09), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 473 HIS 0.023 0.002 HIS E 378 PHE 0.028 0.002 PHE M 72 TYR 0.026 0.002 TYR B 674 ARG 0.012 0.001 ARG M 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 511 time to evaluate : 4.157 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: A 449 TYR cc_start: 0.3441 (OUTLIER) cc_final: 0.2769 (m-80) REVERT: A 528 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.5960 (tppt) REVERT: A 572 THR cc_start: 0.5221 (m) cc_final: 0.4876 (p) REVERT: A 751 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.7023 (p0) REVERT: A 814 LYS cc_start: 0.6452 (tptt) cc_final: 0.6218 (tptt) REVERT: A 823 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 904 TYR cc_start: 0.7770 (m-10) cc_final: 0.7194 (m-10) REVERT: A 969 ASN cc_start: 0.8975 (m110) cc_final: 0.8424 (m-40) REVERT: B 177 MET cc_start: -0.0516 (mmt) cc_final: -0.0958 (ttt) REVERT: B 572 THR cc_start: 0.5506 (m) cc_final: 0.4989 (p) REVERT: B 748 GLU cc_start: 0.6202 (mp0) cc_final: 0.5667 (tp30) REVERT: B 823 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6949 (t80) REVERT: B 979 ASP cc_start: 0.7578 (t70) cc_final: 0.7356 (t0) REVERT: B 1107 ARG cc_start: 0.7156 (ptp90) cc_final: 0.6325 (mtt90) REVERT: C 134 GLN cc_start: 0.5297 (mt0) cc_final: 0.5051 (mt0) REVERT: C 197 ILE cc_start: 0.7467 (pt) cc_final: 0.7251 (tt) REVERT: C 572 THR cc_start: 0.4622 (m) cc_final: 0.4213 (p) REVERT: C 740 MET cc_start: 0.6485 (tpt) cc_final: 0.6040 (tpp) REVERT: C 780 GLU cc_start: 0.7860 (pt0) cc_final: 0.7547 (pt0) REVERT: C 786 LYS cc_start: 0.7373 (mptt) cc_final: 0.6919 (mmmt) REVERT: C 814 LYS cc_start: 0.6755 (tptt) cc_final: 0.6166 (tppt) REVERT: C 979 ASP cc_start: 0.7442 (t70) cc_final: 0.7150 (t0) REVERT: C 1019 ARG cc_start: 0.6904 (tpt-90) cc_final: 0.6691 (ttm110) REVERT: C 1103 PHE cc_start: 0.8082 (m-80) cc_final: 0.7611 (m-80) REVERT: E 26 LYS cc_start: 0.3239 (tptt) cc_final: 0.2762 (mmtt) REVERT: E 91 LEU cc_start: 0.3953 (mm) cc_final: 0.3731 (tp) REVERT: E 293 VAL cc_start: 0.1673 (p) cc_final: 0.1355 (t) REVERT: E 332 MET cc_start: 0.4518 (ttt) cc_final: 0.3084 (mtp) REVERT: E 366 MET cc_start: -0.0140 (mtm) cc_final: -0.0561 (tpp) REVERT: E 459 TRP cc_start: 0.0776 (OUTLIER) cc_final: 0.0023 (t60) REVERT: E 474 MET cc_start: 0.1107 (tpp) cc_final: 0.0072 (mmp) REVERT: H 81 MET cc_start: -0.0959 (tpp) cc_final: -0.1263 (tpp) REVERT: H 110 ASN cc_start: 0.2483 (p0) cc_final: 0.1993 (t0) REVERT: L 64 PHE cc_start: -0.0387 (m-80) cc_final: -0.0700 (m-80) REVERT: G 111 PHE cc_start: 0.2532 (m-80) cc_final: 0.2316 (m-80) REVERT: J 73 LEU cc_start: 0.1065 (tt) cc_final: 0.0749 (mt) REVERT: J 75 GLU cc_start: 0.3204 (pt0) cc_final: 0.2931 (tm-30) REVERT: J 134 ASN cc_start: 0.2334 (m110) cc_final: 0.1869 (t0) REVERT: J 240 LEU cc_start: 0.2931 (pp) cc_final: 0.2601 (pp) REVERT: J 249 MET cc_start: 0.2259 (OUTLIER) cc_final: 0.1986 (tpp) REVERT: J 270 MET cc_start: 0.0144 (tpp) cc_final: -0.2261 (tpp) REVERT: J 271 TRP cc_start: 0.1834 (m-90) cc_final: 0.0515 (t-100) REVERT: J 332 MET cc_start: 0.2007 (ttt) cc_final: 0.0684 (mtt) REVERT: J 356 PHE cc_start: 0.1159 (m-80) cc_final: 0.0852 (m-80) REVERT: J 360 MET cc_start: 0.1857 (ttp) cc_final: 0.1394 (ttm) REVERT: J 505 HIS cc_start: 0.2401 (m170) cc_final: 0.1642 (p-80) REVERT: J 546 ASN cc_start: 0.1941 (m-40) cc_final: 0.1337 (p0) REVERT: M 42 GLN cc_start: 0.6731 (mt0) cc_final: 0.5991 (tp40) REVERT: M 217 TYR cc_start: 0.3800 (t80) cc_final: 0.2817 (m-80) REVERT: M 270 MET cc_start: -0.0390 (tpp) cc_final: -0.1366 (tpp) REVERT: M 271 TRP cc_start: 0.1390 (m-90) cc_final: 0.0875 (t-100) REVERT: M 366 MET cc_start: -0.0156 (mtp) cc_final: -0.0801 (tpp) REVERT: M 482 ARG cc_start: 0.4426 (mtt180) cc_final: 0.4204 (ttm-80) REVERT: M 579 MET cc_start: 0.2248 (ptp) cc_final: 0.1692 (mtm) REVERT: N 105 TYR cc_start: 0.4041 (m-80) cc_final: 0.3571 (m-80) REVERT: O 16 GLN cc_start: 0.0813 (OUTLIER) cc_final: 0.0375 (mm-40) REVERT: O 64 PHE cc_start: -0.0479 (m-80) cc_final: -0.1036 (m-10) outliers start: 71 outliers final: 38 residues processed: 565 average time/residue: 0.5030 time to fit residues: 470.8549 Evaluate side-chains 447 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 401 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 459 TRP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 378 HIS Chi-restraints excluded: chain J residue 524 GLN Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 378 HIS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 471 optimal weight: 20.0000 chunk 385 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 567 optimal weight: 10.0000 chunk 613 optimal weight: 10.0000 chunk 505 optimal weight: 4.9990 chunk 562 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 455 optimal weight: 40.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 99 ASN A 207 HIS A 354 ASN A 450 ASN A 901 GLN A 953 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1023 ASN A1064 HIS B 87 ASN B 99 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 450 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 703 ASN B 787 GLN B 913 GLN B 955 ASN B 992 GLN B1023 ASN B1064 HIS B1101 HIS C 87 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 394 ASN C 409 GLN C 487 ASN C 580 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 901 GLN C 913 GLN C 953 ASN C 955 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN C1064 HIS C1101 HIS C1135 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 345 HIS E 374 HIS H 182 GLN ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN L 193 HIS I 172 GLN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 GLN J 305 GLN ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS J 397 ASN J 401 HIS J 508 ASN J 578 ASN ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 101 GLN M 175 GLN M 305 GLN M 374 HIS M 378 HIS M 401 HIS M 442 GLN M 505 HIS ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 51201 Z= 0.572 Angle : 0.921 18.076 69696 Z= 0.475 Chirality : 0.056 0.427 7857 Planarity : 0.006 0.073 8961 Dihedral : 6.594 53.591 7784 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.93 % Allowed : 15.00 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.09), residues: 6258 helix: -1.78 (0.11), residues: 1599 sheet: -0.54 (0.15), residues: 1206 loop : -2.56 (0.09), residues: 3453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G 114 HIS 0.023 0.002 HIS M 195 PHE 0.043 0.004 PHE A1042 TYR 0.030 0.003 TYR C 695 ARG 0.013 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 407 time to evaluate : 4.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7571 (t80) cc_final: 0.7086 (t80) REVERT: A 238 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5326 (p90) REVERT: A 271 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7296 (mt0) REVERT: A 572 THR cc_start: 0.4652 (m) cc_final: 0.4291 (p) REVERT: A 661 GLU cc_start: 0.7951 (tp30) cc_final: 0.7025 (pm20) REVERT: A 740 MET cc_start: 0.7268 (mmm) cc_final: 0.7002 (mmm) REVERT: A 751 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7881 (p0) REVERT: A 773 GLU cc_start: 0.7643 (tt0) cc_final: 0.7434 (tt0) REVERT: A 814 LYS cc_start: 0.6408 (tptt) cc_final: 0.5883 (tppt) REVERT: B 153 MET cc_start: 0.4163 (mmt) cc_final: 0.3360 (pmm) REVERT: B 177 MET cc_start: -0.0825 (mmt) cc_final: -0.1223 (ttt) REVERT: B 318 PHE cc_start: 0.7467 (t80) cc_final: 0.6969 (t80) REVERT: B 338 PHE cc_start: 0.5548 (OUTLIER) cc_final: 0.4377 (p90) REVERT: B 528 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7028 (mmmt) REVERT: B 565 PHE cc_start: 0.8309 (m-80) cc_final: 0.8040 (m-10) REVERT: B 572 THR cc_start: 0.5433 (m) cc_final: 0.5029 (p) REVERT: B 1017 GLU cc_start: 0.7300 (tt0) cc_final: 0.6719 (tm-30) REVERT: C 134 GLN cc_start: 0.5388 (mt0) cc_final: 0.5081 (mt0) REVERT: C 321 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7118 (tp-100) REVERT: C 347 PHE cc_start: -0.0434 (OUTLIER) cc_final: -0.1145 (m-10) REVERT: C 572 THR cc_start: 0.5287 (m) cc_final: 0.4812 (p) REVERT: C 661 GLU cc_start: 0.8055 (tp30) cc_final: 0.7008 (pm20) REVERT: C 814 LYS cc_start: 0.6604 (tptt) cc_final: 0.6019 (tppt) REVERT: C 979 ASP cc_start: 0.7623 (t70) cc_final: 0.7162 (t0) REVERT: E 26 LYS cc_start: 0.3446 (tptt) cc_final: 0.3055 (mmtt) REVERT: E 152 MET cc_start: 0.1974 (tpt) cc_final: 0.1491 (ppp) REVERT: E 332 MET cc_start: 0.1869 (ttt) cc_final: -0.0011 (mmm) REVERT: H 110 ASN cc_start: 0.2155 (p0) cc_final: 0.1760 (t0) REVERT: L 22 CYS cc_start: 0.5521 (OUTLIER) cc_final: 0.5191 (m) REVERT: G 59 ASN cc_start: 0.3999 (t0) cc_final: 0.3274 (p0) REVERT: G 111 PHE cc_start: 0.2669 (m-80) cc_final: 0.2435 (m-80) REVERT: J 75 GLU cc_start: 0.1942 (pt0) cc_final: 0.1146 (tm-30) REVERT: J 270 MET cc_start: 0.0409 (tpp) cc_final: -0.2134 (tpp) REVERT: J 271 TRP cc_start: 0.2314 (m-90) cc_final: 0.1326 (t-100) REVERT: J 332 MET cc_start: 0.1757 (ttt) cc_final: 0.0574 (mtt) REVERT: J 402 GLU cc_start: 0.1454 (mm-30) cc_final: 0.1001 (mm-30) REVERT: J 421 ILE cc_start: -0.1800 (OUTLIER) cc_final: -0.2047 (mm) REVERT: J 488 VAL cc_start: 0.2510 (OUTLIER) cc_final: 0.2292 (t) REVERT: J 514 ARG cc_start: 0.0682 (OUTLIER) cc_final: -0.0184 (ptt90) REVERT: J 546 ASN cc_start: 0.2805 (m-40) cc_final: 0.2307 (t0) REVERT: M 241 HIS cc_start: 0.1972 (t-90) cc_final: 0.1647 (t70) REVERT: M 270 MET cc_start: -0.0390 (tpp) cc_final: -0.1893 (tpp) REVERT: M 271 TRP cc_start: 0.0977 (m-90) cc_final: 0.0589 (t-100) REVERT: M 400 PHE cc_start: 0.1043 (m-80) cc_final: -0.0382 (t80) REVERT: M 401 HIS cc_start: 0.0887 (OUTLIER) cc_final: 0.0466 (m170) REVERT: M 482 ARG cc_start: 0.4483 (mtt180) cc_final: 0.4248 (ttm-80) REVERT: N 105 TYR cc_start: 0.4747 (m-80) cc_final: 0.4348 (m-80) REVERT: O 64 PHE cc_start: -0.0176 (m-80) cc_final: -0.0708 (m-10) outliers start: 158 outliers final: 86 residues processed: 539 average time/residue: 0.4926 time to fit residues: 453.6206 Evaluate side-chains 423 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 327 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 545 SER Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 401 HIS Chi-restraints excluded: chain J residue 421 ILE Chi-restraints excluded: chain J residue 453 THR Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 514 ARG Chi-restraints excluded: chain J residue 516 TYR Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 401 HIS Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 10.0000 chunk 426 optimal weight: 3.9990 chunk 294 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 381 optimal weight: 0.5980 chunk 569 optimal weight: 9.9990 chunk 603 optimal weight: 0.5980 chunk 297 optimal weight: 0.7980 chunk 539 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A 913 GLN A 992 GLN A1101 HIS B 354 ASN B 474 GLN B 787 GLN B 856 ASN B 901 GLN B 920 GLN B 953 ASN B1002 GLN C 66 HIS C 99 ASN C 580 GLN C 955 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN G 39 GLN I 172 GLN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 305 GLN ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 HIS J 397 ASN J 401 HIS J 437 ASN ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN M 305 GLN M 401 HIS M 505 HIS O 6 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51201 Z= 0.183 Angle : 0.566 9.201 69696 Z= 0.286 Chirality : 0.045 0.358 7857 Planarity : 0.004 0.058 8961 Dihedral : 5.168 46.856 7779 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 17.29 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 6258 helix: -0.98 (0.13), residues: 1605 sheet: -0.37 (0.15), residues: 1185 loop : -2.29 (0.09), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 461 HIS 0.023 0.002 HIS M 378 PHE 0.023 0.001 PHE C 898 TYR 0.022 0.001 TYR B1138 ARG 0.008 0.001 ARG M 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 363 time to evaluate : 3.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5681 (pmm) cc_final: 0.5265 (pmm) REVERT: A 220 PHE cc_start: 0.7352 (t80) cc_final: 0.6827 (t80) REVERT: A 238 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5507 (p90) REVERT: A 572 THR cc_start: 0.4920 (m) cc_final: 0.4493 (p) REVERT: A 661 GLU cc_start: 0.7785 (tp30) cc_final: 0.6995 (pm20) REVERT: A 814 LYS cc_start: 0.6498 (tptt) cc_final: 0.6145 (tptt) REVERT: A 1141 LEU cc_start: 0.7622 (mt) cc_final: 0.7213 (tt) REVERT: B 153 MET cc_start: 0.3849 (mmt) cc_final: 0.3355 (pmm) REVERT: B 177 MET cc_start: -0.1020 (mmt) cc_final: -0.1411 (ttt) REVERT: B 565 PHE cc_start: 0.7883 (m-80) cc_final: 0.7560 (m-10) REVERT: B 572 THR cc_start: 0.5914 (m) cc_final: 0.5504 (p) REVERT: B 740 MET cc_start: 0.6685 (mmm) cc_final: 0.6462 (mmm) REVERT: B 1139 ASP cc_start: 0.7576 (t0) cc_final: 0.7024 (t0) REVERT: C 53 ASP cc_start: 0.6931 (m-30) cc_final: 0.6651 (m-30) REVERT: C 129 LYS cc_start: 0.5272 (tttm) cc_final: 0.5059 (tttp) REVERT: C 134 GLN cc_start: 0.5455 (mt0) cc_final: 0.5239 (mt0) REVERT: C 276 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7493 (tt) REVERT: C 347 PHE cc_start: -0.0647 (OUTLIER) cc_final: -0.0907 (m-80) REVERT: C 558 LYS cc_start: 0.7630 (mptt) cc_final: 0.7360 (mppt) REVERT: C 572 THR cc_start: 0.5174 (m) cc_final: 0.4647 (p) REVERT: C 661 GLU cc_start: 0.7851 (tp30) cc_final: 0.7152 (pm20) REVERT: C 814 LYS cc_start: 0.6578 (tptt) cc_final: 0.6060 (tppt) REVERT: C 823 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6802 (t80) REVERT: C 979 ASP cc_start: 0.7449 (t70) cc_final: 0.7107 (t0) REVERT: E 26 LYS cc_start: 0.3240 (tptt) cc_final: 0.2833 (mmtt) REVERT: E 332 MET cc_start: 0.2332 (ttt) cc_final: 0.0567 (mmm) REVERT: E 455 MET cc_start: 0.3064 (tmm) cc_final: 0.2856 (tmm) REVERT: H 110 ASN cc_start: 0.2386 (p0) cc_final: 0.2046 (t0) REVERT: G 59 ASN cc_start: 0.4125 (t0) cc_final: 0.3427 (p0) REVERT: G 221 LYS cc_start: 0.1985 (pttm) cc_final: -0.1338 (mmmt) REVERT: J 73 LEU cc_start: 0.1908 (tt) cc_final: 0.1695 (mt) REVERT: J 75 GLU cc_start: 0.2048 (pt0) cc_final: 0.1419 (tm-30) REVERT: J 134 ASN cc_start: 0.0842 (m110) cc_final: 0.0536 (t0) REVERT: J 180 TYR cc_start: 0.1002 (t80) cc_final: 0.0752 (m-80) REVERT: J 270 MET cc_start: -0.0243 (tpp) cc_final: -0.2199 (tpp) REVERT: J 271 TRP cc_start: 0.2423 (m-90) cc_final: 0.1389 (t-100) REVERT: J 292 ASP cc_start: 0.3222 (p0) cc_final: 0.3009 (m-30) REVERT: J 546 ASN cc_start: 0.2649 (m-40) cc_final: 0.2043 (p0) REVERT: M 241 HIS cc_start: 0.1977 (t-90) cc_final: 0.1622 (t-90) REVERT: M 270 MET cc_start: -0.0332 (tpp) cc_final: -0.2173 (tpp) REVERT: M 271 TRP cc_start: 0.1036 (m-90) cc_final: 0.0738 (t-100) REVERT: M 400 PHE cc_start: 0.0229 (m-80) cc_final: -0.0119 (t80) REVERT: M 478 TRP cc_start: 0.0119 (m100) cc_final: -0.0301 (m100) REVERT: M 482 ARG cc_start: 0.4538 (mtt180) cc_final: 0.4244 (ttm-80) REVERT: M 503 LEU cc_start: 0.3191 (OUTLIER) cc_final: 0.2318 (tp) REVERT: N 105 TYR cc_start: 0.4286 (m-80) cc_final: 0.3920 (m-80) REVERT: O 64 PHE cc_start: -0.0209 (m-80) cc_final: -0.0762 (m-10) outliers start: 101 outliers final: 63 residues processed: 445 average time/residue: 0.4640 time to fit residues: 355.1238 Evaluate side-chains 369 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 449 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 514 optimal weight: 20.0000 chunk 416 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 0.2980 chunk 541 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 overall best weight: 6.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 787 GLN A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 804 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 195 HIS J 277 ASN J 305 GLN J 397 ASN J 578 ASN ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 GLN M 397 ASN ** M 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.124 51201 Z= 0.738 Angle : 1.007 14.871 69696 Z= 0.512 Chirality : 0.059 0.435 7857 Planarity : 0.007 0.066 8961 Dihedral : 7.402 59.539 7779 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.72 % Favored : 91.22 % Rotamer: Outliers : 4.45 % Allowed : 18.55 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.10), residues: 6258 helix: -1.35 (0.12), residues: 1566 sheet: -0.97 (0.14), residues: 1233 loop : -2.57 (0.09), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP G 114 HIS 0.024 0.004 HIS M 378 PHE 0.046 0.004 PHE A1042 TYR 0.035 0.004 TYR C 612 ARG 0.018 0.002 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 342 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.5822 (mt0) cc_final: 0.5597 (mt0) REVERT: A 220 PHE cc_start: 0.7625 (t80) cc_final: 0.6821 (t80) REVERT: A 238 PHE cc_start: 0.5954 (OUTLIER) cc_final: 0.5435 (p90) REVERT: A 347 PHE cc_start: 0.2035 (OUTLIER) cc_final: 0.1712 (m-80) REVERT: A 572 THR cc_start: 0.6008 (m) cc_final: 0.5467 (p) REVERT: A 745 ASP cc_start: 0.6703 (t70) cc_final: 0.6106 (t0) REVERT: A 814 LYS cc_start: 0.6809 (tptt) cc_final: 0.6253 (tppt) REVERT: A 823 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7270 (t80) REVERT: B 88 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.6876 (p0) REVERT: B 129 LYS cc_start: 0.5538 (tttm) cc_final: 0.5296 (tttp) REVERT: B 153 MET cc_start: 0.4022 (mmt) cc_final: 0.3410 (pmm) REVERT: B 177 MET cc_start: -0.0936 (mmt) cc_final: -0.1457 (ttt) REVERT: B 338 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.4552 (p90) REVERT: B 528 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.7062 (mmmt) REVERT: B 572 THR cc_start: 0.7408 (m) cc_final: 0.6937 (p) REVERT: B 745 ASP cc_start: 0.7538 (m-30) cc_final: 0.6383 (t0) REVERT: B 959 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7995 (mm) REVERT: C 134 GLN cc_start: 0.5637 (mt0) cc_final: 0.5374 (mt0) REVERT: C 276 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7536 (tt) REVERT: C 347 PHE cc_start: 0.0182 (OUTLIER) cc_final: -0.0441 (m-10) REVERT: C 814 LYS cc_start: 0.7197 (tptt) cc_final: 0.6544 (tppt) REVERT: C 1017 GLU cc_start: 0.7635 (tt0) cc_final: 0.6850 (tm-30) REVERT: C 1031 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6477 (mt-10) REVERT: E 26 LYS cc_start: 0.3583 (tptt) cc_final: 0.3008 (mmtt) REVERT: E 323 MET cc_start: 0.0784 (tpt) cc_final: -0.0395 (tpt) REVERT: E 332 MET cc_start: 0.0359 (ttt) cc_final: -0.0673 (mmm) REVERT: E 531 GLN cc_start: 0.4014 (OUTLIER) cc_final: 0.3121 (tp40) REVERT: E 606 TRP cc_start: 0.3549 (OUTLIER) cc_final: 0.3232 (p-90) REVERT: H 36 TRP cc_start: 0.1878 (m100) cc_final: 0.1490 (m-90) REVERT: H 59 ASN cc_start: 0.4426 (t0) cc_final: 0.3702 (p0) REVERT: H 70 ILE cc_start: 0.0939 (mp) cc_final: 0.0287 (mp) REVERT: H 81 MET cc_start: -0.0805 (mmm) cc_final: -0.1387 (mmm) REVERT: J 73 LEU cc_start: 0.1938 (tt) cc_final: 0.1585 (mp) REVERT: J 75 GLU cc_start: 0.1250 (pt0) cc_final: 0.0433 (tm-30) REVERT: J 152 MET cc_start: 0.1704 (ttt) cc_final: 0.1481 (ptm) REVERT: J 233 ILE cc_start: 0.1792 (OUTLIER) cc_final: 0.1459 (tt) REVERT: J 270 MET cc_start: 0.0199 (tpp) cc_final: -0.2414 (tpp) REVERT: J 271 TRP cc_start: 0.2135 (m-90) cc_final: 0.0695 (t-100) REVERT: J 292 ASP cc_start: 0.3519 (OUTLIER) cc_final: 0.2963 (m-30) REVERT: J 421 ILE cc_start: -0.1665 (OUTLIER) cc_final: -0.1876 (mp) REVERT: J 461 TRP cc_start: 0.1585 (m-10) cc_final: 0.0809 (t-100) REVERT: J 514 ARG cc_start: -0.0755 (OUTLIER) cc_final: -0.1280 (ptt90) REVERT: J 516 TYR cc_start: 0.0883 (OUTLIER) cc_final: 0.0627 (m-80) REVERT: M 144 LEU cc_start: 0.2672 (OUTLIER) cc_final: 0.2307 (tt) REVERT: M 270 MET cc_start: 0.0088 (tpp) cc_final: -0.1945 (tpp) REVERT: M 271 TRP cc_start: 0.1059 (m-90) cc_final: 0.0808 (t-100) REVERT: M 400 PHE cc_start: 0.0412 (m-80) cc_final: 0.0122 (t80) REVERT: M 482 ARG cc_start: 0.4772 (mtt180) cc_final: 0.4526 (ttm-80) REVERT: N 70 ILE cc_start: 0.0266 (OUTLIER) cc_final: -0.0345 (mp) REVERT: O 64 PHE cc_start: -0.0002 (m-80) cc_final: -0.0471 (m-10) outliers start: 241 outliers final: 137 residues processed: 559 average time/residue: 0.4941 time to fit residues: 479.9730 Evaluate side-chains 460 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 304 time to evaluate : 3.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 421 ILE Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 514 ARG Chi-restraints excluded: chain J residue 516 TYR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 HIS Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 572 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.9980 chunk 543 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 603 optimal weight: 3.9990 chunk 501 optimal weight: 5.9990 chunk 279 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 316 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 787 GLN A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 374 HIS ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 HIS J 325 GLN J 397 ASN ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 397 ASN M 401 HIS M 437 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 51201 Z= 0.196 Angle : 0.601 8.889 69696 Z= 0.304 Chirality : 0.046 0.451 7857 Planarity : 0.004 0.050 8961 Dihedral : 5.801 56.770 7779 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.40 % Allowed : 20.31 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.10), residues: 6258 helix: -0.67 (0.13), residues: 1566 sheet: -0.71 (0.14), residues: 1218 loop : -2.27 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 353 HIS 0.019 0.001 HIS E 378 PHE 0.022 0.002 PHE B 238 TYR 0.021 0.002 TYR E 515 ARG 0.006 0.001 ARG J 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 329 time to evaluate : 3.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6221 (mt0) cc_final: 0.5969 (mt0) REVERT: A 153 MET cc_start: 0.5593 (pmm) cc_final: 0.5191 (pmm) REVERT: A 220 PHE cc_start: 0.7242 (t80) cc_final: 0.7018 (t80) REVERT: A 238 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5624 (p90) REVERT: A 326 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6425 (tt) REVERT: A 369 TYR cc_start: 0.3202 (m-80) cc_final: 0.2910 (m-80) REVERT: A 572 THR cc_start: 0.6808 (m) cc_final: 0.6152 (p) REVERT: A 814 LYS cc_start: 0.6678 (tptt) cc_final: 0.6269 (tppt) REVERT: A 820 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: A 823 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7132 (t80) REVERT: B 51 THR cc_start: 0.8258 (t) cc_final: 0.7861 (t) REVERT: B 53 ASP cc_start: 0.7005 (m-30) cc_final: 0.6765 (m-30) REVERT: B 129 LYS cc_start: 0.5363 (tttm) cc_final: 0.5106 (tttp) REVERT: B 153 MET cc_start: 0.4079 (mmt) cc_final: 0.3421 (pmm) REVERT: B 177 MET cc_start: -0.1053 (mmt) cc_final: -0.1704 (ttt) REVERT: B 338 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.4434 (p90) REVERT: B 528 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6798 (mmmt) REVERT: B 572 THR cc_start: 0.7455 (m) cc_final: 0.6990 (p) REVERT: B 745 ASP cc_start: 0.7563 (m-30) cc_final: 0.6392 (t0) REVERT: B 820 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: B 919 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7287 (p0) REVERT: C 53 ASP cc_start: 0.6968 (m-30) cc_final: 0.6716 (m-30) REVERT: C 134 GLN cc_start: 0.5822 (mt0) cc_final: 0.5498 (mt0) REVERT: C 353 TRP cc_start: 0.0757 (p-90) cc_final: 0.0257 (p-90) REVERT: C 814 LYS cc_start: 0.6931 (tptt) cc_final: 0.6214 (tppt) REVERT: E 26 LYS cc_start: 0.3226 (tptt) cc_final: 0.2682 (mmtt) REVERT: E 323 MET cc_start: 0.0714 (tpt) cc_final: 0.0440 (tpp) REVERT: E 332 MET cc_start: 0.1751 (ttt) cc_final: 0.0152 (mmm) REVERT: E 531 GLN cc_start: 0.4064 (OUTLIER) cc_final: 0.3136 (tp40) REVERT: E 606 TRP cc_start: 0.3529 (OUTLIER) cc_final: 0.3256 (p-90) REVERT: H 59 ASN cc_start: 0.4885 (t0) cc_final: 0.4238 (p0) REVERT: G 59 ASN cc_start: 0.4284 (t0) cc_final: 0.3150 (p0) REVERT: J 73 LEU cc_start: 0.2203 (OUTLIER) cc_final: 0.1931 (mt) REVERT: J 75 GLU cc_start: 0.1567 (pt0) cc_final: 0.0807 (tm-30) REVERT: J 270 MET cc_start: 0.0058 (tpp) cc_final: -0.2459 (tpp) REVERT: J 271 TRP cc_start: 0.2100 (m-90) cc_final: 0.0647 (t-100) REVERT: J 505 HIS cc_start: 0.1773 (m-70) cc_final: 0.1358 (m-70) REVERT: J 546 ASN cc_start: 0.2838 (m-40) cc_final: 0.2062 (p0) REVERT: M 144 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2458 (tt) REVERT: M 241 HIS cc_start: 0.2269 (t-90) cc_final: 0.1925 (t70) REVERT: M 270 MET cc_start: 0.0129 (tpp) cc_final: -0.2208 (tpp) REVERT: M 271 TRP cc_start: 0.1224 (m-90) cc_final: 0.0665 (t-100) REVERT: M 401 HIS cc_start: 0.1075 (OUTLIER) cc_final: 0.0153 (t-170) REVERT: M 437 ASN cc_start: -0.4785 (OUTLIER) cc_final: -0.5040 (p0) REVERT: M 478 TRP cc_start: 0.0180 (m100) cc_final: -0.0235 (m100) REVERT: M 482 ARG cc_start: 0.4640 (mtt180) cc_final: 0.4345 (ttm-80) outliers start: 129 outliers final: 81 residues processed: 438 average time/residue: 0.4618 time to fit residues: 346.4687 Evaluate side-chains 396 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 301 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 165 TRP Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 401 HIS Chi-restraints excluded: chain M residue 437 ASN Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 343 optimal weight: 10.0000 chunk 440 optimal weight: 0.7980 chunk 341 optimal weight: 0.9980 chunk 508 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 chunk 601 optimal weight: 10.0000 chunk 376 optimal weight: 20.0000 chunk 366 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 578 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 401 HIS M 437 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 51201 Z= 0.257 Angle : 0.613 13.500 69696 Z= 0.307 Chirality : 0.047 0.379 7857 Planarity : 0.004 0.054 8961 Dihedral : 5.587 56.216 7779 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.71 % Allowed : 20.33 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 6258 helix: -0.45 (0.13), residues: 1578 sheet: -0.57 (0.15), residues: 1197 loop : -2.22 (0.10), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 353 HIS 0.024 0.002 HIS M 378 PHE 0.025 0.002 PHE J 525 TYR 0.018 0.002 TYR A 380 ARG 0.006 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 313 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.4690 (mm) cc_final: 0.4028 (tp) REVERT: A 134 GLN cc_start: 0.6331 (mt0) cc_final: 0.5961 (mt0) REVERT: A 136 CYS cc_start: 0.4259 (OUTLIER) cc_final: 0.4015 (p) REVERT: A 220 PHE cc_start: 0.7315 (t80) cc_final: 0.7093 (t80) REVERT: A 238 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5562 (p90) REVERT: A 326 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6342 (tt) REVERT: A 369 TYR cc_start: 0.3132 (m-80) cc_final: 0.2816 (m-80) REVERT: A 814 LYS cc_start: 0.6681 (tptt) cc_final: 0.6273 (tppt) REVERT: A 820 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: B 51 THR cc_start: 0.8293 (t) cc_final: 0.7987 (t) REVERT: B 53 ASP cc_start: 0.7028 (m-30) cc_final: 0.6798 (m-30) REVERT: B 153 MET cc_start: 0.3952 (mmt) cc_final: 0.3425 (pmm) REVERT: B 177 MET cc_start: -0.0991 (mmt) cc_final: -0.1672 (ttt) REVERT: B 338 PHE cc_start: 0.5578 (OUTLIER) cc_final: 0.4478 (p90) REVERT: B 528 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6920 (mmmt) REVERT: B 565 PHE cc_start: 0.8056 (m-80) cc_final: 0.7683 (m-10) REVERT: B 572 THR cc_start: 0.7496 (m) cc_final: 0.7010 (p) REVERT: B 745 ASP cc_start: 0.7585 (m-30) cc_final: 0.6401 (t0) REVERT: B 820 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: B 1117 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7999 (p) REVERT: C 53 ASP cc_start: 0.6958 (m-30) cc_final: 0.6704 (m-30) REVERT: C 129 LYS cc_start: 0.6036 (tttp) cc_final: 0.5728 (tttp) REVERT: C 134 GLN cc_start: 0.5806 (mt0) cc_final: 0.5563 (mt0) REVERT: C 353 TRP cc_start: 0.0892 (p-90) cc_final: 0.0679 (p-90) REVERT: C 814 LYS cc_start: 0.6947 (tptt) cc_final: 0.6248 (tppt) REVERT: C 1031 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: C 1127 ASP cc_start: 0.7859 (m-30) cc_final: 0.7418 (p0) REVERT: E 26 LYS cc_start: 0.3402 (tptt) cc_final: 0.2871 (mmtt) REVERT: E 323 MET cc_start: 0.0671 (tpt) cc_final: 0.0442 (tpp) REVERT: E 332 MET cc_start: 0.1701 (ttt) cc_final: 0.0094 (mmm) REVERT: E 531 GLN cc_start: 0.4081 (OUTLIER) cc_final: 0.3134 (tp40) REVERT: E 606 TRP cc_start: 0.3527 (OUTLIER) cc_final: 0.3236 (p-90) REVERT: H 59 ASN cc_start: 0.4925 (t0) cc_final: 0.4312 (p0) REVERT: G 59 ASN cc_start: 0.4246 (t0) cc_final: 0.3196 (p0) REVERT: J 73 LEU cc_start: 0.2236 (tt) cc_final: 0.1962 (mt) REVERT: J 75 GLU cc_start: 0.1498 (pt0) cc_final: 0.0700 (tm-30) REVERT: J 270 MET cc_start: -0.0296 (tpp) cc_final: -0.2409 (tpp) REVERT: J 271 TRP cc_start: 0.2258 (m-90) cc_final: 0.0696 (t-100) REVERT: J 383 MET cc_start: 0.1582 (tmm) cc_final: 0.0743 (mtt) REVERT: J 408 MET cc_start: 0.2308 (ptp) cc_final: 0.2092 (ptp) REVERT: J 421 ILE cc_start: -0.1894 (OUTLIER) cc_final: -0.2151 (mm) REVERT: J 505 HIS cc_start: 0.1789 (m-70) cc_final: 0.1346 (m-70) REVERT: J 546 ASN cc_start: 0.2943 (m-40) cc_final: 0.2183 (p0) REVERT: M 134 ASN cc_start: 0.1707 (OUTLIER) cc_final: 0.1068 (t0) REVERT: M 144 LEU cc_start: 0.2867 (OUTLIER) cc_final: 0.2446 (tt) REVERT: M 152 MET cc_start: 0.0581 (ttt) cc_final: 0.0298 (ppp) REVERT: M 270 MET cc_start: 0.0289 (tpp) cc_final: -0.1638 (tpp) REVERT: M 271 TRP cc_start: 0.1466 (m-90) cc_final: 0.0353 (m100) REVERT: M 374 HIS cc_start: 0.1112 (OUTLIER) cc_final: 0.0776 (t70) REVERT: M 437 ASN cc_start: -0.4180 (OUTLIER) cc_final: -0.4424 (p0) REVERT: M 478 TRP cc_start: 0.0173 (m100) cc_final: -0.0239 (m100) REVERT: M 482 ARG cc_start: 0.4583 (mtt180) cc_final: 0.4284 (ttm-80) REVERT: N 111 PHE cc_start: 0.2800 (OUTLIER) cc_final: 0.2353 (m-80) outliers start: 146 outliers final: 98 residues processed: 439 average time/residue: 0.4681 time to fit residues: 354.5871 Evaluate side-chains 418 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 303 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 189 GLN Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 378 HIS Chi-restraints excluded: chain J residue 421 ILE Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 165 TRP Chi-restraints excluded: chain M residue 274 PHE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 HIS Chi-restraints excluded: chain M residue 437 ASN Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 111 PHE Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 359 optimal weight: 20.0000 chunk 181 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 382 optimal weight: 0.6980 chunk 409 optimal weight: 0.0570 chunk 297 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 472 optimal weight: 9.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 GLN M 437 ASN M 524 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 51201 Z= 0.216 Angle : 0.580 9.772 69696 Z= 0.291 Chirality : 0.046 0.357 7857 Planarity : 0.004 0.058 8961 Dihedral : 5.258 54.508 7779 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.69 % Allowed : 20.46 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -1.93 (0.10), residues: 6258 helix: -0.27 (0.13), residues: 1581 sheet: -0.51 (0.15), residues: 1167 loop : -2.11 (0.10), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.022 0.001 HIS M 378 PHE 0.025 0.001 PHE O 64 TYR 0.015 0.001 TYR E 516 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 310 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.4581 (mm) cc_final: 0.3991 (tp) REVERT: A 134 GLN cc_start: 0.6357 (mt0) cc_final: 0.5972 (mt0) REVERT: A 136 CYS cc_start: 0.4238 (OUTLIER) cc_final: 0.3984 (p) REVERT: A 238 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.5717 (p90) REVERT: A 369 TYR cc_start: 0.3418 (m-80) cc_final: 0.3194 (m-10) REVERT: A 814 LYS cc_start: 0.6666 (tptt) cc_final: 0.6256 (tppt) REVERT: B 51 THR cc_start: 0.8222 (t) cc_final: 0.7898 (t) REVERT: B 53 ASP cc_start: 0.6920 (m-30) cc_final: 0.6698 (m-30) REVERT: B 153 MET cc_start: 0.4084 (mmt) cc_final: 0.3427 (pmm) REVERT: B 177 MET cc_start: -0.0988 (mmt) cc_final: -0.1692 (ttt) REVERT: B 528 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6909 (mmmt) REVERT: B 565 PHE cc_start: 0.7978 (m-80) cc_final: 0.7625 (m-10) REVERT: B 572 THR cc_start: 0.7531 (m) cc_final: 0.7083 (p) REVERT: B 745 ASP cc_start: 0.7684 (m-30) cc_final: 0.6421 (t0) REVERT: B 820 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: B 1055 SER cc_start: 0.8989 (t) cc_final: 0.8715 (p) REVERT: B 1130 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7979 (mm) REVERT: C 53 ASP cc_start: 0.6927 (m-30) cc_final: 0.6655 (m-30) REVERT: C 129 LYS cc_start: 0.5752 (tttp) cc_final: 0.5478 (tttp) REVERT: C 134 GLN cc_start: 0.5829 (mt0) cc_final: 0.5527 (mt0) REVERT: C 814 LYS cc_start: 0.6904 (tptt) cc_final: 0.6222 (tppt) REVERT: C 1031 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: C 1127 ASP cc_start: 0.7881 (m-30) cc_final: 0.7436 (p0) REVERT: E 26 LYS cc_start: 0.3188 (tptt) cc_final: 0.2653 (mmtt) REVERT: E 332 MET cc_start: 0.1699 (ttt) cc_final: 0.0081 (mmm) REVERT: E 531 GLN cc_start: 0.4061 (OUTLIER) cc_final: 0.3165 (tp40) REVERT: E 606 TRP cc_start: 0.3041 (OUTLIER) cc_final: 0.2806 (p-90) REVERT: H 59 ASN cc_start: 0.4760 (t0) cc_final: 0.4190 (p0) REVERT: J 73 LEU cc_start: 0.1936 (OUTLIER) cc_final: 0.1666 (mt) REVERT: J 75 GLU cc_start: 0.1452 (pt0) cc_final: 0.0815 (tm-30) REVERT: J 270 MET cc_start: -0.0254 (tpp) cc_final: -0.2385 (tpp) REVERT: J 271 TRP cc_start: 0.2249 (m-90) cc_final: 0.0686 (t-100) REVERT: J 408 MET cc_start: 0.2308 (ptp) cc_final: 0.2098 (ptp) REVERT: J 421 ILE cc_start: -0.1896 (OUTLIER) cc_final: -0.2153 (mm) REVERT: J 505 HIS cc_start: 0.1917 (m-70) cc_final: 0.1499 (m-70) REVERT: M 134 ASN cc_start: 0.2981 (m-40) cc_final: 0.2554 (t0) REVERT: M 144 LEU cc_start: 0.2759 (OUTLIER) cc_final: 0.2347 (tt) REVERT: M 183 TYR cc_start: -0.0774 (OUTLIER) cc_final: -0.0984 (m-10) REVERT: M 270 MET cc_start: 0.0300 (tpp) cc_final: -0.1697 (tpp) REVERT: M 271 TRP cc_start: 0.1490 (m-90) cc_final: 0.0387 (m100) REVERT: M 360 MET cc_start: 0.3534 (mtp) cc_final: 0.0039 (ppp) REVERT: M 437 ASN cc_start: -0.3993 (OUTLIER) cc_final: -0.4199 (p0) REVERT: M 478 TRP cc_start: 0.0163 (m100) cc_final: -0.0239 (m100) REVERT: M 482 ARG cc_start: 0.4591 (mtt180) cc_final: 0.4291 (ttm-80) REVERT: M 504 PHE cc_start: 0.0178 (m-10) cc_final: -0.0359 (m-10) REVERT: N 111 PHE cc_start: 0.2834 (OUTLIER) cc_final: 0.2378 (m-80) outliers start: 145 outliers final: 111 residues processed: 435 average time/residue: 0.4609 time to fit residues: 347.3936 Evaluate side-chains 426 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 301 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 378 HIS Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 421 ILE Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 165 TRP Chi-restraints excluded: chain M residue 183 TYR Chi-restraints excluded: chain M residue 274 PHE Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 437 ASN Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 524 GLN Chi-restraints excluded: chain N residue 111 PHE Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 10.0000 chunk 576 optimal weight: 0.8980 chunk 525 optimal weight: 5.9990 chunk 560 optimal weight: 0.5980 chunk 337 optimal weight: 0.4980 chunk 244 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 chunk 171 optimal weight: 0.0870 chunk 506 optimal weight: 9.9990 chunk 530 optimal weight: 6.9990 chunk 558 optimal weight: 9.9990 overall best weight: 1.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 GLN M 437 ASN M 524 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 51201 Z= 0.222 Angle : 0.583 12.727 69696 Z= 0.291 Chirality : 0.045 0.353 7857 Planarity : 0.004 0.060 8961 Dihedral : 5.155 54.043 7779 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.60 % Allowed : 20.75 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -1.84 (0.10), residues: 6258 helix: -0.18 (0.13), residues: 1581 sheet: -0.46 (0.15), residues: 1167 loop : -2.06 (0.10), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 163 HIS 0.018 0.001 HIS M 378 PHE 0.040 0.001 PHE J 525 TYR 0.020 0.001 TYR J 196 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 313 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.4749 (mm) cc_final: 0.4189 (tp) REVERT: A 134 GLN cc_start: 0.6409 (mt0) cc_final: 0.6021 (mt0) REVERT: A 238 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5701 (p90) REVERT: A 369 TYR cc_start: 0.3134 (m-80) cc_final: 0.2915 (m-10) REVERT: A 814 LYS cc_start: 0.6756 (tptt) cc_final: 0.6321 (tppt) REVERT: B 51 THR cc_start: 0.8215 (t) cc_final: 0.7891 (t) REVERT: B 129 LYS cc_start: 0.5839 (tttp) cc_final: 0.5590 (tmtm) REVERT: B 153 MET cc_start: 0.4084 (mmt) cc_final: 0.3434 (pmm) REVERT: B 177 MET cc_start: -0.0973 (mmt) cc_final: -0.1700 (ttt) REVERT: B 326 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.5994 (tp) REVERT: B 565 PHE cc_start: 0.7961 (m-80) cc_final: 0.7606 (m-10) REVERT: B 745 ASP cc_start: 0.7743 (m-30) cc_final: 0.6388 (t0) REVERT: B 820 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: B 1117 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7987 (p) REVERT: B 1130 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7999 (mm) REVERT: C 53 ASP cc_start: 0.6658 (m-30) cc_final: 0.6337 (m-30) REVERT: C 129 LYS cc_start: 0.5805 (tttp) cc_final: 0.5541 (tttp) REVERT: C 134 GLN cc_start: 0.5977 (mt0) cc_final: 0.5663 (mt0) REVERT: C 518 LEU cc_start: 0.1167 (OUTLIER) cc_final: 0.0942 (pp) REVERT: C 814 LYS cc_start: 0.6912 (tptt) cc_final: 0.6236 (tppt) REVERT: C 1031 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: C 1127 ASP cc_start: 0.7842 (m-30) cc_final: 0.7386 (p0) REVERT: E 26 LYS cc_start: 0.3189 (tptt) cc_final: 0.2651 (mmtt) REVERT: E 332 MET cc_start: 0.1680 (ttt) cc_final: 0.0051 (mmm) REVERT: E 531 GLN cc_start: 0.4092 (OUTLIER) cc_final: 0.3148 (tp40) REVERT: E 606 TRP cc_start: 0.3040 (OUTLIER) cc_final: 0.2806 (p-90) REVERT: H 59 ASN cc_start: 0.4503 (t0) cc_final: 0.3877 (p0) REVERT: H 81 MET cc_start: -0.1349 (mmm) cc_final: -0.1631 (tpp) REVERT: J 73 LEU cc_start: 0.1881 (tt) cc_final: 0.1606 (mt) REVERT: J 75 GLU cc_start: 0.1444 (pt0) cc_final: 0.0810 (tm-30) REVERT: J 270 MET cc_start: 0.0062 (tpp) cc_final: -0.2211 (tpp) REVERT: J 271 TRP cc_start: 0.2145 (m-90) cc_final: 0.0683 (t-100) REVERT: J 421 ILE cc_start: -0.1912 (OUTLIER) cc_final: -0.2167 (mm) REVERT: J 505 HIS cc_start: 0.1929 (m-70) cc_final: 0.1510 (m-70) REVERT: J 525 PHE cc_start: 0.0342 (m-80) cc_final: 0.0060 (m-80) REVERT: M 134 ASN cc_start: 0.4403 (m-40) cc_final: 0.3825 (t0) REVERT: M 144 LEU cc_start: 0.2826 (OUTLIER) cc_final: 0.2430 (tt) REVERT: M 270 MET cc_start: 0.0273 (tpp) cc_final: -0.1468 (tpp) REVERT: M 271 TRP cc_start: 0.1643 (m-90) cc_final: 0.0339 (m100) REVERT: M 360 MET cc_start: 0.3601 (mtp) cc_final: 0.0091 (ppp) REVERT: M 478 TRP cc_start: 0.0200 (m100) cc_final: -0.0223 (m100) REVERT: M 482 ARG cc_start: 0.4593 (mtt180) cc_final: 0.4289 (ttm-80) REVERT: M 504 PHE cc_start: 0.0193 (m-10) cc_final: -0.0348 (m-10) REVERT: N 111 PHE cc_start: 0.2832 (OUTLIER) cc_final: 0.2450 (m-80) outliers start: 140 outliers final: 115 residues processed: 435 average time/residue: 0.5089 time to fit residues: 389.7387 Evaluate side-chains 422 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 295 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 378 HIS Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 421 ILE Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 165 TRP Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 HIS Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 111 PHE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 1.9990 chunk 592 optimal weight: 2.9990 chunk 361 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 621 optimal weight: 20.0000 chunk 572 optimal weight: 2.9990 chunk 495 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 382 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN A1083 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 460 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 401 HIS J 578 ASN ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 GLN M 524 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.7538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 51201 Z= 0.201 Angle : 0.572 13.220 69696 Z= 0.284 Chirality : 0.045 0.354 7857 Planarity : 0.004 0.061 8961 Dihedral : 4.971 53.210 7779 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.56 % Allowed : 20.68 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -1.72 (0.10), residues: 6258 helix: -0.07 (0.13), residues: 1581 sheet: -0.40 (0.16), residues: 1098 loop : -1.96 (0.10), residues: 3579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 36 HIS 0.019 0.001 HIS M 378 PHE 0.032 0.001 PHE J 525 TYR 0.017 0.001 TYR M 183 ARG 0.004 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 304 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.4949 (mm) cc_final: 0.4456 (tp) REVERT: A 134 GLN cc_start: 0.6230 (mt0) cc_final: 0.5980 (mt0) REVERT: A 238 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5745 (p90) REVERT: A 814 LYS cc_start: 0.6764 (tptt) cc_final: 0.6328 (tppt) REVERT: A 969 ASN cc_start: 0.9135 (m110) cc_final: 0.8464 (m-40) REVERT: B 51 THR cc_start: 0.7979 (t) cc_final: 0.7754 (t) REVERT: B 129 LYS cc_start: 0.5826 (tttp) cc_final: 0.5568 (tmtm) REVERT: B 153 MET cc_start: 0.4124 (mmt) cc_final: 0.3508 (pmm) REVERT: B 177 MET cc_start: -0.1058 (mmt) cc_final: -0.1855 (ttt) REVERT: B 326 ILE cc_start: 0.6245 (OUTLIER) cc_final: 0.5948 (tp) REVERT: B 338 PHE cc_start: 0.5537 (OUTLIER) cc_final: 0.4365 (p90) REVERT: B 565 PHE cc_start: 0.7993 (m-80) cc_final: 0.7664 (m-10) REVERT: B 745 ASP cc_start: 0.7741 (m-30) cc_final: 0.6405 (t0) REVERT: B 820 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: B 1055 SER cc_start: 0.9007 (t) cc_final: 0.8718 (p) REVERT: B 1117 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 1130 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7983 (mm) REVERT: C 53 ASP cc_start: 0.6653 (m-30) cc_final: 0.6318 (m-30) REVERT: C 129 LYS cc_start: 0.5638 (tttp) cc_final: 0.5414 (tttp) REVERT: C 134 GLN cc_start: 0.5894 (mt0) cc_final: 0.5587 (mt0) REVERT: C 196 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.6850 (m110) REVERT: C 814 LYS cc_start: 0.6921 (tptt) cc_final: 0.6260 (tppt) REVERT: C 1031 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: E 26 LYS cc_start: 0.3187 (tptt) cc_final: 0.2651 (mmtt) REVERT: E 332 MET cc_start: 0.1534 (ttt) cc_final: 0.0584 (mmm) REVERT: E 531 GLN cc_start: 0.4082 (OUTLIER) cc_final: 0.3115 (tp40) REVERT: E 606 TRP cc_start: 0.3051 (OUTLIER) cc_final: 0.2823 (p-90) REVERT: J 73 LEU cc_start: 0.2387 (OUTLIER) cc_final: 0.2133 (mt) REVERT: J 75 GLU cc_start: 0.1436 (pt0) cc_final: 0.0804 (tm-30) REVERT: J 270 MET cc_start: 0.0080 (tpp) cc_final: -0.2181 (tpp) REVERT: J 271 TRP cc_start: 0.2165 (m-90) cc_final: 0.0678 (t-100) REVERT: J 505 HIS cc_start: 0.1762 (m-70) cc_final: 0.1366 (m-70) REVERT: J 546 ASN cc_start: 0.3251 (m-40) cc_final: 0.2383 (p0) REVERT: M 152 MET cc_start: -0.0164 (ppp) cc_final: -0.0411 (ppp) REVERT: M 271 TRP cc_start: 0.1418 (m-90) cc_final: 0.0507 (m-90) REVERT: M 360 MET cc_start: 0.3589 (mtp) cc_final: 0.0347 (ppp) REVERT: M 383 MET cc_start: 0.1169 (tmm) cc_final: 0.0866 (ttt) REVERT: M 478 TRP cc_start: 0.0202 (m100) cc_final: -0.0219 (m100) REVERT: M 482 ARG cc_start: 0.4508 (mtt180) cc_final: 0.4170 (ttm-80) REVERT: M 504 PHE cc_start: 0.0186 (m-10) cc_final: -0.0203 (m-10) REVERT: N 111 PHE cc_start: 0.2607 (OUTLIER) cc_final: 0.2287 (m-80) outliers start: 138 outliers final: 114 residues processed: 423 average time/residue: 0.4582 time to fit residues: 336.2390 Evaluate side-chains 417 residues out of total 5457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 291 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 378 HIS Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 165 TRP Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 HIS Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 111 PHE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.6980 chunk 527 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 456 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 495 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 509 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN M 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.202861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.189217 restraints weight = 167186.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.187182 restraints weight = 219202.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.184897 restraints weight = 188398.220| |-----------------------------------------------------------------------------| r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4573 r_free = 0.4573 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4573 r_free = 0.4573 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.4573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 moved from start: 0.7554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 51201 Z= 0.172 Angle : 0.558 12.928 69696 Z= 0.277 Chirality : 0.045 0.352 7857 Planarity : 0.004 0.060 8961 Dihedral : 4.803 52.132 7779 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.27 % Allowed : 20.99 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % 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: -1.61 (0.10), residues: 6258 helix: 0.04 (0.13), residues: 1578 sheet: -0.35 (0.16), residues: 1098 loop : -1.89 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 36 HIS 0.017 0.001 HIS M 378 PHE 0.039 0.001 PHE J 525 TYR 0.023 0.001 TYR J 515 ARG 0.005 0.000 ARG M 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8517.48 seconds wall clock time: 152 minutes 33.02 seconds (9153.02 seconds total)