Starting phenix.real_space_refine on Tue Aug 26 06:53:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgl_34741/08_2025/8hgl_34741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgl_34741/08_2025/8hgl_34741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hgl_34741/08_2025/8hgl_34741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgl_34741/08_2025/8hgl_34741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgl_34741/08_2025/8hgl_34741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgl_34741/08_2025/8hgl_34741.map" } resolution = 2.9 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= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21669 2.51 5 N 5631 2.21 5 O 6723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34170 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "B" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 7.12, per 1000 atoms: 0.21 Number of scatterers: 34170 At special positions: 0 Unit cell: (138.414, 138.414, 260.406, 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 147 16.00 O 6723 8.00 N 5631 7.00 C 21669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 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=2.04 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=2.04 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 H 20 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 20 " - pdb=" SG CYS F 94 " distance=2.04 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG E1301 " - " ASN E 282 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 122 " " NAG E1304 " - " ASN E 165 " " NAG E1305 " - " ASN E 234 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1098 " " NAG E1312 " - " ASN E1134 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN E 331 " " NAG S 1 " - " ASN E 343 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.4 microseconds 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 77 sheets defined 20.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.718A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.020A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.709A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.879A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.557A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.506A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.706A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.765A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'H' and resid 26 through 29 removed outlier: 3.820A pdb=" N TYR H 29 " --> pdb=" O THR H 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 29' Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.994A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.001A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.774A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.563A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.889A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.563A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.552A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.541A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.667A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.787A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.974A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.738A pdb=" N LYS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.697A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.008A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.506A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.555A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.863A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.516A pdb=" N ILE E 870 " --> pdb=" O THR E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 removed outlier: 3.559A pdb=" N ALA E 890 " --> pdb=" O THR E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 removed outlier: 4.011A pdb=" N SER E 939 " --> pdb=" O GLN E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 967 removed outlier: 3.891A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 956 " --> pdb=" O VAL E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.511A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.738A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 993 " --> pdb=" O ALA E 989 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 996 " --> pdb=" O GLN E 992 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E1006 " --> pdb=" O GLN E1002 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR E1007 " --> pdb=" O SER E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.968A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.778A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.325A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 4.124A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.605A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.286A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.741A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.519A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.925A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.576A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.642A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.227A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.638A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.611A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AC2, first strand: chain 'H' and resid 8 through 10 removed outlier: 6.782A pdb=" N VAL H 32 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP H 48 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 8 through 10 Processing sheet with id=AC4, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.774A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.774A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.133A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.615A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.561A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.170A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.572A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 119 through 122 removed outlier: 3.547A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.935A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.304A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 574 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.689A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.269A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.660A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.049A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.648A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AF1, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.799A pdb=" N VAL C 32 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP C 48 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP C 34 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AF3, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.773A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.773A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AF6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.171A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.638A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AG1, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.912A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 93 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 90 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 47 through 51 removed outlier: 4.180A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AG4, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.607A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 241 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU E 118 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 130 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.969A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.767A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AG8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AG9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 711 through 713 removed outlier: 3.670A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.516A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.668A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AH5, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AH6, first strand: chain 'F' and resid 8 through 10 removed outlier: 6.793A pdb=" N VAL F 32 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP F 48 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.500A pdb=" N LEU F 110 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.771A pdb=" N GLY F 147 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.771A pdb=" N GLY F 147 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.506A pdb=" N THR F 159 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AI3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.141A pdb=" N LEU G 11 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.626A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN G 161 " --> pdb=" O THR G 179 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 154 through 155 1363 hydrogen bonds defined for protein. 3633 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: 8.97 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10766 1.34 - 1.46: 7769 1.46 - 1.58: 16220 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 34935 Sorted by residual: bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" C1 NAG E1304 " pdb=" O5 NAG E1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 ... (remaining 34930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 45919 1.64 - 3.28: 1432 3.28 - 4.92: 160 4.92 - 6.56: 41 6.56 - 8.20: 7 Bond angle restraints: 47559 Sorted by residual: angle pdb=" C ASN E 122 " pdb=" CA ASN E 122 " pdb=" CB ASN E 122 " ideal model delta sigma weight residual 111.68 103.48 8.20 1.68e+00 3.54e-01 2.38e+01 angle pdb=" C ASN E 234 " pdb=" CA ASN E 234 " pdb=" CB ASN E 234 " ideal model delta sigma weight residual 110.74 118.02 -7.28 1.61e+00 3.86e-01 2.05e+01 angle pdb=" C LYS F 151 " pdb=" N ASP F 152 " pdb=" CA ASP F 152 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.82e+01 angle pdb=" C LYS C 151 " pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.81e+01 angle pdb=" C LYS H 151 " pdb=" N ASP H 152 " pdb=" CA ASP H 152 " ideal model delta sigma weight residual 122.82 128.51 -5.69 1.42e+00 4.96e-01 1.61e+01 ... (remaining 47554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 20300 22.06 - 44.12: 1092 44.12 - 66.18: 184 66.18 - 88.24: 55 88.24 - 110.31: 26 Dihedral angle restraints: 21657 sinusoidal: 9132 harmonic: 12525 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.87 66.87 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.33 66.33 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.30 63.30 1 1.00e+01 1.00e-02 5.29e+01 ... (remaining 21654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4830 0.077 - 0.154: 722 0.154 - 0.231: 21 0.231 - 0.308: 2 0.308 - 0.384: 2 Chirality restraints: 5577 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG E1303 " pdb=" ND2 ASN E 122 " pdb=" C2 NAG E1303 " pdb=" O5 NAG E1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5574 not shown) Planarity restraints: 6114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " -0.006 2.00e-02 2.50e+03 5.11e-02 3.26e+01 pdb=" CG ASN E 122 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG E1303 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.003 2.00e-02 2.50e+03 4.63e-02 2.68e+01 pdb=" CG ASN E 234 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " 0.004 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" CG ASN B 717 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.044 2.00e-02 2.50e+03 ... (remaining 6111 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2072 2.73 - 3.27: 33123 3.27 - 3.81: 52689 3.81 - 4.36: 61870 4.36 - 4.90: 110122 Nonbonded interactions: 259876 Sorted by model distance: nonbonded pdb=" OD1 ASN L 139 " pdb=" OG1 THR L 173 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASN D 139 " pdb=" OG1 THR D 173 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASN G 139 " pdb=" OG1 THR G 173 " model vdw 2.196 3.040 nonbonded pdb=" OG SER D 66 " pdb=" OG1 THR D 73 " model vdw 2.198 3.040 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.201 3.040 ... (remaining 259871 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 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 32.650 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.006 0.052 35049 Z= 0.273 Angle : 0.739 17.049 47847 Z= 0.372 Chirality : 0.050 0.384 5577 Planarity : 0.004 0.047 6066 Dihedral : 14.180 110.306 13449 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.39 (0.13), residues: 4257 helix: 1.28 (0.20), residues: 699 sheet: 0.26 (0.14), residues: 1311 loop : -1.09 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 815 TYR 0.044 0.002 TYR B 160 PHE 0.064 0.002 PHE E 906 TRP 0.051 0.002 TRP B 886 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00640 (34935) covalent geometry : angle 0.67179 (47559) SS BOND : bond 0.00343 ( 54) SS BOND : angle 1.24969 ( 108) hydrogen bonds : bond 0.16317 ( 1300) hydrogen bonds : angle 6.86346 ( 3633) link_BETA1-4 : bond 0.01258 ( 12) link_BETA1-4 : angle 4.67766 ( 36) link_NAG-ASN : bond 0.00917 ( 48) link_NAG-ASN : angle 5.06438 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.850 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: H 111 TRP cc_start: 0.2761 (m100) cc_final: 0.1056 (m100) REVERT: D 174 TYR cc_start: 0.5804 (m-80) cc_final: 0.5570 (m-80) REVERT: F 29 TYR cc_start: 0.6080 (m-80) cc_final: 0.5744 (m-10) REVERT: G 174 TYR cc_start: 0.5838 (m-80) cc_final: 0.5567 (m-80) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.6468 time to fit residues: 208.7903 Evaluate side-chains 147 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 50.0000 chunk 155 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 388 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 139 ASN B 66 HIS B 211 ASN B 239 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN D 27 GLN E 196 ASN E 239 GLN E 493 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.134325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072046 restraints weight = 89548.218| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.65 r_work: 0.2811 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35049 Z= 0.149 Angle : 0.672 14.135 47847 Z= 0.327 Chirality : 0.046 0.277 5577 Planarity : 0.005 0.064 6066 Dihedral : 8.880 79.661 5889 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 0.94 % Allowed : 6.47 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.18 (0.13), residues: 4257 helix: 1.53 (0.20), residues: 711 sheet: 0.43 (0.14), residues: 1311 loop : -1.02 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 65 TYR 0.032 0.001 TYR D 141 PHE 0.024 0.002 PHE E 168 TRP 0.021 0.001 TRP E 64 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00334 (34935) covalent geometry : angle 0.61988 (47559) SS BOND : bond 0.00268 ( 54) SS BOND : angle 0.92790 ( 108) hydrogen bonds : bond 0.05591 ( 1300) hydrogen bonds : angle 5.56907 ( 3633) link_BETA1-4 : bond 0.01063 ( 12) link_BETA1-4 : angle 3.52502 ( 36) link_NAG-ASN : bond 0.00828 ( 48) link_NAG-ASN : angle 4.38221 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8335 (pt) cc_final: 0.7821 (tp) REVERT: A 374 PHE cc_start: 0.8275 (p90) cc_final: 0.7967 (p90) REVERT: A 453 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7289 (p90) REVERT: A 869 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8308 (mtt) REVERT: L 32 ASN cc_start: 0.8097 (t0) cc_final: 0.7825 (p0) REVERT: E 160 TYR cc_start: 0.4810 (t80) cc_final: 0.4362 (t80) REVERT: E 242 LEU cc_start: 0.8286 (pt) cc_final: 0.7825 (tp) REVERT: E 374 PHE cc_start: 0.8352 (p90) cc_final: 0.8082 (p90) REVERT: F 78 TYR cc_start: 0.8058 (m-80) cc_final: 0.7826 (m-80) REVERT: G 50 TYR cc_start: 0.7701 (p90) cc_final: 0.7500 (p90) outliers start: 35 outliers final: 11 residues processed: 181 average time/residue: 0.5498 time to fit residues: 120.4179 Evaluate side-chains 145 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 346 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 38 GLN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.132930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072260 restraints weight = 89546.889| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.88 r_work: 0.2750 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 35049 Z= 0.197 Angle : 0.673 13.789 47847 Z= 0.329 Chirality : 0.047 0.254 5577 Planarity : 0.004 0.049 6066 Dihedral : 7.687 59.281 5889 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 1.48 % Allowed : 8.94 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.19 (0.13), residues: 4257 helix: 1.49 (0.20), residues: 714 sheet: 0.39 (0.14), residues: 1347 loop : -1.02 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 109 TYR 0.022 0.002 TYR A1067 PHE 0.022 0.002 PHE E 906 TRP 0.016 0.001 TRP B 64 HIS 0.010 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00478 (34935) covalent geometry : angle 0.62370 (47559) SS BOND : bond 0.00243 ( 54) SS BOND : angle 0.96620 ( 108) hydrogen bonds : bond 0.06077 ( 1300) hydrogen bonds : angle 5.39178 ( 3633) link_BETA1-4 : bond 0.01045 ( 12) link_BETA1-4 : angle 3.47259 ( 36) link_NAG-ASN : bond 0.00801 ( 48) link_NAG-ASN : angle 4.29993 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 1.275 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 374 PHE cc_start: 0.8305 (p90) cc_final: 0.7983 (p90) REVERT: A 1029 MET cc_start: 0.9142 (tpp) cc_final: 0.8925 (tpp) REVERT: L 50 TYR cc_start: 0.7811 (p90) cc_final: 0.7505 (p90) REVERT: B 374 PHE cc_start: 0.8281 (p90) cc_final: 0.7832 (p90) REVERT: B 455 LEU cc_start: 0.6991 (mt) cc_final: 0.6669 (mt) REVERT: E 374 PHE cc_start: 0.8419 (p90) cc_final: 0.8011 (p90) REVERT: F 49 MET cc_start: 0.7135 (pmt) cc_final: 0.5857 (pp-130) outliers start: 55 outliers final: 17 residues processed: 179 average time/residue: 0.5817 time to fit residues: 129.6335 Evaluate side-chains 139 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 33 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 45 optimal weight: 3.9990 chunk 401 optimal weight: 30.0000 chunk 124 optimal weight: 40.0000 chunk 3 optimal weight: 4.9990 chunk 368 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 374 optimal weight: 0.7980 chunk 308 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 194 optimal weight: 0.0770 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN H 41 GLN L 32 ASN L 138 ASN B 66 HIS B 360 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 762 GLN D 32 ASN E 115 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN G 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.134975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.072740 restraints weight = 89215.927| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.73 r_work: 0.2863 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35049 Z= 0.107 Angle : 0.608 13.498 47847 Z= 0.292 Chirality : 0.045 0.246 5577 Planarity : 0.004 0.039 6066 Dihedral : 6.825 58.362 5889 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.29 % Allowed : 10.39 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.10 (0.13), residues: 4257 helix: 1.88 (0.20), residues: 717 sheet: 0.55 (0.14), residues: 1317 loop : -0.85 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 109 TYR 0.031 0.001 TYR A 453 PHE 0.029 0.001 PHE E 168 TRP 0.012 0.001 TRP E 64 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00226 (34935) covalent geometry : angle 0.55820 (47559) SS BOND : bond 0.00279 ( 54) SS BOND : angle 0.80418 ( 108) hydrogen bonds : bond 0.04246 ( 1300) hydrogen bonds : angle 5.00885 ( 3633) link_BETA1-4 : bond 0.01251 ( 12) link_BETA1-4 : angle 3.39955 ( 36) link_NAG-ASN : bond 0.00823 ( 48) link_NAG-ASN : angle 4.09181 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8460 (p90) cc_final: 0.8078 (p90) REVERT: A 387 LEU cc_start: 0.8708 (tp) cc_final: 0.8116 (mm) REVERT: A 464 PHE cc_start: 0.7862 (m-80) cc_final: 0.7134 (m-80) REVERT: L 50 TYR cc_start: 0.7873 (p90) cc_final: 0.7654 (p90) REVERT: B 374 PHE cc_start: 0.8641 (p90) cc_final: 0.8266 (p90) REVERT: B 390 LEU cc_start: 0.8027 (mm) cc_final: 0.7730 (OUTLIER) REVERT: C 29 TYR cc_start: 0.5935 (m-10) cc_final: 0.5715 (m-10) REVERT: E 242 LEU cc_start: 0.8211 (pt) cc_final: 0.7762 (tp) REVERT: E 374 PHE cc_start: 0.8425 (p90) cc_final: 0.7970 (p90) REVERT: F 49 MET cc_start: 0.7155 (pmt) cc_final: 0.5873 (tmt) outliers start: 48 outliers final: 15 residues processed: 166 average time/residue: 0.4830 time to fit residues: 100.6147 Evaluate side-chains 130 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 283 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 375 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 360 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN H 41 GLN L 32 ASN L 138 ASN L 167 GLN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 32 ASN E 66 HIS E 196 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.133398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.070602 restraints weight = 89645.137| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.68 r_work: 0.2794 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35049 Z= 0.168 Angle : 0.638 14.074 47847 Z= 0.309 Chirality : 0.046 0.252 5577 Planarity : 0.004 0.051 6066 Dihedral : 6.776 58.461 5889 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.32 % Allowed : 11.35 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.01 (0.13), residues: 4257 helix: 1.81 (0.20), residues: 714 sheet: 0.41 (0.14), residues: 1368 loop : -0.88 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 55 TYR 0.036 0.001 TYR B 160 PHE 0.021 0.001 PHE A 377 TRP 0.013 0.001 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00406 (34935) covalent geometry : angle 0.58780 (47559) SS BOND : bond 0.00222 ( 54) SS BOND : angle 0.88114 ( 108) hydrogen bonds : bond 0.05339 ( 1300) hydrogen bonds : angle 5.05279 ( 3633) link_BETA1-4 : bond 0.01031 ( 12) link_BETA1-4 : angle 3.32626 ( 36) link_NAG-ASN : bond 0.00721 ( 48) link_NAG-ASN : angle 4.21044 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.894 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 374 PHE cc_start: 0.8451 (p90) cc_final: 0.8042 (p90) REVERT: A 387 LEU cc_start: 0.8745 (tp) cc_final: 0.8218 (mm) REVERT: A 464 PHE cc_start: 0.8009 (m-80) cc_final: 0.7297 (m-80) REVERT: A 869 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: L 50 TYR cc_start: 0.7910 (p90) cc_final: 0.7691 (p90) REVERT: B 374 PHE cc_start: 0.8688 (p90) cc_final: 0.8233 (p90) REVERT: B 455 LEU cc_start: 0.6845 (mt) cc_final: 0.6312 (mt) REVERT: E 66 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.6163 (t-90) REVERT: E 374 PHE cc_start: 0.8510 (p90) cc_final: 0.8026 (p90) REVERT: F 49 MET cc_start: 0.7186 (pmt) cc_final: 0.6129 (pp-130) outliers start: 49 outliers final: 22 residues processed: 162 average time/residue: 0.5196 time to fit residues: 105.3717 Evaluate side-chains 139 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 344 optimal weight: 0.0970 chunk 103 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 361 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 325 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.0010 chunk 244 optimal weight: 0.4980 chunk 300 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 32 ASN L 138 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.134005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073440 restraints weight = 89025.323| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.01 r_work: 0.2853 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35049 Z= 0.126 Angle : 0.614 14.115 47847 Z= 0.296 Chirality : 0.045 0.482 5577 Planarity : 0.004 0.040 6066 Dihedral : 6.636 57.774 5889 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.26 % Allowed : 12.00 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.09 (0.13), residues: 4257 helix: 1.89 (0.20), residues: 717 sheet: 0.49 (0.14), residues: 1338 loop : -0.84 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.028 0.001 TYR B 160 PHE 0.020 0.001 PHE E 133 TRP 0.026 0.001 TRP E 64 HIS 0.021 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00289 (34935) covalent geometry : angle 0.56541 (47559) SS BOND : bond 0.00226 ( 54) SS BOND : angle 0.76741 ( 108) hydrogen bonds : bond 0.04747 ( 1300) hydrogen bonds : angle 4.94789 ( 3633) link_BETA1-4 : bond 0.01084 ( 12) link_BETA1-4 : angle 3.29795 ( 36) link_NAG-ASN : bond 0.00747 ( 48) link_NAG-ASN : angle 4.05824 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 1.342 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 374 PHE cc_start: 0.8486 (p90) cc_final: 0.8060 (p90) REVERT: A 387 LEU cc_start: 0.8728 (tp) cc_final: 0.8297 (tm) REVERT: A 464 PHE cc_start: 0.7990 (m-80) cc_final: 0.7257 (m-80) REVERT: L 50 TYR cc_start: 0.7901 (p90) cc_final: 0.7681 (p90) REVERT: B 374 PHE cc_start: 0.8805 (p90) cc_final: 0.8311 (p90) REVERT: E 117 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7674 (tt) REVERT: E 374 PHE cc_start: 0.8557 (p90) cc_final: 0.8066 (p90) REVERT: F 49 MET cc_start: 0.7139 (pmt) cc_final: 0.6017 (tmt) outliers start: 47 outliers final: 25 residues processed: 153 average time/residue: 0.4909 time to fit residues: 94.5109 Evaluate side-chains 139 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 210 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 216 optimal weight: 0.5980 chunk 310 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 chunk 378 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 32 ASN L 138 ASN L 139 ASN L 167 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.134441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.070565 restraints weight = 89489.411| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.00 r_work: 0.2876 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35049 Z= 0.111 Angle : 0.596 14.903 47847 Z= 0.286 Chirality : 0.044 0.338 5577 Planarity : 0.004 0.038 6066 Dihedral : 6.481 58.934 5889 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.18 % Allowed : 12.51 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.19 (0.13), residues: 4257 helix: 2.02 (0.20), residues: 717 sheet: 0.58 (0.14), residues: 1332 loop : -0.81 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 55 TYR 0.023 0.001 TYR B 160 PHE 0.031 0.001 PHE A 168 TRP 0.011 0.001 TRP C 48 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00249 (34935) covalent geometry : angle 0.54624 (47559) SS BOND : bond 0.00276 ( 54) SS BOND : angle 0.74613 ( 108) hydrogen bonds : bond 0.04317 ( 1300) hydrogen bonds : angle 4.81538 ( 3633) link_BETA1-4 : bond 0.01099 ( 12) link_BETA1-4 : angle 3.24576 ( 36) link_NAG-ASN : bond 0.00754 ( 48) link_NAG-ASN : angle 4.04225 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.893 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 374 PHE cc_start: 0.8455 (p90) cc_final: 0.8107 (p90) REVERT: A 387 LEU cc_start: 0.8738 (tp) cc_final: 0.8304 (tm) REVERT: A 464 PHE cc_start: 0.8035 (m-80) cc_final: 0.7308 (m-80) REVERT: A 740 MET cc_start: 0.9143 (tpp) cc_final: 0.8889 (ttt) REVERT: L 50 TYR cc_start: 0.7967 (p90) cc_final: 0.7752 (p90) REVERT: L 106 GLU cc_start: 0.3818 (pt0) cc_final: 0.3566 (tt0) REVERT: L 141 TYR cc_start: 0.3803 (t80) cc_final: 0.3531 (t80) REVERT: B 374 PHE cc_start: 0.8779 (p90) cc_final: 0.8207 (p90) REVERT: C 72 MET cc_start: 0.6535 (mpt) cc_final: 0.5062 (mmt) REVERT: E 117 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7692 (tt) REVERT: E 374 PHE cc_start: 0.8592 (p90) cc_final: 0.8020 (p90) REVERT: E 390 LEU cc_start: 0.7927 (mt) cc_final: 0.7600 (mt) outliers start: 44 outliers final: 27 residues processed: 163 average time/residue: 0.4934 time to fit residues: 100.1529 Evaluate side-chains 151 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 128 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 385 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 136 optimal weight: 50.0000 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN E 360 ASN ** E 501 ASN ** 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 = 0.4293 r_free = 0.4293 target = 0.134004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071326 restraints weight = 89172.009| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.65 r_work: 0.2817 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35049 Z= 0.136 Angle : 0.610 13.501 47847 Z= 0.295 Chirality : 0.045 0.311 5577 Planarity : 0.004 0.069 6066 Dihedral : 6.413 58.134 5889 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.15 % Allowed : 12.86 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.16 (0.13), residues: 4257 helix: 1.98 (0.20), residues: 717 sheet: 0.55 (0.14), residues: 1362 loop : -0.83 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 55 TYR 0.038 0.001 TYR B 160 PHE 0.028 0.001 PHE B 168 TRP 0.011 0.001 TRP C 48 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00321 (34935) covalent geometry : angle 0.56231 (47559) SS BOND : bond 0.00222 ( 54) SS BOND : angle 0.75772 ( 108) hydrogen bonds : bond 0.04728 ( 1300) hydrogen bonds : angle 4.84151 ( 3633) link_BETA1-4 : bond 0.01054 ( 12) link_BETA1-4 : angle 3.25957 ( 36) link_NAG-ASN : bond 0.00706 ( 48) link_NAG-ASN : angle 4.01819 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 1.195 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 374 PHE cc_start: 0.8435 (p90) cc_final: 0.8087 (p90) REVERT: A 387 LEU cc_start: 0.8739 (tp) cc_final: 0.8353 (tm) REVERT: A 464 PHE cc_start: 0.8026 (m-80) cc_final: 0.7335 (m-80) REVERT: A 740 MET cc_start: 0.9064 (tpp) cc_final: 0.8779 (ttt) REVERT: L 50 TYR cc_start: 0.7942 (p90) cc_final: 0.7720 (p90) REVERT: L 106 GLU cc_start: 0.3812 (pt0) cc_final: 0.3557 (tt0) REVERT: L 124 GLU cc_start: 0.5363 (pm20) cc_final: 0.4730 (pp20) REVERT: L 141 TYR cc_start: 0.3803 (t80) cc_final: 0.3431 (t80) REVERT: B 374 PHE cc_start: 0.8790 (p90) cc_final: 0.8334 (m-10) REVERT: C 72 MET cc_start: 0.6469 (mpt) cc_final: 0.5053 (mmt) REVERT: E 117 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7565 (tt) REVERT: E 374 PHE cc_start: 0.8570 (p90) cc_final: 0.8019 (p90) REVERT: E 390 LEU cc_start: 0.7913 (mt) cc_final: 0.7580 (mt) REVERT: F 49 MET cc_start: 0.7329 (pmt) cc_final: 0.5955 (tmt) outliers start: 43 outliers final: 32 residues processed: 160 average time/residue: 0.5251 time to fit residues: 103.6395 Evaluate side-chains 154 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 426 optimal weight: 40.0000 chunk 3 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 420 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 138 ASN E 66 HIS E 196 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.131522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.070216 restraints weight = 88506.020| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.65 r_work: 0.2714 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 35049 Z= 0.296 Angle : 0.718 14.035 47847 Z= 0.354 Chirality : 0.049 0.270 5577 Planarity : 0.005 0.076 6066 Dihedral : 6.694 59.813 5889 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.15 % Allowed : 13.18 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.17 (0.13), residues: 4257 helix: 1.54 (0.20), residues: 711 sheet: 0.31 (0.14), residues: 1338 loop : -0.94 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1107 TYR 0.049 0.002 TYR B 160 PHE 0.031 0.002 PHE E 168 TRP 0.025 0.002 TRP B 64 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00727 (34935) covalent geometry : angle 0.67166 (47559) SS BOND : bond 0.00239 ( 54) SS BOND : angle 1.05023 ( 108) hydrogen bonds : bond 0.06825 ( 1300) hydrogen bonds : angle 5.21486 ( 3633) link_BETA1-4 : bond 0.00910 ( 12) link_BETA1-4 : angle 3.54956 ( 36) link_NAG-ASN : bond 0.00734 ( 48) link_NAG-ASN : angle 4.26435 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 1.371 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 374 PHE cc_start: 0.8353 (p90) cc_final: 0.8021 (p90) REVERT: A 387 LEU cc_start: 0.8829 (tp) cc_final: 0.8540 (tm) REVERT: A 464 PHE cc_start: 0.8115 (m-80) cc_final: 0.7545 (m-80) REVERT: A 740 MET cc_start: 0.9101 (tpp) cc_final: 0.8802 (ttt) REVERT: A 869 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: L 50 TYR cc_start: 0.7967 (p90) cc_final: 0.7746 (p90) REVERT: B 374 PHE cc_start: 0.8728 (p90) cc_final: 0.8288 (m-10) REVERT: B 786 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8410 (pmtt) REVERT: C 72 MET cc_start: 0.6549 (mpt) cc_final: 0.4924 (mmt) REVERT: E 374 PHE cc_start: 0.8439 (p90) cc_final: 0.7961 (p90) REVERT: E 390 LEU cc_start: 0.8071 (mt) cc_final: 0.7742 (mt) REVERT: F 49 MET cc_start: 0.7331 (pmt) cc_final: 0.5977 (tmt) outliers start: 43 outliers final: 27 residues processed: 147 average time/residue: 0.5151 time to fit residues: 95.5146 Evaluate side-chains 140 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 152 optimal weight: 5.9990 chunk 69 optimal weight: 0.0000 chunk 183 optimal weight: 8.9990 chunk 287 optimal weight: 0.9990 chunk 248 optimal weight: 50.0000 chunk 218 optimal weight: 0.7980 chunk 153 optimal weight: 0.0570 chunk 204 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 361 optimal weight: 0.7980 overall best weight: 0.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN L 32 ASN L 138 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.134285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071782 restraints weight = 89211.914| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.65 r_work: 0.2839 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35049 Z= 0.111 Angle : 0.613 13.620 47847 Z= 0.295 Chirality : 0.044 0.263 5577 Planarity : 0.004 0.068 6066 Dihedral : 6.353 58.772 5889 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.94 % Allowed : 13.71 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.11 (0.13), residues: 4257 helix: 1.90 (0.20), residues: 717 sheet: 0.49 (0.14), residues: 1332 loop : -0.80 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 408 TYR 0.022 0.001 TYR B 160 PHE 0.033 0.001 PHE B 168 TRP 0.016 0.001 TRP C 34 HIS 0.003 0.000 HIS E1088 Details of bonding type rmsd covalent geometry : bond 0.00241 (34935) covalent geometry : angle 0.56512 (47559) SS BOND : bond 0.00242 ( 54) SS BOND : angle 0.73734 ( 108) hydrogen bonds : bond 0.04335 ( 1300) hydrogen bonds : angle 4.82722 ( 3633) link_BETA1-4 : bond 0.01198 ( 12) link_BETA1-4 : angle 3.26879 ( 36) link_NAG-ASN : bond 0.00755 ( 48) link_NAG-ASN : angle 4.01298 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 1.070 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 374 PHE cc_start: 0.8476 (p90) cc_final: 0.8057 (p90) REVERT: A 387 LEU cc_start: 0.8816 (tp) cc_final: 0.8486 (tm) REVERT: A 464 PHE cc_start: 0.8032 (m-80) cc_final: 0.7390 (m-80) REVERT: A 492 LEU cc_start: 0.8583 (mp) cc_final: 0.8202 (tp) REVERT: A 740 MET cc_start: 0.9039 (tpp) cc_final: 0.8739 (ttt) REVERT: L 30 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6762 (p0) REVERT: L 50 TYR cc_start: 0.7883 (p90) cc_final: 0.7641 (p90) REVERT: B 374 PHE cc_start: 0.8754 (p90) cc_final: 0.8308 (m-10) REVERT: C 49 MET cc_start: 0.5569 (mpt) cc_final: 0.4275 (tmm) REVERT: C 72 MET cc_start: 0.6419 (mpt) cc_final: 0.4998 (mmt) REVERT: D 30 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6713 (p0) REVERT: E 374 PHE cc_start: 0.8622 (p90) cc_final: 0.8056 (p90) REVERT: E 390 LEU cc_start: 0.7897 (mt) cc_final: 0.7536 (mt) REVERT: F 49 MET cc_start: 0.7336 (pmt) cc_final: 0.5884 (tmt) outliers start: 35 outliers final: 23 residues processed: 143 average time/residue: 0.4936 time to fit residues: 88.5709 Evaluate side-chains 136 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 167 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 242 optimal weight: 0.2980 chunk 189 optimal weight: 2.9990 chunk 411 optimal weight: 40.0000 chunk 70 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 356 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.133916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071392 restraints weight = 88990.026| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.60 r_work: 0.2822 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35049 Z= 0.121 Angle : 0.609 13.512 47847 Z= 0.294 Chirality : 0.044 0.262 5577 Planarity : 0.004 0.064 6066 Dihedral : 6.307 58.136 5889 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.78 % Allowed : 13.74 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.17 (0.13), residues: 4257 helix: 1.98 (0.20), residues: 717 sheet: 0.46 (0.14), residues: 1371 loop : -0.76 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 65 TYR 0.030 0.001 TYR E 160 PHE 0.031 0.001 PHE E 168 TRP 0.016 0.001 TRP C 34 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00278 (34935) covalent geometry : angle 0.56158 (47559) SS BOND : bond 0.00224 ( 54) SS BOND : angle 0.75906 ( 108) hydrogen bonds : bond 0.04531 ( 1300) hydrogen bonds : angle 4.79125 ( 3633) link_BETA1-4 : bond 0.01069 ( 12) link_BETA1-4 : angle 3.24284 ( 36) link_NAG-ASN : bond 0.00696 ( 48) link_NAG-ASN : angle 3.99889 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14926.93 seconds wall clock time: 253 minutes 39.23 seconds (15219.23 seconds total)