Starting phenix.real_space_refine on Mon Jul 6 20:50:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ye9_33766/07_2026/7ye9_33766.cif" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 22320 2.51 5 N 5832 2.21 5 O 6903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 254 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35208 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "H" Number of atoms: 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: "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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 8 Time building chain proxies: 7.94, per 1000 atoms: 0.23 Number of scatterers: 35208 At special positions: 0 Unit cell: (211.2, 214.72, 197.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 6903 8.00 N 5832 7.00 C 22320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG 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=2.04 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 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 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 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.5 seconds 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8388 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 90 sheets defined 13.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 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: 3.518A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.906A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.527A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.918A 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: 3.818A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.686A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 777 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: 3.643A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 4.217A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.509A 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: 3.826A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.189A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.560A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.545A pdb=" N GLU A1144 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.525A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.778A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.065A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 777 removed outlier: 3.517A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.585A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.648A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 removed outlier: 4.190A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 857 " --> pdb=" O LYS B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.603A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.526A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.813A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.142A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1032 removed outlier: 3.653A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.501A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.541A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 777 Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.631A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.644A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 removed outlier: 4.190A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.557A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 949 through 966 removed outlier: 3.819A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.200A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.644A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.504A pdb=" N GLU L 129 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 130 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.224A 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: 3.750A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.068A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 200 No H-bonds generated for 'chain 'N' and resid 198 through 200' Processing helix chain 'O' and resid 129 through 133 removed outlier: 3.764A pdb=" N ASN O 133 " --> pdb=" O LEU O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 191 removed outlier: 4.203A 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: 8.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.851A 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: 3.643A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.968A 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: 8.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.851A 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: 3.643A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.688A 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: 4.328A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.371A 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: 3.696A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 158 removed outlier: 5.174A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.058A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.710A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.787A 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: 4.111A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.543A 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: 3.656A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.836A 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: 3.602A 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: 7.474A 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: 3.594A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.172A 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: 3.710A 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: 3.598A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.387A 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: 3.711A 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: 3.519A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.368A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.359A 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: 6.166A 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: 3.704A 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: 8.820A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.862A 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: 3.687A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.883A 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: 4.340A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.547A 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: 5.143A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.998A 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: 6.109A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.550A 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: 3.691A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.777A 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: 4.122A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.453A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.777A pdb=" N ARG B 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY N 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.521A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD6, 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=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.451A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.615A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.621A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, 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=AE2, first strand: chain 'B' and resid 724 through 727 removed outlier: 3.509A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 735 removed outlier: 4.335A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.680A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.812A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.033A 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: 3.724A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.650A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.727A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.964A 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) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 313 removed outlier: 4.093A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.525A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.815A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.596A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.418A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.568A 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: 7.125A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.633A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.731A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.731A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.467A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.689A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.205A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.531A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.531A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.808A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.758A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN H 210 " --> pdb=" O THR H 162 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AH1, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.882A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.882A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.973A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AH5, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.600A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.033A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.955A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 33 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 131 through 134 removed outlier: 3.673A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL G 192 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS G 175 " --> pdb=" O VAL G 192 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.868A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AI2, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.876A 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: 3.676A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.876A 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: 3.676A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.794A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AI6, first strand: chain 'I' and resid 150 through 154 removed outlier: 3.977A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 150 through 154 removed outlier: 3.977A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I 211 " --> pdb=" O TYR I 196 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 3 through 6 removed outlier: 4.411A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.357A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AJ1, 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=AJ2, first strand: chain 'N' and resid 131 through 134 removed outlier: 3.614A pdb=" N SER N 191 " --> pdb=" O CYS N 151 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL N 153 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU N 189 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP N 155 " --> pdb=" O TYR N 187 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR N 187 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 162 through 165 removed outlier: 3.737A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN N 210 " --> pdb=" O THR N 162 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL N 209 " --> pdb=" O VAL N 218 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL N 218 " --> pdb=" O VAL N 209 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'O' and resid 17 through 23 Processing sheet with id=AJ5, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.882A 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: 4.083A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.882A 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: 4.083A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 119 through 123 removed outlier: 3.960A pdb=" N PHE O 123 " --> pdb=" O VAL O 138 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA O 178 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER O 170 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 135 through 136 Processing sheet with id=AJ9, first strand: chain 'O' and resid 159 through 160 removed outlier: 4.606A pdb=" N TRP O 153 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR O 201 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS O 154 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL O 211 " --> pdb=" O TYR O 196 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.94 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11239 1.34 - 1.46: 7805 1.46 - 1.58: 16794 1.58 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 36027 Sorted by residual: bond pdb=" CA LYS A 528 " pdb=" C LYS A 528 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.28e-02 6.10e+03 1.27e+01 bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.328 1.354 -0.026 1.25e-02 6.40e+03 4.24e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 36022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 47819 1.42 - 2.84: 1084 2.84 - 4.26: 136 4.26 - 5.69: 25 5.69 - 7.11: 13 Bond angle restraints: 49077 Sorted by residual: angle pdb=" C ILE A 896 " pdb=" N PRO A 897 " pdb=" CA PRO A 897 " ideal model delta sigma weight residual 120.03 116.14 3.89 9.90e-01 1.02e+00 1.54e+01 angle pdb=" CA THR A 523 " pdb=" C THR A 523 " pdb=" N VAL A 524 " ideal model delta sigma weight residual 119.46 117.17 2.29 6.10e-01 2.69e+00 1.41e+01 angle pdb=" O GLY O 112 " pdb=" C GLY O 112 " pdb=" N GLN O 113 " ideal model delta sigma weight residual 122.41 125.88 -3.47 9.80e-01 1.04e+00 1.26e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.76 116.23 3.53 1.03e+00 9.43e-01 1.17e+01 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 105.48 6.86 2.04e+00 2.40e-01 1.13e+01 ... (remaining 49072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 19579 17.82 - 35.64: 1331 35.64 - 53.46: 249 53.46 - 71.27: 44 71.27 - 89.09: 34 Dihedral angle restraints: 21237 sinusoidal: 8142 harmonic: 13095 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.29 83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.66 82.34 1 1.00e+01 1.00e-02 8.32e+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 93.00 174.13 -81.13 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 21234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5007 0.068 - 0.136: 647 0.136 - 0.204: 10 0.204 - 0.272: 3 0.272 - 0.340: 3 Chirality restraints: 5670 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+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 -2.06 -0.34 2.00e-01 2.50e+01 2.86e+00 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 2.84e+00 ... (remaining 5667 not shown) Planarity restraints: 6336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 527 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO C 987 " 0.097 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 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 987 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.031 5.00e-02 4.00e+02 ... (remaining 6333 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1764 2.73 - 3.27: 31840 3.27 - 3.81: 55124 3.81 - 4.36: 63877 4.36 - 4.90: 111611 Nonbonded interactions: 264216 Sorted by model distance: nonbonded pdb=" OE2 GLU O 208 " pdb=" OG1 THR O 210 " model vdw 2.182 3.040 nonbonded pdb=" O PHE A 318 " pdb=" OG SER A 591 " model vdw 2.210 3.040 nonbonded pdb=" OG SER L 197 " pdb=" OE2 GLU L 208 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.259 3.040 ... (remaining 264211 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 35.010 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 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 0.049 36120 Z= 0.129 Angle : 0.510 9.426 49299 Z= 0.273 Chirality : 0.043 0.340 5670 Planarity : 0.004 0.059 6306 Dihedral : 12.413 89.093 12678 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 0.82 % Allowed : 2.76 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.10), residues: 4476 helix: -4.50 (0.07), residues: 555 sheet: -1.15 (0.15), residues: 1041 loop : -3.04 (0.09), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 194 TYR 0.005 0.000 TYR C 351 PHE 0.025 0.000 PHE A 392 TRP 0.004 0.000 TRP O 153 HIS 0.002 0.000 HIS N 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (36027) covalent geometry : angle 0.49775 / 0.27 (49077) SS BOND : bond 0.00221 / 0.14 ( 57) SS BOND : angle 1.23962 / 0.87 ( 114) hydrogen bonds : bond 0.29880 / 19.62 ( 970) hydrogen bonds : angle 9.57594 / 6.70 ( 2660) link_BETA1-4 : bond 0.00251 / 0.14 ( 6) link_BETA1-4 : angle 0.90776 / 0.57 ( 18) link_NAG-ASN : bond 0.00528 / 0.37 ( 30) link_NAG-ASN : angle 2.31757 / 1.61 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 534 time to evaluate : 1.354 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: A 52 GLN cc_start: 0.8516 (tt0) cc_final: 0.8263 (tp-100) REVERT: A 69 HIS cc_start: 0.3125 (t-170) cc_final: 0.2896 (t-170) REVERT: A 91 TYR cc_start: 0.7030 (t80) cc_final: 0.6269 (t80) REVERT: A 133 PHE cc_start: 0.5720 (m-80) cc_final: 0.5434 (m-80) REVERT: A 145 TYR cc_start: 0.4905 (t80) cc_final: 0.3821 (t80) REVERT: A 169 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6954 (tp30) REVERT: A 177 MET cc_start: 0.0619 (mmt) cc_final: 0.0314 (mmt) REVERT: A 191 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7613 (tp30) REVERT: A 203 ILE cc_start: 0.8656 (mt) cc_final: 0.8197 (pt) REVERT: A 208 THR cc_start: 0.7907 (m) cc_final: 0.7661 (t) REVERT: A 299 THR cc_start: 0.8475 (m) cc_final: 0.8114 (p) REVERT: A 309 GLU cc_start: 0.8298 (mp0) cc_final: 0.8095 (mm-30) REVERT: A 528 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6632 (tttm) REVERT: A 529 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6504 (tttt) REVERT: A 599 THR cc_start: 0.8136 (m) cc_final: 0.7740 (m) REVERT: A 612 TYR cc_start: 0.6503 (m-10) cc_final: 0.6226 (m-10) REVERT: A 747 THR cc_start: 0.8413 (m) cc_final: 0.8036 (p) REVERT: A 1019 ARG cc_start: 0.7266 (tpt-90) cc_final: 0.6966 (tpt170) REVERT: A 1077 THR cc_start: 0.7414 (t) cc_final: 0.7165 (m) REVERT: A 1111 GLU cc_start: 0.7520 (tp30) cc_final: 0.7308 (tm-30) REVERT: B 130 VAL cc_start: 0.7483 (t) cc_final: 0.7272 (t) REVERT: B 145 TYR cc_start: 0.6117 (t80) cc_final: 0.5189 (t80) REVERT: B 170 TYR cc_start: 0.7556 (t80) cc_final: 0.7149 (t80) REVERT: B 200 TYR cc_start: 0.7008 (m-10) cc_final: 0.6252 (m-80) REVERT: B 530 SER cc_start: 0.4115 (OUTLIER) cc_final: 0.3243 (m) REVERT: B 740 MET cc_start: 0.7241 (ttm) cc_final: 0.6878 (mtt) REVERT: B 776 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7432 (tptm) REVERT: B 983 ARG cc_start: 0.7541 (ptp-170) cc_final: 0.7022 (ptt180) REVERT: B 995 ARG cc_start: 0.8234 (mmt90) cc_final: 0.7964 (ttm110) REVERT: B 1111 GLU cc_start: 0.7240 (tp30) cc_final: 0.6882 (tm-30) REVERT: C 52 GLN cc_start: 0.9255 (tt0) cc_final: 0.8652 (tp-100) REVERT: C 101 ILE cc_start: 0.7811 (mp) cc_final: 0.7311 (mm) REVERT: C 173 GLN cc_start: 0.8018 (pm20) cc_final: 0.7816 (mm-40) REVERT: C 177 MET cc_start: 0.0211 (mmt) cc_final: -0.0145 (mmt) REVERT: C 200 TYR cc_start: 0.7263 (m-10) cc_final: 0.6720 (m-80) REVERT: C 203 ILE cc_start: 0.8591 (mt) cc_final: 0.8266 (pt) REVERT: C 235 ILE cc_start: 0.5137 (mt) cc_final: 0.4337 (mt) REVERT: C 286 THR cc_start: 0.8059 (m) cc_final: 0.7804 (p) REVERT: C 529 LYS cc_start: 0.5623 (mmtt) cc_final: 0.5245 (ttmt) REVERT: C 553 THR cc_start: 0.7367 (t) cc_final: 0.7163 (p) REVERT: C 697 MET cc_start: 0.7913 (ptm) cc_final: 0.7676 (ptm) REVERT: C 731 MET cc_start: 0.8526 (ptt) cc_final: 0.8269 (ptt) REVERT: C 751 ASN cc_start: 0.8375 (m-40) cc_final: 0.7708 (t0) REVERT: C 869 MET cc_start: 0.8016 (mtt) cc_final: 0.7632 (mtm) REVERT: C 902 MET cc_start: 0.4838 (tpp) cc_final: 0.4412 (tpp) REVERT: C 1047 TYR cc_start: 0.6146 (m-10) cc_final: 0.5816 (m-10) REVERT: H 158 PRO cc_start: 0.0833 (Cg_endo) cc_final: 0.0377 (Cg_exo) REVERT: L 94 ASP cc_start: 0.5996 (t0) cc_final: 0.5241 (p0) REVERT: G 74 LYS cc_start: 0.5055 (mmmt) cc_final: 0.3374 (tptm) REVERT: G 105 TYR cc_start: 0.2334 (m-80) cc_final: 0.1673 (p90) REVERT: I 102 PHE cc_start: 0.1387 (m-80) cc_final: 0.0956 (m-80) REVERT: I 108 LEU cc_start: 0.3383 (OUTLIER) cc_final: 0.3113 (mt) REVERT: I 110 VAL cc_start: 0.5604 (OUTLIER) cc_final: 0.5323 (t) REVERT: N 14 PRO cc_start: 0.3472 (Cg_endo) cc_final: 0.3253 (Cg_exo) REVERT: N 74 LYS cc_start: 0.4212 (mmmt) cc_final: 0.3228 (tttt) REVERT: N 158 PRO cc_start: 0.2163 (Cg_endo) cc_final: 0.1815 (Cg_exo) REVERT: O 108 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3843 (tp) outliers start: 30 outliers final: 6 residues processed: 558 average time/residue: 0.2313 time to fit residues: 209.0746 Evaluate side-chains 261 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.5980 chunk 424 optimal weight: 30.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 99 ASN A 137 ASN A 146 HIS A 164 ASN A 173 GLN A 183 GLN A 196 ASN A 218 GLN A 271 GLN A 409 GLN A 440 ASN A 474 GLN A 493 GLN A 506 GLN A 901 GLN A 926 GLN A 992 GLN A1023 ASN A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 81 ASN B 99 ASN B 137 ASN B 146 HIS B 173 GLN B 183 GLN B 196 ASN B 218 GLN B 271 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 580 GLN B 751 ASN B 920 GLN B 926 GLN B 992 GLN B1023 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 52 GLN C 99 ASN C 137 ASN C 165 ASN C 183 GLN C 196 ASN C 218 GLN C 271 GLN C 314 GLN C 448 ASN C 450 ASN C 474 GLN C 493 GLN C 556 ASN C 580 GLN C 613 GLN C 920 GLN C 926 GLN C 992 GLN C1054 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN H 175 HIS ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 189 GLN G 39 GLN G 203 GLN N 3 GLN ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 ASN O 189 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.129073 restraints weight = 226155.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.127162 restraints weight = 306035.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.125763 restraints weight = 220429.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.124854 restraints weight = 234896.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.123526 restraints weight = 225610.917| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4112 r_free = 0.4112 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4112 r_free = 0.4112 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 36120 Z= 0.220 Angle : 0.691 12.784 49299 Z= 0.350 Chirality : 0.048 0.319 5670 Planarity : 0.005 0.062 6306 Dihedral : 3.521 20.386 4842 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.13 % Allowed : 6.03 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.11), residues: 4476 helix: -0.84 (0.18), residues: 624 sheet: -0.62 (0.15), residues: 1062 loop : -2.54 (0.10), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 815 TYR 0.038 0.002 TYR A 313 PHE 0.029 0.002 PHE B 906 TRP 0.013 0.002 TRP B 436 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (36027) covalent geometry : angle 0.67927 / 0.35 (49077) SS BOND : bond 0.01878 / 1.39 ( 57) SS BOND : angle 1.63800 / 1.13 ( 114) hydrogen bonds : bond 0.04259 / 2.78 ( 970) hydrogen bonds : angle 5.80707 / 3.94 ( 2660) link_BETA1-4 : bond 0.00485 / 0.24 ( 6) link_BETA1-4 : angle 1.05165 / 0.69 ( 18) link_NAG-ASN : bond 0.00513 / 0.35 ( 30) link_NAG-ASN : angle 2.56239 / 1.78 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.6394 (mppt) cc_final: 0.5743 (tttt) REVERT: A 902 MET cc_start: 0.8151 (tpp) cc_final: 0.7834 (tpp) REVERT: A 1050 MET cc_start: 0.7817 (ptm) cc_final: 0.7556 (ptp) REVERT: B 153 MET cc_start: 0.6170 (mpp) cc_final: 0.5628 (mpp) REVERT: B 541 PHE cc_start: 0.7302 (p90) cc_final: 0.7046 (p90) REVERT: B 869 MET cc_start: 0.7124 (mtm) cc_final: 0.6838 (mtm) REVERT: C 153 MET cc_start: 0.5997 (mpp) cc_final: 0.5387 (mpp) REVERT: C 200 TYR cc_start: 0.6289 (m-10) cc_final: 0.6081 (m-80) REVERT: C 731 MET cc_start: 0.9018 (ptt) cc_final: 0.8801 (ptm) REVERT: L 28 ASN cc_start: 0.1258 (t0) cc_final: 0.0476 (p0) REVERT: L 119 SER cc_start: 0.5695 (m) cc_final: 0.5283 (p) REVERT: G 105 TYR cc_start: 0.2558 (m-80) cc_final: 0.1791 (p90) REVERT: N 158 PRO cc_start: 0.1122 (Cg_endo) cc_final: 0.0351 (Cg_exo) outliers start: 3 outliers final: 0 residues processed: 268 average time/residue: 0.2090 time to fit residues: 95.0357 Evaluate side-chains 165 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 57 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 442 optimal weight: 10.0000 chunk 415 optimal weight: 30.0000 chunk 320 optimal weight: 30.0000 chunk 390 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1113 GLN B 49 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 394 ASN B 901 GLN B1048 HIS B1064 HIS C 52 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1023 ASN C1064 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN G 175 HIS I 39 GLN N 43 GLN O 189 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.137451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.121094 restraints weight = 211653.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.118550 restraints weight = 305627.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.117595 restraints weight = 256123.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.116793 restraints weight = 241178.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.115420 restraints weight = 233126.921| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36120 Z= 0.241 Angle : 0.701 11.687 49299 Z= 0.352 Chirality : 0.048 0.331 5670 Planarity : 0.005 0.081 6306 Dihedral : 4.057 21.908 4842 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.26 % Allowed : 4.51 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.11), residues: 4476 helix: 0.16 (0.21), residues: 636 sheet: -0.36 (0.15), residues: 1098 loop : -2.43 (0.10), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 328 TYR 0.032 0.002 TYR O 145 PHE 0.028 0.002 PHE A 543 TRP 0.030 0.002 TRP C 886 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (36027) covalent geometry : angle 0.68712 / 0.35 (49077) SS BOND : bond 0.00473 / 0.30 ( 57) SS BOND : angle 1.60767 / 1.16 ( 114) hydrogen bonds : bond 0.05112 / 3.30 ( 970) hydrogen bonds : angle 5.63746 / 3.82 ( 2660) link_BETA1-4 : bond 0.00529 / 0.31 ( 6) link_BETA1-4 : angle 0.97697 / 0.64 ( 18) link_NAG-ASN : bond 0.00572 / 0.39 ( 30) link_NAG-ASN : angle 2.81354 / 1.95 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.6763 (mppt) cc_final: 0.6143 (ttmt) REVERT: B 153 MET cc_start: 0.6516 (mpp) cc_final: 0.6083 (mpp) REVERT: B 200 TYR cc_start: 0.6682 (m-80) cc_final: 0.6450 (m-10) REVERT: B 697 MET cc_start: 0.7571 (ptm) cc_final: 0.7358 (ptm) REVERT: B 900 MET cc_start: 0.8523 (mmm) cc_final: 0.7978 (mtp) REVERT: C 153 MET cc_start: 0.6036 (mpp) cc_final: 0.5498 (mpp) REVERT: C 189 LEU cc_start: 0.9309 (tp) cc_final: 0.8834 (tp) REVERT: C 191 GLU cc_start: 0.7448 (mp0) cc_final: 0.7183 (mp0) REVERT: C 529 LYS cc_start: 0.4610 (mmtt) cc_final: 0.4277 (ttmt) REVERT: C 786 LYS cc_start: 0.8578 (mttt) cc_final: 0.8267 (mmmm) REVERT: L 119 SER cc_start: 0.5593 (m) cc_final: 0.5192 (p) REVERT: G 105 TYR cc_start: 0.1841 (m-80) cc_final: 0.1282 (p90) outliers start: 8 outliers final: 4 residues processed: 196 average time/residue: 0.2087 time to fit residues: 70.2208 Evaluate side-chains 132 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 429 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 409 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1054 GLN B 49 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN N 43 GLN O 189 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.137648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.121431 restraints weight = 238890.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.118679 restraints weight = 298574.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.117709 restraints weight = 243015.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.116879 restraints weight = 242368.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.115523 restraints weight = 233442.450| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36120 Z= 0.140 Angle : 0.552 13.592 49299 Z= 0.274 Chirality : 0.045 0.485 5670 Planarity : 0.004 0.071 6306 Dihedral : 3.643 20.172 4842 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.12), residues: 4476 helix: 0.77 (0.21), residues: 630 sheet: -0.39 (0.16), residues: 1089 loop : -2.23 (0.10), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.014 0.001 TYR A 313 PHE 0.020 0.001 PHE B 133 TRP 0.027 0.001 TRP B 436 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (36027) covalent geometry : angle 0.53577 / 0.27 (49077) SS BOND : bond 0.00389 / 0.25 ( 57) SS BOND : angle 1.34986 / 0.90 ( 114) hydrogen bonds : bond 0.03604 / 2.34 ( 970) hydrogen bonds : angle 5.15990 / 3.49 ( 2660) link_BETA1-4 : bond 0.00306 / 0.14 ( 6) link_BETA1-4 : angle 0.76937 / 0.49 ( 18) link_NAG-ASN : bond 0.00659 / 0.50 ( 30) link_NAG-ASN : angle 2.81765 / 1.99 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.6437 (mppt) cc_final: 0.6039 (ttmt) REVERT: B 153 MET cc_start: 0.6503 (mpp) cc_final: 0.6014 (mpp) REVERT: C 731 MET cc_start: 0.9001 (ptt) cc_final: 0.8698 (ptt) REVERT: H 48 MET cc_start: -0.0459 (mpp) cc_final: -0.0716 (mpp) REVERT: L 119 SER cc_start: 0.5341 (m) cc_final: 0.5100 (p) REVERT: G 48 MET cc_start: -0.0169 (mpp) cc_final: -0.1338 (mtm) REVERT: G 105 TYR cc_start: 0.1905 (m-80) cc_final: 0.1291 (p90) REVERT: N 123 SER cc_start: -0.1745 (p) cc_final: -0.2376 (t) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.2120 time to fit residues: 65.4313 Evaluate side-chains 127 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 221 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 377 optimal weight: 50.0000 chunk 219 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 319 optimal weight: 0.0470 chunk 171 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 901 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 751 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN I 39 GLN I 172 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.132556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.107240 restraints weight = 220179.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.103172 restraints weight = 314112.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101192 restraints weight = 201882.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.100547 restraints weight = 204094.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.100365 restraints weight = 164227.721| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 36120 Z= 0.257 Angle : 0.720 11.518 49299 Z= 0.358 Chirality : 0.048 0.319 5670 Planarity : 0.005 0.066 6306 Dihedral : 4.409 22.133 4842 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.12), residues: 4476 helix: 0.61 (0.21), residues: 612 sheet: -0.35 (0.15), residues: 1134 loop : -2.25 (0.10), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 905 TYR 0.020 0.002 TYR C 917 PHE 0.035 0.003 PHE C 275 TRP 0.017 0.002 TRP C 886 HIS 0.011 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.26 (36027) covalent geometry : angle 0.70425 / 0.35 (49077) SS BOND : bond 0.00493 / 0.32 ( 57) SS BOND : angle 1.63413 / 1.14 ( 114) hydrogen bonds : bond 0.04343 / 2.81 ( 970) hydrogen bonds : angle 5.55888 / 3.77 ( 2660) link_BETA1-4 : bond 0.00626 / 0.31 ( 6) link_BETA1-4 : angle 1.08764 / 0.74 ( 18) link_NAG-ASN : bond 0.00696 / 0.49 ( 30) link_NAG-ASN : angle 3.19860 / 2.27 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 1.285 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 170 TYR cc_start: 0.7118 (t80) cc_final: 0.6914 (t80) REVERT: A 869 MET cc_start: 0.7602 (mtm) cc_final: 0.7161 (mtm) REVERT: A 895 GLN cc_start: 0.8414 (pt0) cc_final: 0.8180 (pt0) REVERT: A 906 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: A 1050 MET cc_start: 0.8157 (ptp) cc_final: 0.7937 (ptp) REVERT: B 153 MET cc_start: 0.6862 (mpp) cc_final: 0.6106 (mpp) REVERT: C 731 MET cc_start: 0.9000 (ptt) cc_final: 0.8690 (ptt) REVERT: C 900 MET cc_start: 0.8262 (mmm) cc_final: 0.7896 (mtp) REVERT: H 48 MET cc_start: 0.1262 (mpp) cc_final: -0.0204 (mtp) REVERT: L 119 SER cc_start: 0.5710 (m) cc_final: 0.5315 (p) REVERT: G 48 MET cc_start: -0.0174 (mpp) cc_final: -0.1258 (mtm) REVERT: N 116 ARG cc_start: 0.3139 (tmt-80) cc_final: 0.2045 (tmm160) outliers start: 5 outliers final: 2 residues processed: 169 average time/residue: 0.2015 time to fit residues: 58.7419 Evaluate side-chains 120 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 10 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 152 optimal weight: 4.9990 chunk 361 optimal weight: 0.4980 chunk 441 optimal weight: 40.0000 chunk 241 optimal weight: 3.9990 chunk 322 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 420 optimal weight: 2.9990 chunk 390 optimal weight: 40.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 HIS ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.133139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.106315 restraints weight = 201443.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.101256 restraints weight = 293589.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.099233 restraints weight = 199849.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098750 restraints weight = 178684.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098631 restraints weight = 154045.757| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36120 Z= 0.147 Angle : 0.571 10.408 49299 Z= 0.284 Chirality : 0.045 0.346 5670 Planarity : 0.004 0.062 6306 Dihedral : 3.974 23.662 4842 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.10 % Allowed : 1.44 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4476 helix: 1.04 (0.22), residues: 615 sheet: -0.31 (0.15), residues: 1116 loop : -2.12 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 905 TYR 0.018 0.001 TYR B 453 PHE 0.021 0.002 PHE B 133 TRP 0.017 0.001 TRP C 436 HIS 0.014 0.001 HIS N 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (36027) covalent geometry : angle 0.55516 / 0.28 (49077) SS BOND : bond 0.00375 / 0.21 ( 57) SS BOND : angle 1.47391 / 1.01 ( 114) hydrogen bonds : bond 0.03528 / 2.29 ( 970) hydrogen bonds : angle 5.17259 / 3.51 ( 2660) link_BETA1-4 : bond 0.00357 / 0.15 ( 6) link_BETA1-4 : angle 0.80756 / 0.53 ( 18) link_NAG-ASN : bond 0.00488 / 0.34 ( 30) link_NAG-ASN : angle 2.76654 / 1.93 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.337 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 133 PHE cc_start: 0.5077 (m-80) cc_final: 0.4870 (m-80) REVERT: A 153 MET cc_start: 0.6930 (mpp) cc_final: 0.6724 (mpp) REVERT: A 170 TYR cc_start: 0.7157 (t80) cc_final: 0.6886 (t80) REVERT: A 529 LYS cc_start: 0.6552 (mppt) cc_final: 0.5627 (ttmt) REVERT: A 740 MET cc_start: 0.8178 (mtt) cc_final: 0.7416 (mtm) REVERT: A 869 MET cc_start: 0.7864 (mtm) cc_final: 0.7519 (mtm) REVERT: A 895 GLN cc_start: 0.8537 (pt0) cc_final: 0.8333 (pt0) REVERT: A 1141 LEU cc_start: 0.8385 (mm) cc_final: 0.8056 (mt) REVERT: B 153 MET cc_start: 0.6841 (mpp) cc_final: 0.6327 (mpp) REVERT: B 242 LEU cc_start: 0.6847 (mt) cc_final: 0.6599 (mt) REVERT: B 921 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7615 (mttp) REVERT: C 101 ILE cc_start: 0.8106 (mp) cc_final: 0.7895 (tp) REVERT: C 153 MET cc_start: 0.5740 (mpp) cc_final: 0.5445 (mpp) REVERT: C 248 TYR cc_start: 0.4795 (m-10) cc_final: 0.4499 (p90) REVERT: C 731 MET cc_start: 0.9000 (ptt) cc_final: 0.8751 (ptt) REVERT: C 900 MET cc_start: 0.8127 (mmm) cc_final: 0.7866 (mtp) REVERT: H 48 MET cc_start: 0.1434 (mpp) cc_final: 0.0824 (tpp) REVERT: H 81 MET cc_start: -0.1334 (ttm) cc_final: -0.1756 (mtm) REVERT: L 119 SER cc_start: 0.5677 (m) cc_final: 0.5342 (p) REVERT: G 48 MET cc_start: -0.0202 (mpp) cc_final: -0.0868 (mtm) REVERT: N 116 ARG cc_start: 0.3023 (tmt-80) cc_final: 0.1811 (tmm160) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.1973 time to fit residues: 58.2460 Evaluate side-chains 121 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 386 optimal weight: 20.0000 chunk 416 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 330 optimal weight: 0.0770 chunk 323 optimal weight: 10.0000 chunk 318 optimal weight: 40.0000 chunk 55 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 895 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 580 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN H 100 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.131158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.105236 restraints weight = 183723.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.100678 restraints weight = 280750.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.097844 restraints weight = 210961.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098017 restraints weight = 201434.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097775 restraints weight = 151896.498| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 36120 Z= 0.251 Angle : 0.701 9.867 49299 Z= 0.348 Chirality : 0.048 0.360 5670 Planarity : 0.005 0.082 6306 Dihedral : 4.495 24.787 4842 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.10 % Allowed : 1.62 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.12), residues: 4476 helix: 0.52 (0.21), residues: 639 sheet: -0.29 (0.16), residues: 1059 loop : -2.15 (0.11), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 905 TYR 0.017 0.002 TYR B 453 PHE 0.035 0.002 PHE N 64 TRP 0.018 0.002 TRP N 47 HIS 0.012 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (36027) covalent geometry : angle 0.68455 / 0.34 (49077) SS BOND : bond 0.00480 / 0.29 ( 57) SS BOND : angle 1.72728 / 1.20 ( 114) hydrogen bonds : bond 0.04115 / 2.67 ( 970) hydrogen bonds : angle 5.52073 / 3.74 ( 2660) link_BETA1-4 : bond 0.00595 / 0.31 ( 6) link_BETA1-4 : angle 1.04264 / 0.69 ( 18) link_NAG-ASN : bond 0.00582 / 0.40 ( 30) link_NAG-ASN : angle 3.14759 / 2.19 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 1.328 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: 0.6773 (mpp) cc_final: 0.6548 (mpp) REVERT: A 529 LYS cc_start: 0.6814 (mppt) cc_final: 0.5959 (ttmt) REVERT: A 895 GLN cc_start: 0.8496 (pt0) cc_final: 0.8090 (pt0) REVERT: A 1050 MET cc_start: 0.8042 (ptp) cc_final: 0.7730 (ptp) REVERT: B 153 MET cc_start: 0.6856 (mpp) cc_final: 0.6267 (mpp) REVERT: C 153 MET cc_start: 0.5786 (mpp) cc_final: 0.5433 (mpp) REVERT: C 731 MET cc_start: 0.8968 (ptt) cc_final: 0.8659 (ptt) REVERT: C 900 MET cc_start: 0.8061 (mmm) cc_final: 0.7785 (mtp) REVERT: H 48 MET cc_start: 0.1484 (mpp) cc_final: -0.0010 (mtp) REVERT: H 80 TYR cc_start: 0.4370 (m-80) cc_final: 0.4152 (m-80) REVERT: L 119 SER cc_start: 0.5571 (m) cc_final: 0.5191 (p) REVERT: G 48 MET cc_start: -0.0075 (mpp) cc_final: -0.0611 (mtm) REVERT: N 116 ARG cc_start: 0.3094 (tmt-80) cc_final: 0.1657 (tmm160) outliers start: 2 outliers final: 2 residues processed: 161 average time/residue: 0.2050 time to fit residues: 56.7210 Evaluate side-chains 114 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 10 optimal weight: 0.5980 chunk 255 optimal weight: 30.0000 chunk 238 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 389 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 239 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.132552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.109607 restraints weight = 236239.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.105618 restraints weight = 290798.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.102553 restraints weight = 244239.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.103065 restraints weight = 232343.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.102657 restraints weight = 169203.850| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36120 Z= 0.112 Angle : 0.555 9.105 49299 Z= 0.276 Chirality : 0.045 0.347 5670 Planarity : 0.004 0.074 6306 Dihedral : 3.976 22.099 4842 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.08 % Allowed : 0.70 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4476 helix: 1.04 (0.21), residues: 633 sheet: -0.25 (0.16), residues: 1071 loop : -2.01 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.017 0.001 TYR B 453 PHE 0.021 0.001 PHE B 275 TRP 0.023 0.001 TRP B 436 HIS 0.016 0.001 HIS O 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (36027) covalent geometry : angle 0.53879 / 0.27 (49077) SS BOND : bond 0.00363 / 0.23 ( 57) SS BOND : angle 1.51839 / 1.02 ( 114) hydrogen bonds : bond 0.03384 / 2.19 ( 970) hydrogen bonds : angle 5.04287 / 3.43 ( 2660) link_BETA1-4 : bond 0.00354 / 0.17 ( 6) link_BETA1-4 : angle 0.86662 / 0.55 ( 18) link_NAG-ASN : bond 0.00511 / 0.35 ( 30) link_NAG-ASN : angle 2.71403 / 1.88 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.096 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 153 MET cc_start: 0.6447 (mpp) cc_final: 0.6161 (mpp) REVERT: A 276 LEU cc_start: 0.8850 (tp) cc_final: 0.8546 (tp) REVERT: A 323 THR cc_start: 0.7088 (p) cc_final: 0.6756 (t) REVERT: A 342 PHE cc_start: 0.3774 (m-10) cc_final: 0.3484 (m-10) REVERT: A 529 LYS cc_start: 0.6753 (mppt) cc_final: 0.5909 (ttmt) REVERT: A 895 GLN cc_start: 0.8465 (pt0) cc_final: 0.8190 (pt0) REVERT: A 1050 MET cc_start: 0.7804 (ptp) cc_final: 0.7568 (ptp) REVERT: B 153 MET cc_start: 0.6694 (mpp) cc_final: 0.6060 (mpp) REVERT: C 153 MET cc_start: 0.5595 (mpp) cc_final: 0.5178 (mpp) REVERT: C 248 TYR cc_start: 0.3752 (p90) cc_final: 0.3472 (p90) REVERT: H 48 MET cc_start: 0.1479 (mpp) cc_final: 0.0111 (mtt) REVERT: H 81 MET cc_start: -0.0226 (ttm) cc_final: -0.0873 (mtm) REVERT: L 119 SER cc_start: 0.5468 (m) cc_final: 0.5185 (p) REVERT: G 48 MET cc_start: -0.0471 (mpp) cc_final: -0.0814 (mtm) REVERT: N 116 ARG cc_start: 0.2668 (tmt-80) cc_final: 0.1138 (tmm160) REVERT: O 5 THR cc_start: 0.6034 (p) cc_final: 0.5784 (p) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1993 time to fit residues: 55.4091 Evaluate side-chains 126 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 42 optimal weight: 0.0970 chunk 164 optimal weight: 0.7980 chunk 253 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 427 optimal weight: 7.9990 chunk 222 optimal weight: 0.0980 chunk 51 optimal weight: 0.0770 chunk 260 optimal weight: 0.1980 chunk 172 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 189 GLN I 39 GLN I 172 GLN ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.133870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.108221 restraints weight = 210953.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104407 restraints weight = 293131.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.101584 restraints weight = 192312.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.101834 restraints weight = 187792.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.101889 restraints weight = 143859.705| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36120 Z= 0.092 Angle : 0.517 8.923 49299 Z= 0.259 Chirality : 0.044 0.340 5670 Planarity : 0.004 0.069 6306 Dihedral : 3.609 18.576 4842 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.08 % Allowed : 0.36 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.12), residues: 4476 helix: 1.38 (0.22), residues: 633 sheet: -0.09 (0.16), residues: 1032 loop : -1.90 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 355 TYR 0.019 0.001 TYR B 453 PHE 0.023 0.001 PHE C 329 TRP 0.063 0.002 TRP I 37 HIS 0.004 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (36027) covalent geometry : angle 0.50374 / 0.26 (49077) SS BOND : bond 0.00247 / 0.16 ( 57) SS BOND : angle 1.16351 / 0.78 ( 114) hydrogen bonds : bond 0.03049 / 1.97 ( 970) hydrogen bonds : angle 4.74003 / 3.23 ( 2660) link_BETA1-4 : bond 0.00539 / 0.28 ( 6) link_BETA1-4 : angle 0.82503 / 0.53 ( 18) link_NAG-ASN : bond 0.00538 / 0.37 ( 30) link_NAG-ASN : angle 2.48527 / 1.72 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.221 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 153 MET cc_start: 0.6571 (mpp) cc_final: 0.6241 (mpp) REVERT: A 276 LEU cc_start: 0.8925 (tp) cc_final: 0.8565 (tp) REVERT: A 529 LYS cc_start: 0.6754 (mppt) cc_final: 0.5733 (ttmt) REVERT: A 895 GLN cc_start: 0.8491 (pt0) cc_final: 0.8103 (pt0) REVERT: A 1050 MET cc_start: 0.7981 (ptp) cc_final: 0.7608 (ptp) REVERT: A 1141 LEU cc_start: 0.8353 (mm) cc_final: 0.7928 (mt) REVERT: B 153 MET cc_start: 0.6617 (mpp) cc_final: 0.5839 (mpp) REVERT: B 177 MET cc_start: 0.2961 (mmm) cc_final: 0.2752 (mmp) REVERT: B 242 LEU cc_start: 0.6940 (mt) cc_final: 0.6684 (mt) REVERT: C 153 MET cc_start: 0.6038 (mpp) cc_final: 0.5731 (mpp) REVERT: C 248 TYR cc_start: 0.3862 (p90) cc_final: 0.3508 (p90) REVERT: C 731 MET cc_start: 0.8869 (ptt) cc_final: 0.8571 (ptt) REVERT: H 48 MET cc_start: 0.1530 (mpp) cc_final: 0.0967 (tpp) REVERT: H 81 MET cc_start: -0.0892 (ttm) cc_final: -0.1541 (mtm) REVERT: L 119 SER cc_start: 0.5704 (m) cc_final: 0.5233 (p) REVERT: G 48 MET cc_start: -0.0648 (mpp) cc_final: -0.0994 (mtm) REVERT: N 116 ARG cc_start: 0.2591 (tmt-80) cc_final: 0.1129 (tmm160) REVERT: O 5 THR cc_start: 0.6530 (p) cc_final: 0.6300 (p) REVERT: O 6 GLN cc_start: 0.2329 (tp-100) cc_final: 0.1161 (tp-100) outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.1994 time to fit residues: 58.2796 Evaluate side-chains 125 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 341 optimal weight: 4.9990 chunk 279 optimal weight: 0.0000 chunk 405 optimal weight: 0.8980 chunk 320 optimal weight: 0.0010 chunk 439 optimal weight: 40.0000 chunk 209 optimal weight: 8.9990 chunk 399 optimal weight: 40.0000 chunk 408 optimal weight: 30.0000 chunk 203 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN I 39 GLN I 172 GLN ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.132584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.108132 restraints weight = 204727.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.102874 restraints weight = 267366.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099576 restraints weight = 224707.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100326 restraints weight = 192443.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.099811 restraints weight = 146523.062| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36120 Z= 0.133 Angle : 0.537 9.071 49299 Z= 0.268 Chirality : 0.044 0.333 5670 Planarity : 0.004 0.069 6306 Dihedral : 3.661 18.113 4842 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.10 % Allowed : 0.23 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.12), residues: 4476 helix: 1.31 (0.22), residues: 633 sheet: -0.06 (0.16), residues: 1068 loop : -1.86 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.021 0.001 TYR B1138 PHE 0.023 0.001 PHE B 275 TRP 0.032 0.002 TRP I 37 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (36027) covalent geometry : angle 0.52368 / 0.26 (49077) SS BOND : bond 0.00271 / 0.17 ( 57) SS BOND : angle 1.25394 / 0.84 ( 114) hydrogen bonds : bond 0.03183 / 2.06 ( 970) hydrogen bonds : angle 4.75753 / 3.22 ( 2660) link_BETA1-4 : bond 0.00352 / 0.17 ( 6) link_BETA1-4 : angle 0.87987 / 0.59 ( 18) link_NAG-ASN : bond 0.00452 / 0.31 ( 30) link_NAG-ASN : angle 2.55209 / 1.77 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.041 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: 0.6479 (mpp) cc_final: 0.6128 (mpp) REVERT: A 276 LEU cc_start: 0.8989 (tp) cc_final: 0.8623 (tp) REVERT: A 323 THR cc_start: 0.7138 (p) cc_final: 0.6816 (t) REVERT: A 529 LYS cc_start: 0.6566 (mppt) cc_final: 0.5702 (ttmt) REVERT: A 869 MET cc_start: 0.8104 (mtm) cc_final: 0.7652 (mtm) REVERT: A 895 GLN cc_start: 0.8494 (pt0) cc_final: 0.8232 (pt0) REVERT: A 1050 MET cc_start: 0.8074 (ptp) cc_final: 0.7865 (ptp) REVERT: A 1141 LEU cc_start: 0.8393 (mm) cc_final: 0.7894 (mt) REVERT: B 153 MET cc_start: 0.6589 (mpp) cc_final: 0.5848 (mpp) REVERT: B 242 LEU cc_start: 0.6737 (mt) cc_final: 0.6495 (mt) REVERT: C 153 MET cc_start: 0.6037 (mpp) cc_final: 0.5739 (mpp) REVERT: C 248 TYR cc_start: 0.3779 (p90) cc_final: 0.3508 (p90) REVERT: C 731 MET cc_start: 0.8991 (ptt) cc_final: 0.8758 (ptt) REVERT: H 48 MET cc_start: 0.1529 (mpp) cc_final: 0.0099 (mtt) REVERT: H 81 MET cc_start: -0.0443 (ttm) cc_final: -0.1337 (mtm) REVERT: L 119 SER cc_start: 0.5697 (m) cc_final: 0.5224 (p) REVERT: N 116 ARG cc_start: 0.2398 (tmt-80) cc_final: 0.1015 (tmm160) REVERT: O 6 GLN cc_start: 0.2551 (tp-100) cc_final: 0.1227 (tp-100) outliers start: 2 outliers final: 0 residues processed: 152 average time/residue: 0.1816 time to fit residues: 47.6171 Evaluate side-chains 117 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 422 optimal weight: 4.9990 chunk 387 optimal weight: 10.0000 chunk 353 optimal weight: 0.8980 chunk 116 optimal weight: 0.1980 chunk 144 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 263 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN I 39 GLN N 166 ASN ** N 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.133552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.109109 restraints weight = 276514.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.107991 restraints weight = 341886.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104537 restraints weight = 189944.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.104904 restraints weight = 200814.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.103971 restraints weight = 173106.826| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36120 Z= 0.089 Angle : 0.500 8.792 49299 Z= 0.249 Chirality : 0.044 0.334 5670 Planarity : 0.004 0.067 6306 Dihedral : 3.473 16.589 4842 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.12), residues: 4476 helix: 1.50 (0.22), residues: 642 sheet: -0.10 (0.16), residues: 1095 loop : -1.75 (0.11), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.018 0.001 TYR B 453 PHE 0.021 0.001 PHE B 275 TRP 0.032 0.002 TRP B 436 HIS 0.004 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (36027) covalent geometry : angle 0.48766 / 0.25 (49077) SS BOND : bond 0.00227 / 0.15 ( 57) SS BOND : angle 1.09281 / 0.73 ( 114) hydrogen bonds : bond 0.02954 / 1.91 ( 970) hydrogen bonds : angle 4.55916 / 3.10 ( 2660) link_BETA1-4 : bond 0.00406 / 0.19 ( 6) link_BETA1-4 : angle 0.79747 / 0.52 ( 18) link_NAG-ASN : bond 0.00521 / 0.36 ( 30) link_NAG-ASN : angle 2.39180 / 1.65 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5512.26 seconds wall clock time: 96 minutes 31.69 seconds (5791.69 seconds total)