Starting phenix.real_space_refine on Mon Jul 6 09:33:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hgl_34741/07_2026/8hgl_34741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgl_34741/07_2026/8hgl_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_34741/07_2026/8hgl_34741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgl_34741/07_2026/8hgl_34741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgl_34741/07_2026/8hgl_34741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgl_34741/07_2026/8hgl_34741.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hgl_34741/07_2026/8hgl_34741.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hgl_34741/07_2026/8hgl_34741.cif" } 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-dev-6108/lib/python3.11/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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 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 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 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 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 chiralities: 12 Time building chain proxies: 6.76, per 1000 atoms: 0.20 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: 2.57 Conformation dependent library (CDL) restraints added in 939.6 milliseconds 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: 1.49 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: 9.86 Time building geometry restraints manager: 3.34 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 - 17.99: 18738 17.99 - 35.98: 1391 35.98 - 53.96: 176 53.96 - 71.95: 59 71.95 - 89.94: 33 Dihedral angle restraints: 20397 sinusoidal: 7872 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 20394 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: 0.04 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: 3.530 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.460 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.130 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 13.073 89.939 12189 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 are 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/Z covalent geometry : bond 0.00640 / 0.27 (34935) covalent geometry : angle 0.67179 / 0.36 (47559) SS BOND : bond 0.00343 / 0.24 ( 54) SS BOND : angle 1.24969 / 0.81 ( 108) hydrogen bonds : bond 0.16317 / 10.35 ( 1300) hydrogen bonds : angle 6.86346 / 4.70 ( 3633) link_BETA1-4 : bond 0.01258 / 0.78 ( 12) link_BETA1-4 : angle 4.67766 / 3.08 ( 36) link_NAG-ASN : bond 0.00917 / 0.53 ( 48) link_NAG-ASN : angle 5.06438 / 3.20 ( 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 : 1.250 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: 0.5803 (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: 0.7135 time to fit residues: 232.7641 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 : 1.374 ------------------------------------------------------------------------------- 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... 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 = 0.4299 r_free = 0.4299 target = 0.134338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.071999 restraints weight = 89523.461| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.60 r_work: 0.2825 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35049 Z= 0.148 Angle : 0.664 14.133 47847 Z= 0.325 Chirality : 0.046 0.271 5577 Planarity : 0.005 0.066 6066 Dihedral : 4.478 28.501 4629 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 0.94 % Allowed : 6.60 % Favored : 92.46 % 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 are not related in a simple way. whole: -0.17 (0.13), residues: 4257 helix: 1.54 (0.20), residues: 711 sheet: 0.44 (0.14), residues: 1311 loop : -1.02 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 109 TYR 0.028 0.001 TYR D 141 PHE 0.024 0.002 PHE E 906 TRP 0.020 0.001 TRP E 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (34935) covalent geometry : angle 0.61368 / 0.31 (47559) SS BOND : bond 0.00263 / 0.17 ( 54) SS BOND : angle 0.93680 / 0.60 ( 108) hydrogen bonds : bond 0.05570 / 3.63 ( 1300) hydrogen bonds : angle 5.55494 / 3.80 ( 3633) link_BETA1-4 : bond 0.01108 / 0.65 ( 12) link_BETA1-4 : angle 3.30968 / 2.17 ( 36) link_NAG-ASN : bond 0.00789 / 0.47 ( 48) link_NAG-ASN : angle 4.32063 / 2.83 ( 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 198 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 1.407 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: 0.8296 (pt) cc_final: 0.7811 (tp) REVERT: A 374 PHE cc_start: 0.8291 (p90) cc_final: 0.7999 (p90) REVERT: A 453 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7176 (p90) REVERT: L 32 ASN cc_start: 0.8085 (t0) cc_final: 0.7804 (p0) REVERT: E 160 TYR cc_start: 0.4797 (t80) cc_final: 0.4356 (t80) REVERT: E 242 LEU cc_start: 0.8242 (pt) cc_final: 0.7810 (tp) REVERT: E 374 PHE cc_start: 0.8374 (p90) cc_final: 0.8107 (p90) REVERT: F 78 TYR cc_start: 0.8061 (m-80) cc_final: 0.7802 (m-80) REVERT: G 174 TYR cc_start: 0.5414 (m-80) cc_final: 0.5176 (m-80) outliers start: 35 outliers final: 11 residues processed: 183 average time/residue: 0.6843 time to fit residues: 151.7650 Evaluate side-chains 146 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 128 optimal weight: 20.0000 chunk 254 optimal weight: 40.0000 chunk 8 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 346 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN 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 360 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.132071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071082 restraints weight = 89374.142| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 4.87 r_work: 0.2699 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 35049 Z= 0.300 Angle : 0.741 13.857 47847 Z= 0.368 Chirality : 0.049 0.241 5577 Planarity : 0.005 0.053 6066 Dihedral : 4.738 21.318 4629 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 1.61 % Allowed : 9.23 % Favored : 89.16 % 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 are not related in a simple way. whole: -0.41 (0.13), residues: 4257 helix: 1.23 (0.19), residues: 711 sheet: 0.20 (0.14), residues: 1350 loop : -1.09 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 109 TYR 0.030 0.002 TYR G 141 PHE 0.027 0.002 PHE E 86 TRP 0.021 0.001 TRP B 64 HIS 0.011 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.30 (34935) covalent geometry : angle 0.69454 / 0.36 (47559) SS BOND : bond 0.00254 / 0.17 ( 54) SS BOND : angle 1.11892 / 0.70 ( 108) hydrogen bonds : bond 0.07284 / 4.74 ( 1300) hydrogen bonds : angle 5.60493 / 3.83 ( 3633) link_BETA1-4 : bond 0.00859 / 0.51 ( 12) link_BETA1-4 : angle 3.39109 / 2.15 ( 36) link_NAG-ASN : bond 0.00823 / 0.50 ( 48) link_NAG-ASN : angle 4.40323 / 2.86 ( 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 198 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 1.267 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 214 ARG cc_start: 0.8131 (pmm-80) cc_final: 0.7690 (pmm-80) REVERT: A 374 PHE cc_start: 0.8397 (p90) cc_final: 0.8094 (p90) REVERT: A 464 PHE cc_start: 0.8135 (m-80) cc_final: 0.7331 (m-80) REVERT: A 1029 MET cc_start: 0.9207 (tpp) cc_final: 0.9000 (tpp) REVERT: L 32 ASN cc_start: 0.8007 (t0) cc_final: 0.7804 (p0) REVERT: L 50 TYR cc_start: 0.7906 (p90) cc_final: 0.7619 (p90) REVERT: B 374 PHE cc_start: 0.8159 (p90) cc_final: 0.7897 (p90) REVERT: B 455 LEU cc_start: 0.6996 (mt) cc_final: 0.6562 (mp) REVERT: E 374 PHE cc_start: 0.8334 (p90) cc_final: 0.7924 (p90) REVERT: F 49 MET cc_start: 0.6903 (pmt) cc_final: 0.5728 (pp-130) REVERT: F 78 TYR cc_start: 0.8316 (m-80) cc_final: 0.8046 (m-80) REVERT: G 174 TYR cc_start: 0.5186 (m-80) cc_final: 0.4937 (m-80) outliers start: 60 outliers final: 26 residues processed: 182 average time/residue: 0.5600 time to fit residues: 126.7641 Evaluate side-chains 147 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 980 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 84 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 242 LEU 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 534 VAL Chi-restraints excluded: chain E residue 934 ILE 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: 2.9990 chunk 401 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 374 optimal weight: 0.5980 chunk 308 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 138 ASN L 167 GLN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN D 32 ASN E 115 GLN E 134 GLN E 196 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.133153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070269 restraints weight = 88910.909| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.67 r_work: 0.2786 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35049 Z= 0.159 Angle : 0.639 13.659 47847 Z= 0.312 Chirality : 0.046 0.237 5577 Planarity : 0.004 0.049 6066 Dihedral : 4.505 22.011 4629 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 1.61 % Allowed : 10.57 % Favored : 87.82 % 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 are not related in a simple way. whole: -0.23 (0.13), residues: 4257 helix: 1.57 (0.20), residues: 714 sheet: 0.26 (0.14), residues: 1332 loop : -0.99 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 46 TYR 0.036 0.001 TYR A 453 PHE 0.027 0.001 PHE E 168 TRP 0.015 0.001 TRP B 64 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (34935) covalent geometry : angle 0.59085 / 0.30 (47559) SS BOND : bond 0.00298 / 0.25 ( 54) SS BOND : angle 0.88762 / 0.57 ( 108) hydrogen bonds : bond 0.05523 / 3.60 ( 1300) hydrogen bonds : angle 5.25882 / 3.60 ( 3633) link_BETA1-4 : bond 0.01229 / 0.72 ( 12) link_BETA1-4 : angle 3.21792 / 2.09 ( 36) link_NAG-ASN : bond 0.00750 / 0.47 ( 48) link_NAG-ASN : angle 4.15705 / 2.72 ( 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 196 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8364 (p90) cc_final: 0.8049 (p90) REVERT: A 386 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9243 (pptt) REVERT: A 387 LEU cc_start: 0.8725 (tp) cc_final: 0.8148 (mm) REVERT: A 464 PHE cc_start: 0.8001 (m-80) cc_final: 0.7345 (m-80) REVERT: A 869 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: L 50 TYR cc_start: 0.7884 (p90) cc_final: 0.7629 (p90) REVERT: L 106 GLU cc_start: 0.3921 (pt0) cc_final: 0.3636 (tt0) REVERT: L 141 TYR cc_start: 0.4109 (t80) cc_final: 0.3655 (t80) REVERT: B 374 PHE cc_start: 0.8303 (p90) cc_final: 0.7980 (p90) REVERT: E 374 PHE cc_start: 0.8482 (p90) cc_final: 0.8046 (p90) REVERT: F 49 MET cc_start: 0.7020 (pmt) cc_final: 0.5761 (tmt) REVERT: F 78 TYR cc_start: 0.8265 (m-80) cc_final: 0.8054 (m-80) REVERT: F 79 MET cc_start: -0.1080 (mmm) cc_final: -0.1367 (mmm) outliers start: 60 outliers final: 22 residues processed: 179 average time/residue: 0.6070 time to fit residues: 134.8870 Evaluate side-chains 147 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 386 LYS 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 A residue 1050 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 233 ILE 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 B residue 973 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 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 1010 GLN 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: 5.9990 chunk 0 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 197 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 375 optimal weight: 0.0980 chunk 250 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 32 ASN L 138 ASN B 66 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.068594 restraints weight = 89344.826| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.58 r_work: 0.2773 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 35049 Z= 0.192 Angle : 0.662 13.567 47847 Z= 0.322 Chirality : 0.046 0.339 5577 Planarity : 0.004 0.051 6066 Dihedral : 4.512 21.919 4629 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.74 % Allowed : 11.49 % Favored : 86.77 % 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 are not related in a simple way. whole: -0.23 (0.13), residues: 4257 helix: 1.56 (0.20), residues: 714 sheet: 0.26 (0.14), residues: 1332 loop : -0.99 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.022 0.002 TYR A1067 PHE 0.019 0.002 PHE E 86 TRP 0.015 0.001 TRP B 64 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (34935) covalent geometry : angle 0.61450 / 0.31 (47559) SS BOND : bond 0.00227 / 0.14 ( 54) SS BOND : angle 0.94198 / 0.60 ( 108) hydrogen bonds : bond 0.05948 / 3.88 ( 1300) hydrogen bonds : angle 5.22143 / 3.57 ( 3633) link_BETA1-4 : bond 0.01053 / 0.61 ( 12) link_BETA1-4 : angle 3.16130 / 2.03 ( 36) link_NAG-ASN : bond 0.00695 / 0.42 ( 48) link_NAG-ASN : angle 4.18742 / 2.71 ( 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 196 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 1.444 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 214 ARG cc_start: 0.8088 (pmm-80) cc_final: 0.7878 (pmt-80) REVERT: A 374 PHE cc_start: 0.8375 (p90) cc_final: 0.8049 (p90) REVERT: A 386 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9356 (pptt) REVERT: A 387 LEU cc_start: 0.8759 (tp) cc_final: 0.8324 (tm) REVERT: A 464 PHE cc_start: 0.8043 (m-80) cc_final: 0.7377 (m-80) REVERT: A 869 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8476 (mtt) REVERT: H 72 MET cc_start: 0.6422 (mmp) cc_final: 0.5276 (mmm) REVERT: L 50 TYR cc_start: 0.7906 (p90) cc_final: 0.7662 (p90) REVERT: L 106 GLU cc_start: 0.3828 (pt0) cc_final: 0.3527 (tt0) REVERT: L 124 GLU cc_start: 0.5102 (pm20) cc_final: 0.4410 (pp20) REVERT: L 141 TYR cc_start: 0.4320 (t80) cc_final: 0.3897 (t80) REVERT: B 374 PHE cc_start: 0.8402 (p90) cc_final: 0.7997 (p90) REVERT: E 374 PHE cc_start: 0.8538 (p90) cc_final: 0.8062 (p90) REVERT: F 32 VAL cc_start: 0.6440 (OUTLIER) cc_final: 0.6023 (p) outliers start: 65 outliers final: 35 residues processed: 182 average time/residue: 0.5885 time to fit residues: 133.3793 Evaluate side-chains 159 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 603 ASN 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 66 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 434 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 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 84 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 323 THR 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 534 VAL Chi-restraints excluded: chain E residue 776 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 344 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 361 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 244 optimal weight: 0.0470 chunk 300 optimal weight: 8.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 675 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.133183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070333 restraints weight = 88750.887| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.95 r_work: 0.2879 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2608 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= 0.138 Angle : 0.629 15.244 47847 Z= 0.304 Chirality : 0.045 0.450 5577 Planarity : 0.004 0.046 6066 Dihedral : 4.406 22.083 4629 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.69 % Allowed : 12.43 % Favored : 85.88 % 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 are not related in a simple way. whole: -0.07 (0.13), residues: 4257 helix: 1.72 (0.20), residues: 714 sheet: 0.41 (0.14), residues: 1335 loop : -0.93 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.019 0.001 TYR A 453 PHE 0.031 0.001 PHE A 168 TRP 0.012 0.001 TRP E 64 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34935) covalent geometry : angle 0.58276 / 0.29 (47559) SS BOND : bond 0.00251 / 0.17 ( 54) SS BOND : angle 0.81068 / 0.52 ( 108) hydrogen bonds : bond 0.05208 / 3.40 ( 1300) hydrogen bonds : angle 5.08281 / 3.47 ( 3633) link_BETA1-4 : bond 0.01161 / 0.68 ( 12) link_BETA1-4 : angle 3.09782 / 2.00 ( 36) link_NAG-ASN : bond 0.00706 / 0.45 ( 48) link_NAG-ASN : angle 4.06025 / 2.61 ( 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 191 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 1.330 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: 0.8369 (p90) cc_final: 0.8002 (p90) REVERT: A 386 LYS cc_start: 0.9575 (OUTLIER) cc_final: 0.9369 (pptt) REVERT: A 387 LEU cc_start: 0.8809 (tp) cc_final: 0.8418 (tm) REVERT: A 464 PHE cc_start: 0.8034 (m-80) cc_final: 0.7344 (m-80) REVERT: A 869 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8486 (mtt) REVERT: H 72 MET cc_start: 0.6935 (mmp) cc_final: 0.5951 (mmm) REVERT: L 50 TYR cc_start: 0.8010 (p90) cc_final: 0.7807 (p90) REVERT: L 106 GLU cc_start: 0.3879 (pt0) cc_final: 0.3612 (tt0) REVERT: L 141 TYR cc_start: 0.4458 (t80) cc_final: 0.3987 (t80) REVERT: B 374 PHE cc_start: 0.8398 (p90) cc_final: 0.8009 (p90) REVERT: B 675 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8437 (pp30) REVERT: C 72 MET cc_start: 0.7065 (mpm) cc_final: 0.5670 (mmp) REVERT: E 374 PHE cc_start: 0.8566 (p90) cc_final: 0.8056 (p90) REVERT: E 390 LEU cc_start: 0.7918 (mt) cc_final: 0.7486 (mt) REVERT: F 49 MET cc_start: 0.7094 (pmt) cc_final: 0.5814 (tmt) outliers start: 63 outliers final: 33 residues processed: 175 average time/residue: 0.5775 time to fit residues: 125.8600 Evaluate side-chains 156 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 386 LYS 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 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 233 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 675 GLN 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 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 386 LYS 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 E residue 1043 CYS 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: 0.9990 chunk 226 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 216 optimal weight: 0.5980 chunk 310 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 378 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 32 ASN E 196 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 = 0.4278 r_free = 0.4278 target = 0.132851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069793 restraints weight = 89086.510| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.47 r_work: 0.2789 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35049 Z= 0.157 Angle : 0.637 13.419 47847 Z= 0.308 Chirality : 0.046 0.348 5577 Planarity : 0.004 0.053 6066 Dihedral : 4.405 20.770 4629 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.64 % Allowed : 12.91 % Favored : 85.45 % 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 are not related in a simple way. whole: -0.06 (0.13), residues: 4257 helix: 1.72 (0.20), residues: 714 sheet: 0.46 (0.14), residues: 1329 loop : -0.96 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 55 TYR 0.032 0.001 TYR E 160 PHE 0.029 0.001 PHE B 168 TRP 0.010 0.001 TRP E 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (34935) covalent geometry : angle 0.59240 / 0.30 (47559) SS BOND : bond 0.00238 / 0.16 ( 54) SS BOND : angle 0.84559 / 0.54 ( 108) hydrogen bonds : bond 0.05350 / 3.49 ( 1300) hydrogen bonds : angle 5.05581 / 3.45 ( 3633) link_BETA1-4 : bond 0.01060 / 0.61 ( 12) link_BETA1-4 : angle 3.07246 / 1.97 ( 36) link_NAG-ASN : bond 0.00642 / 0.41 ( 48) link_NAG-ASN : angle 3.99926 / 2.56 ( 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 176 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 115 time to evaluate : 1.262 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: 0.8325 (p90) cc_final: 0.8030 (p90) REVERT: A 387 LEU cc_start: 0.8760 (tp) cc_final: 0.8307 (tm) REVERT: A 464 PHE cc_start: 0.8057 (m-80) cc_final: 0.7434 (m-80) REVERT: A 869 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8219 (mtt) REVERT: H 72 MET cc_start: 0.6914 (mmp) cc_final: 0.5967 (mmm) REVERT: B 374 PHE cc_start: 0.8374 (p90) cc_final: 0.7984 (p90) REVERT: C 72 MET cc_start: 0.6926 (mpm) cc_final: 0.5904 (mmp) REVERT: E 117 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7978 (tt) REVERT: E 374 PHE cc_start: 0.8516 (p90) cc_final: 0.8037 (p90) REVERT: F 49 MET cc_start: 0.7038 (pmt) cc_final: 0.5792 (tmt) REVERT: F 79 MET cc_start: -0.0997 (mmm) cc_final: -0.1248 (mmm) outliers start: 61 outliers final: 36 residues processed: 162 average time/residue: 0.5264 time to fit residues: 108.0408 Evaluate side-chains 149 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE 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 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 289 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 858 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 66 HIS 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 323 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 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 E residue 1043 CYS 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: 20.0000 chunk 120 optimal weight: 30.0000 chunk 229 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 385 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 136 optimal weight: 40.0000 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.0030 chunk 91 optimal weight: 0.0770 overall best weight: 0.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN L 139 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 32 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 = 0.4292 r_free = 0.4292 target = 0.133820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071234 restraints weight = 88985.724| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.63 r_work: 0.2823 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2829 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= 0.113 Angle : 0.611 15.494 47847 Z= 0.293 Chirality : 0.045 0.402 5577 Planarity : 0.004 0.111 6066 Dihedral : 4.276 24.616 4629 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.34 % Allowed : 13.45 % Favored : 85.21 % 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 are not related in a simple way. whole: 0.07 (0.13), residues: 4257 helix: 1.89 (0.20), residues: 717 sheet: 0.53 (0.14), residues: 1332 loop : -0.89 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 55 TYR 0.019 0.001 TYR B 160 PHE 0.035 0.001 PHE A 168 TRP 0.010 0.001 TRP C 48 HIS 0.003 0.000 HIS E1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (34935) covalent geometry : angle 0.56627 / 0.28 (47559) SS BOND : bond 0.00233 / 0.14 ( 54) SS BOND : angle 0.74473 / 0.48 ( 108) hydrogen bonds : bond 0.04505 / 2.94 ( 1300) hydrogen bonds : angle 4.89379 / 3.34 ( 3633) link_BETA1-4 : bond 0.01135 / 0.66 ( 12) link_BETA1-4 : angle 3.00320 / 1.93 ( 36) link_NAG-ASN : bond 0.00736 / 0.47 ( 48) link_NAG-ASN : angle 3.91960 / 2.51 ( 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 169 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 1.219 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: 0.8328 (p90) cc_final: 0.8024 (p90) REVERT: A 387 LEU cc_start: 0.8841 (tp) cc_final: 0.8360 (mm) REVERT: A 464 PHE cc_start: 0.8044 (m-80) cc_final: 0.7425 (m-80) REVERT: H 72 MET cc_start: 0.6796 (mmp) cc_final: 0.5837 (mmm) REVERT: B 374 PHE cc_start: 0.8388 (p90) cc_final: 0.7920 (p90) REVERT: C 72 MET cc_start: 0.6898 (mpm) cc_final: 0.5738 (mmp) REVERT: E 66 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.6282 (t-90) REVERT: E 374 PHE cc_start: 0.8513 (p90) cc_final: 0.7987 (p90) REVERT: F 49 MET cc_start: 0.7383 (pmt) cc_final: 0.6135 (tmt) REVERT: F 79 MET cc_start: -0.0861 (mmm) cc_final: -0.1106 (mmm) REVERT: G 50 TYR cc_start: 0.7783 (p90) cc_final: 0.7567 (p90) outliers start: 50 outliers final: 30 residues processed: 156 average time/residue: 0.5345 time to fit residues: 106.0232 Evaluate side-chains 145 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE 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 791 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL 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 66 HIS 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 858 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 426 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 143 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 420 optimal weight: 40.0000 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN L 138 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.131938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067650 restraints weight = 88408.140| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.05 r_work: 0.2786 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35049 Z= 0.223 Angle : 0.668 13.506 47847 Z= 0.326 Chirality : 0.047 0.376 5577 Planarity : 0.004 0.090 6066 Dihedral : 4.442 20.941 4629 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.23 % Allowed : 13.82 % Favored : 84.94 % 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 are not related in a simple way. whole: -0.07 (0.13), residues: 4257 helix: 1.68 (0.20), residues: 714 sheet: 0.45 (0.14), residues: 1332 loop : -0.96 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.029 0.002 TYR E 160 PHE 0.058 0.002 PHE B 168 TRP 0.014 0.001 TRP E 64 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.22 (34935) covalent geometry : angle 0.62493 / 0.32 (47559) SS BOND : bond 0.00222 / 0.15 ( 54) SS BOND : angle 0.92675 / 0.58 ( 108) hydrogen bonds : bond 0.06024 / 3.92 ( 1300) hydrogen bonds : angle 5.08178 / 3.47 ( 3633) link_BETA1-4 : bond 0.01053 / 0.60 ( 12) link_BETA1-4 : angle 3.13339 / 2.00 ( 36) link_NAG-ASN : bond 0.00642 / 0.41 ( 48) link_NAG-ASN : angle 4.01428 / 2.56 ( 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 162 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 1.443 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: 0.8385 (p90) cc_final: 0.8064 (OUTLIER) REVERT: A 387 LEU cc_start: 0.8827 (tp) cc_final: 0.8500 (tm) REVERT: A 464 PHE cc_start: 0.8068 (m-80) cc_final: 0.7445 (m-80) REVERT: H 72 MET cc_start: 0.6933 (mmp) cc_final: 0.5965 (mmm) REVERT: L 30 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6960 (p0) REVERT: B 374 PHE cc_start: 0.8432 (p90) cc_final: 0.7968 (p90) REVERT: B 786 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8350 (pmtt) REVERT: C 72 MET cc_start: 0.7040 (mpm) cc_final: 0.5638 (mmt) REVERT: E 168 PHE cc_start: 0.8242 (t80) cc_final: 0.8023 (t80) REVERT: E 374 PHE cc_start: 0.8559 (p90) cc_final: 0.7993 (p90) REVERT: F 49 MET cc_start: 0.7115 (pmt) cc_final: 0.5936 (tmt) REVERT: G 50 TYR cc_start: 0.7804 (p90) cc_final: 0.7600 (p90) outliers start: 46 outliers final: 36 residues processed: 154 average time/residue: 0.5502 time to fit residues: 107.3133 Evaluate side-chains 150 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE 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 H residue 178 LEU Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL 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 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 323 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 534 VAL 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 E residue 1043 CYS 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: 0.6980 chunk 69 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 287 optimal weight: 0.9980 chunk 248 optimal weight: 40.0000 chunk 218 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 303 optimal weight: 7.9990 chunk 361 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.132476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069460 restraints weight = 88817.598| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.61 r_work: 0.2775 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.367 35049 Z= 0.214 Angle : 0.832 59.195 47847 Z= 0.441 Chirality : 0.046 0.423 5577 Planarity : 0.005 0.148 6066 Dihedral : 4.486 33.357 4629 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.19 % Favored : 94.79 % Rotamer: Outliers : 1.21 % Allowed : 13.85 % Favored : 84.94 % Cbeta Deviations : 0.02 % 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 are not related in a simple way. whole: -0.08 (0.13), residues: 4257 helix: 1.67 (0.20), residues: 714 sheet: 0.45 (0.14), residues: 1332 loop : -0.96 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 55 TYR 0.278 0.002 TYR E 160 PHE 0.034 0.002 PHE B 168 TRP 0.021 0.001 TRP C 34 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (34935) covalent geometry : angle 0.77514 / 0.43 (47559) SS BOND : bond 0.02137 / 1.75 ( 54) SS BOND : angle 4.20792 / 2.48 ( 108) hydrogen bonds : bond 0.05782 / 3.77 ( 1300) hydrogen bonds : angle 5.08069 / 3.46 ( 3633) link_BETA1-4 : bond 0.00846 / 0.49 ( 12) link_BETA1-4 : angle 3.15299 / 2.01 ( 36) link_NAG-ASN : bond 0.00620 / 0.40 ( 48) link_NAG-ASN : angle 4.00908 / 2.56 ( 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 158 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 1.400 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: A 374 PHE cc_start: 0.8355 (p90) cc_final: 0.8042 (OUTLIER) REVERT: A 387 LEU cc_start: 0.8829 (tp) cc_final: 0.8503 (tm) REVERT: A 464 PHE cc_start: 0.8073 (m-80) cc_final: 0.7462 (m-80) REVERT: H 72 MET cc_start: 0.6946 (mmp) cc_final: 0.6026 (mmm) REVERT: L 30 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.6633 (p0) REVERT: B 374 PHE cc_start: 0.8412 (p90) cc_final: 0.7954 (p90) REVERT: C 72 MET cc_start: 0.7043 (mpm) cc_final: 0.5707 (mmt) REVERT: E 374 PHE cc_start: 0.8499 (p90) cc_final: 0.7953 (p90) REVERT: F 49 MET cc_start: 0.7074 (pmt) cc_final: 0.6006 (tmt) outliers start: 45 outliers final: 37 residues processed: 151 average time/residue: 0.5585 time to fit residues: 106.7548 Evaluate side-chains 147 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL 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 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 323 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 534 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS 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: 1.9990 chunk 326 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 374 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 411 optimal weight: 40.0000 chunk 70 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 356 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.132461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069375 restraints weight = 88653.193| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.65 r_work: 0.2773 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.372 35049 Z= 0.222 Angle : 0.826 59.198 47847 Z= 0.435 Chirality : 0.046 0.430 5577 Planarity : 0.005 0.154 6066 Dihedral : 4.483 31.128 4629 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.19 % Favored : 94.79 % Rotamer: Outliers : 1.13 % Allowed : 13.90 % Favored : 84.97 % Cbeta Deviations : 0.05 % 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 are not related in a simple way. whole: -0.08 (0.13), residues: 4257 helix: 1.67 (0.20), residues: 714 sheet: 0.45 (0.14), residues: 1332 loop : -0.96 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 55 TYR 0.292 0.002 TYR E 160 PHE 0.030 0.001 PHE B 168 TRP 0.021 0.001 TRP C 34 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.20 (34935) covalent geometry : angle 0.76373 / 0.42 (47559) SS BOND : bond 0.04404 / 3.00 ( 54) SS BOND : angle 4.52942 / 2.66 ( 108) hydrogen bonds : bond 0.05794 / 3.77 ( 1300) hydrogen bonds : angle 5.08102 / 3.46 ( 3633) link_BETA1-4 : bond 0.01076 / 0.64 ( 12) link_BETA1-4 : angle 3.20919 / 2.06 ( 36) link_NAG-ASN : bond 0.00621 / 0.40 ( 48) link_NAG-ASN : angle 4.00843 / 2.56 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17002.05 seconds wall clock time: 288 minutes 56.77 seconds (17336.77 seconds total)