Starting phenix.real_space_refine on Sun Jul 5 13:01:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v2a_31639/07_2026/7v2a_31639.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 123 5.16 5 C 17871 2.51 5 N 4620 2.21 5 O 5403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 28017 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7464 Classifications: {'peptide': 988} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 940} Chain breaks: 11 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 8, 'GLN:plan1': 6, 'PHE:plan': 4, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 190 Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "B" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7464 Classifications: {'peptide': 988} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 940} Chain breaks: 11 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 8, 'GLN:plan1': 6, 'PHE:plan': 4, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 190 Chain: "C" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7464 Classifications: {'peptide': 988} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 940} Chain breaks: 11 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 8, 'GLN:plan1': 6, 'PHE:plan': 4, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 190 Chain: "F" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.48, per 1000 atoms: 0.20 Number of scatterers: 28017 At special positions: 0 Unit cell: (131.04, 135.2, 200.72, 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 123 16.00 O 5403 8.00 N 4620 7.00 C 17871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.49 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.36 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.49 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 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.49 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.37 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.36 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 282 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 282 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 282 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 988.8 milliseconds 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6774 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 63 sheets defined 22.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 5.036A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.165A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.572A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.707A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.852A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.802A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.826A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.596A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.622A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.526A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.473A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.667A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.728A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.546A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 5.035A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.166A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.572A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.706A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.852A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.802A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.826A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.596A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.622A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.525A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.474A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.667A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.037A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.166A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.573A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.707A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.853A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.802A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.826A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.597A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.622A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.527A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.473A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.667A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'H' and resid 80 through 84 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.728A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.545A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.728A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.545A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.848A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.618A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.559A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.442A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.611A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.425A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.531A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.326A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 4.250A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP E 33 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.848A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.616A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.560A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.442A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.610A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.425A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.531A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD3, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.326A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.150A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.899A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.899A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.250A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 29 through 30 removed outlier: 8.637A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.617A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.559A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.441A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.611A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.425A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.530A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AF1, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.326A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.150A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF8, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.251A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AG1, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.879A pdb=" N ALA F 12 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.879A pdb=" N ALA F 12 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AG4, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA H 12 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA H 12 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP G 33 " --> pdb=" O HIS G 99 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP I 33 " --> pdb=" O HIS I 99 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2595 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: 6.10 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5537 1.32 - 1.45: 7273 1.45 - 1.57: 15684 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28650 Sorted by residual: bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.211 0.120 2.07e-02 2.33e+03 3.37e+01 bond pdb=" C HIS A1088 " pdb=" N PHE A1089 " ideal model delta sigma weight residual 1.331 1.211 0.120 2.07e-02 2.33e+03 3.34e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.212 0.119 2.07e-02 2.33e+03 3.33e+01 bond pdb=" C LEU C 335 " pdb=" N CYS C 336 " ideal model delta sigma weight residual 1.328 1.396 -0.068 1.44e-02 4.82e+03 2.23e+01 bond pdb=" C LEU B 335 " pdb=" N CYS B 336 " ideal model delta sigma weight residual 1.328 1.395 -0.067 1.44e-02 4.82e+03 2.18e+01 ... (remaining 28645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 38706 3.51 - 7.02: 329 7.02 - 10.53: 13 10.53 - 14.04: 1 14.04 - 17.56: 2 Bond angle restraints: 39051 Sorted by residual: angle pdb=" C TYR G 110 " pdb=" CA TYR G 110 " pdb=" CB TYR G 110 " ideal model delta sigma weight residual 112.82 95.26 17.56 2.17e+00 2.12e-01 6.55e+01 angle pdb=" C TYR I 110 " pdb=" CA TYR I 110 " pdb=" CB TYR I 110 " ideal model delta sigma weight residual 112.82 95.39 17.43 2.17e+00 2.12e-01 6.45e+01 angle pdb=" N LYS B 41 " pdb=" CA LYS B 41 " pdb=" C LYS B 41 " ideal model delta sigma weight residual 114.56 107.60 6.96 1.27e+00 6.20e-01 3.01e+01 angle pdb=" N LYS A 41 " pdb=" CA LYS A 41 " pdb=" C LYS A 41 " ideal model delta sigma weight residual 113.43 106.60 6.83 1.26e+00 6.30e-01 2.94e+01 angle pdb=" C GLU C 324 " pdb=" CA GLU C 324 " pdb=" CB GLU C 324 " ideal model delta sigma weight residual 114.11 100.98 13.13 2.44e+00 1.68e-01 2.90e+01 ... (remaining 39046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14701 17.56 - 35.13: 1567 35.13 - 52.69: 320 52.69 - 70.26: 52 70.26 - 87.82: 37 Dihedral angle restraints: 16677 sinusoidal: 6117 harmonic: 10560 Sorted by residual: dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ASP H 51 " pdb=" CA ASP H 51 " ideal model delta harmonic sigma weight residual -180.00 -125.61 -54.39 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA TYR D 50 " pdb=" C TYR D 50 " pdb=" N ASP D 51 " pdb=" CA ASP D 51 " ideal model delta harmonic sigma weight residual -180.00 -125.61 -54.39 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA TYR F 50 " pdb=" C TYR F 50 " pdb=" N ASP F 51 " pdb=" CA ASP F 51 " ideal model delta harmonic sigma weight residual -180.00 -125.62 -54.38 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 16674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3863 0.077 - 0.153: 635 0.153 - 0.230: 32 0.230 - 0.307: 7 0.307 - 0.384: 5 Chirality restraints: 4542 Sorted by residual: chirality pdb=" CA GLU A 324 " pdb=" N GLU A 324 " pdb=" C GLU A 324 " pdb=" CB GLU A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA GLU C 324 " pdb=" N GLU C 324 " pdb=" C GLU C 324 " pdb=" CB GLU C 324 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA TYR E 110 " pdb=" N TYR E 110 " pdb=" C TYR E 110 " pdb=" CB TYR E 110 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 4539 not shown) Planarity restraints: 5025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.333 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG A1308 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG B1308 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " -0.120 2.00e-02 2.50e+03 9.76e-02 1.19e+02 pdb=" C7 NAG C1308 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " 0.025 2.00e-02 2.50e+03 ... (remaining 5022 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 48 1.96 - 2.69: 1762 2.69 - 3.43: 39774 3.43 - 4.16: 64788 4.16 - 4.90: 116584 Nonbonded interactions: 222956 Sorted by model distance: nonbonded pdb=" NZ LYS A1045 " pdb=" O GLY B 889 " model vdw 1.225 3.120 nonbonded pdb=" O GLY A 889 " pdb=" NZ LYS C1045 " model vdw 1.241 3.120 nonbonded pdb=" NZ LYS B1045 " pdb=" O GLY C 889 " model vdw 1.246 3.120 nonbonded pdb=" CB LYS A 790 " pdb=" OG SER C 704 " model vdw 1.489 3.440 nonbonded pdb=" CD1 ILE A 896 " pdb=" CG1 ILE C 712 " model vdw 1.493 3.860 ... (remaining 222951 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 5.280 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.290 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.013 0.463 28719 Z= 0.714 Angle : 1.036 25.886 39201 Z= 0.587 Chirality : 0.055 0.384 4542 Planarity : 0.008 0.289 5001 Dihedral : 15.248 87.822 9786 Min Nonbonded Distance : 1.225 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.54 % Favored : 90.20 % Rotamer: Outliers : 2.50 % Allowed : 18.17 % Favored : 79.33 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.95 (0.12), residues: 3573 helix: -3.84 (0.13), residues: 654 sheet: -1.74 (0.17), residues: 876 loop : -2.66 (0.11), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 577 TYR 0.028 0.003 TYR G 107 PHE 0.017 0.002 PHE B1089 TRP 0.022 0.003 TRP H 36 HIS 0.006 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01106 / 0.52 (28650) covalent geometry : angle 0.95517 / 0.56 (39051) SS BOND : bond 0.15836 / 11.71 ( 39) SS BOND : angle 7.56986 / 5.32 ( 78) hydrogen bonds : bond 0.23869 / 15.53 ( 958) hydrogen bonds : angle 10.00116 / 6.97 ( 2595) Misc. bond : bond 0.26987 / 16.01 ( 6) link_NAG-ASN : bond 0.00681 / 0.38 ( 24) link_NAG-ASN : angle 5.19365 / 3.29 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 367 time to evaluate : 0.769 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 202 LYS cc_start: 0.7622 (pttt) cc_final: 0.7395 (pttm) REVERT: D 107 LEU cc_start: 0.7772 (tp) cc_final: 0.7125 (tp) REVERT: E 57 ASP cc_start: 0.8679 (t0) cc_final: 0.8399 (t0) REVERT: E 65 GLN cc_start: 0.8803 (mm110) cc_final: 0.8279 (tp40) REVERT: B 202 LYS cc_start: 0.7689 (pttt) cc_final: 0.7291 (pttt) REVERT: B 994 ASP cc_start: 0.8280 (t0) cc_final: 0.8034 (t0) REVERT: C 202 LYS cc_start: 0.7673 (pttt) cc_final: 0.7070 (pttm) REVERT: G 65 GLN cc_start: 0.8733 (mm110) cc_final: 0.8254 (tp40) REVERT: G 87 LYS cc_start: 0.6050 (ptpp) cc_final: 0.5799 (ptpp) REVERT: G 100 GLN cc_start: 0.8819 (mp10) cc_final: 0.8466 (mp10) REVERT: I 65 GLN cc_start: 0.8749 (mm110) cc_final: 0.7985 (tp40) REVERT: I 67 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7997 (mp10) REVERT: I 87 LYS cc_start: 0.6352 (ptpp) cc_final: 0.6064 (ptpp) outliers start: 74 outliers final: 61 residues processed: 441 average time/residue: 0.1524 time to fit residues: 110.5920 Evaluate side-chains 288 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 227 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 89 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 66 HIS A 99 ASN A 437 ASN A 448 ASN A 536 ASN A 644 GLN A 751 ASN A 755 GLN A 901 GLN A 965 GLN A1002 GLN A1101 HIS ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 66 HIS B 437 ASN B 448 ASN B 487 ASN B 536 ASN B 644 GLN B 751 ASN B 755 GLN B 901 GLN B 965 GLN B1002 GLN B1088 HIS B1101 HIS C 61 ASN C 66 HIS C 437 ASN C 448 ASN C 487 ASN C 536 ASN C 644 GLN C 751 ASN C 901 GLN C 965 GLN C1002 GLN C1088 HIS C1101 HIS H 32 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.097706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073397 restraints weight = 78851.428| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.91 r_work: 0.3044 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28719 Z= 0.143 Angle : 0.675 9.369 39201 Z= 0.348 Chirality : 0.045 0.256 4542 Planarity : 0.005 0.058 5001 Dihedral : 6.407 53.407 3964 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.53 % Favored : 95.30 % Rotamer: Outliers : 3.01 % Allowed : 19.89 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.13), residues: 3573 helix: -1.60 (0.19), residues: 633 sheet: -1.17 (0.17), residues: 897 loop : -1.96 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 38 TYR 0.020 0.002 TYR I 101 PHE 0.013 0.001 PHE C1121 TRP 0.025 0.002 TRP F 92 HIS 0.007 0.001 HIS I 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (28650) covalent geometry : angle 0.65840 / 0.34 (39051) SS BOND : bond 0.00311 / 0.20 ( 39) SS BOND : angle 1.67866 / 1.14 ( 78) hydrogen bonds : bond 0.04650 / 3.10 ( 958) hydrogen bonds : angle 6.01519 / 4.14 ( 2595) Misc. bond : bond 0.00121 / 0.07 ( 6) link_NAG-ASN : bond 0.00244 / 0.16 ( 24) link_NAG-ASN : angle 3.15021 / 2.01 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 289 time to evaluate : 1.112 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 887 THR cc_start: 0.8926 (p) cc_final: 0.8427 (t) REVERT: D 28 ASN cc_start: 0.6834 (OUTLIER) cc_final: 0.6196 (p0) REVERT: D 92 TRP cc_start: 0.8523 (t-100) cc_final: 0.8197 (t-100) REVERT: E 48 MET cc_start: 0.8203 (mtp) cc_final: 0.7859 (mpp) REVERT: E 57 ASP cc_start: 0.8872 (t0) cc_final: 0.8493 (t0) REVERT: E 65 GLN cc_start: 0.8913 (mm110) cc_final: 0.8424 (tp40) REVERT: E 81 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5996 (mp) REVERT: B 896 ILE cc_start: 0.7975 (mm) cc_final: 0.7612 (tp) REVERT: B 994 ASP cc_start: 0.8830 (t0) cc_final: 0.8596 (t0) REVERT: C 887 THR cc_start: 0.8912 (p) cc_final: 0.8475 (t) REVERT: C 979 ASP cc_start: 0.8360 (m-30) cc_final: 0.8143 (t70) REVERT: C 1123 SER cc_start: 0.8305 (p) cc_final: 0.7989 (p) REVERT: F 50 TYR cc_start: 0.7900 (p90) cc_final: 0.7660 (p90) REVERT: F 92 TRP cc_start: 0.8735 (t-100) cc_final: 0.7618 (t-100) REVERT: H 50 TYR cc_start: 0.7890 (p90) cc_final: 0.7646 (p90) REVERT: G 48 MET cc_start: 0.8363 (mtp) cc_final: 0.8048 (mpp) REVERT: G 57 ASP cc_start: 0.8771 (t0) cc_final: 0.8500 (t0) REVERT: G 65 GLN cc_start: 0.8770 (mm110) cc_final: 0.8090 (tp40) REVERT: G 67 GLN cc_start: 0.8193 (mm110) cc_final: 0.7834 (mp10) REVERT: I 48 MET cc_start: 0.8161 (mtp) cc_final: 0.7913 (mpp) REVERT: I 65 GLN cc_start: 0.8978 (mm110) cc_final: 0.8098 (tp40) REVERT: I 67 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8127 (mp10) REVERT: I 110 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7283 (t80) REVERT: I 111 TYR cc_start: 0.7911 (m-80) cc_final: 0.7491 (m-10) outliers start: 89 outliers final: 57 residues processed: 353 average time/residue: 0.1459 time to fit residues: 86.7386 Evaluate side-chains 291 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 231 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 215 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 265 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1106 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 804 GLN B1106 GLN C 762 GLN C1106 GLN ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073827 restraints weight = 79600.031| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.98 r_work: 0.3056 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28719 Z= 0.126 Angle : 0.593 9.120 39201 Z= 0.303 Chirality : 0.044 0.308 4542 Planarity : 0.004 0.066 5001 Dihedral : 5.669 59.215 3904 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 3.48 % Allowed : 21.41 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3573 helix: -0.33 (0.20), residues: 630 sheet: -0.83 (0.17), residues: 930 loop : -1.59 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.022 0.001 TYR G 107 PHE 0.014 0.001 PHE C 855 TRP 0.016 0.001 TRP H 92 HIS 0.006 0.001 HIS I 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (28650) covalent geometry : angle 0.58049 / 0.30 (39051) SS BOND : bond 0.00267 / 0.17 ( 39) SS BOND : angle 1.29536 / 0.85 ( 78) hydrogen bonds : bond 0.03643 / 2.42 ( 958) hydrogen bonds : angle 5.25405 / 3.61 ( 2595) Misc. bond : bond 0.00086 / 0.05 ( 6) link_NAG-ASN : bond 0.00240 / 0.15 ( 24) link_NAG-ASN : angle 2.64554 / 1.67 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 259 time to evaluate : 0.874 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 202 LYS cc_start: 0.8082 (pttm) cc_final: 0.7741 (pttm) REVERT: A 488 CYS cc_start: 0.4882 (OUTLIER) cc_final: 0.4363 (m) REVERT: A 585 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 887 THR cc_start: 0.8860 (p) cc_final: 0.8362 (t) REVERT: D 92 TRP cc_start: 0.8549 (t-100) cc_final: 0.8187 (t-100) REVERT: E 48 MET cc_start: 0.8052 (mtp) cc_final: 0.7817 (mpp) REVERT: E 57 ASP cc_start: 0.8838 (t0) cc_final: 0.8444 (t0) REVERT: E 65 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8364 (tp40) REVERT: E 67 GLN cc_start: 0.8403 (mm110) cc_final: 0.7916 (mp-120) REVERT: E 100 GLN cc_start: 0.8995 (mp10) cc_final: 0.8765 (mp10) REVERT: B 488 CYS cc_start: 0.4975 (OUTLIER) cc_final: 0.4487 (m) REVERT: B 780 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: B 896 ILE cc_start: 0.7899 (mm) cc_final: 0.7620 (tp) REVERT: C 320 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8780 (m) REVERT: C 421 TYR cc_start: 0.8749 (m-80) cc_final: 0.8512 (m-80) REVERT: C 488 CYS cc_start: 0.4761 (OUTLIER) cc_final: 0.4322 (m) REVERT: C 585 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8511 (mt) REVERT: C 887 THR cc_start: 0.8812 (p) cc_final: 0.8425 (t) REVERT: C 1123 SER cc_start: 0.8358 (p) cc_final: 0.8013 (p) REVERT: F 92 TRP cc_start: 0.8688 (t-100) cc_final: 0.7590 (t-100) REVERT: H 50 TYR cc_start: 0.7772 (p90) cc_final: 0.7419 (p90) REVERT: G 48 MET cc_start: 0.8363 (mtp) cc_final: 0.7910 (mpp) REVERT: G 57 ASP cc_start: 0.8773 (t0) cc_final: 0.8453 (t0) REVERT: G 65 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8141 (tp40) REVERT: G 67 GLN cc_start: 0.8183 (mm110) cc_final: 0.7954 (mp10) REVERT: I 48 MET cc_start: 0.8101 (mtp) cc_final: 0.7829 (mpp) REVERT: I 65 GLN cc_start: 0.8939 (mm110) cc_final: 0.8108 (tp40) REVERT: I 67 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8090 (mp10) REVERT: I 110 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7105 (t80) outliers start: 103 outliers final: 58 residues processed: 345 average time/residue: 0.1365 time to fit residues: 80.6398 Evaluate side-chains 290 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 2 optimal weight: 8.9990 chunk 338 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 chunk 214 optimal weight: 0.0970 chunk 200 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 191 optimal weight: 0.5980 chunk 289 optimal weight: 0.7980 chunk 307 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1106 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN B 804 GLN B1011 GLN B1106 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN I 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.099223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075063 restraints weight = 78335.236| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.92 r_work: 0.3083 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28719 Z= 0.106 Angle : 0.575 12.758 39201 Z= 0.290 Chirality : 0.044 0.313 4542 Planarity : 0.004 0.067 5001 Dihedral : 5.295 52.128 3896 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 3.07 % Allowed : 22.70 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 3573 helix: 0.32 (0.20), residues: 633 sheet: -0.49 (0.17), residues: 903 loop : -1.49 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 38 TYR 0.018 0.001 TYR D 50 PHE 0.011 0.001 PHE B 490 TRP 0.014 0.001 TRP I 47 HIS 0.003 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (28650) covalent geometry : angle 0.56460 / 0.29 (39051) SS BOND : bond 0.00253 / 0.16 ( 39) SS BOND : angle 1.15520 / 0.75 ( 78) hydrogen bonds : bond 0.03280 / 2.19 ( 958) hydrogen bonds : angle 4.98092 / 3.42 ( 2595) Misc. bond : bond 0.00054 / 0.03 ( 6) link_NAG-ASN : bond 0.00233 / 0.16 ( 24) link_NAG-ASN : angle 2.41706 / 1.52 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 258 time to evaluate : 0.995 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 202 LYS cc_start: 0.8066 (pttm) cc_final: 0.7715 (pttm) REVERT: A 488 CYS cc_start: 0.4845 (OUTLIER) cc_final: 0.4365 (m) REVERT: A 585 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 887 THR cc_start: 0.8783 (p) cc_final: 0.8322 (t) REVERT: D 92 TRP cc_start: 0.8689 (t-100) cc_final: 0.8153 (t-100) REVERT: D 110 LEU cc_start: 0.7102 (mt) cc_final: 0.6495 (pp) REVERT: E 48 MET cc_start: 0.8101 (mtp) cc_final: 0.7841 (mpp) REVERT: E 57 ASP cc_start: 0.8848 (t0) cc_final: 0.8427 (t0) REVERT: E 65 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8332 (tp40) REVERT: E 67 GLN cc_start: 0.8357 (mm110) cc_final: 0.7916 (mp-120) REVERT: B 488 CYS cc_start: 0.4818 (OUTLIER) cc_final: 0.4541 (m) REVERT: B 780 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: B 896 ILE cc_start: 0.7912 (mm) cc_final: 0.7579 (tp) REVERT: B 990 GLU cc_start: 0.8651 (pp20) cc_final: 0.8380 (pp20) REVERT: C 346 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7780 (mtt90) REVERT: C 488 CYS cc_start: 0.5034 (OUTLIER) cc_final: 0.4625 (m) REVERT: C 585 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8491 (mt) REVERT: C 887 THR cc_start: 0.8776 (p) cc_final: 0.8311 (t) REVERT: C 988 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 1123 SER cc_start: 0.8379 (p) cc_final: 0.8050 (p) REVERT: F 92 TRP cc_start: 0.8680 (t-100) cc_final: 0.7671 (t-100) REVERT: H 50 TYR cc_start: 0.7757 (p90) cc_final: 0.7230 (p90) REVERT: H 92 TRP cc_start: 0.8550 (t-100) cc_final: 0.7779 (t-100) REVERT: G 48 MET cc_start: 0.8256 (mtp) cc_final: 0.7871 (mpp) REVERT: G 57 ASP cc_start: 0.8763 (t0) cc_final: 0.8411 (t0) REVERT: G 65 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8135 (tp40) REVERT: I 48 MET cc_start: 0.8075 (mtp) cc_final: 0.7792 (mpp) REVERT: I 55 ASP cc_start: 0.7593 (m-30) cc_final: 0.7196 (m-30) REVERT: I 65 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: I 67 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8162 (mp10) REVERT: I 110 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7202 (t80) outliers start: 91 outliers final: 45 residues processed: 334 average time/residue: 0.1404 time to fit residues: 79.1277 Evaluate side-chains 292 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 136 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.096339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.071905 restraints weight = 79255.414| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.89 r_work: 0.3012 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28719 Z= 0.255 Angle : 0.650 12.184 39201 Z= 0.332 Chirality : 0.046 0.311 4542 Planarity : 0.004 0.070 5001 Dihedral : 5.403 41.425 3888 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.82 % Favored : 94.01 % Rotamer: Outliers : 3.88 % Allowed : 22.83 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3573 helix: 0.02 (0.20), residues: 657 sheet: -0.59 (0.17), residues: 942 loop : -1.39 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 38 TYR 0.018 0.002 TYR I 101 PHE 0.013 0.001 PHE C1121 TRP 0.013 0.002 TRP E 47 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (28650) covalent geometry : angle 0.63883 / 0.33 (39051) SS BOND : bond 0.00421 / 0.30 ( 39) SS BOND : angle 1.45946 / 0.97 ( 78) hydrogen bonds : bond 0.03862 / 2.57 ( 958) hydrogen bonds : angle 5.22368 / 3.59 ( 2595) Misc. bond : bond 0.00034 / 0.02 ( 6) link_NAG-ASN : bond 0.00241 / 0.16 ( 24) link_NAG-ASN : angle 2.49629 / 1.55 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 229 time to evaluate : 0.999 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 559 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: A 585 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 780 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8533 (mp0) REVERT: A 887 THR cc_start: 0.9035 (p) cc_final: 0.8537 (t) REVERT: D 92 TRP cc_start: 0.8826 (t-100) cc_final: 0.8190 (t-100) REVERT: E 48 MET cc_start: 0.8288 (mtp) cc_final: 0.7940 (mpp) REVERT: E 57 ASP cc_start: 0.8831 (t0) cc_final: 0.8445 (t0) REVERT: E 65 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8426 (tp40) REVERT: B 495 TYR cc_start: 0.5807 (OUTLIER) cc_final: 0.3735 (t80) REVERT: B 780 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: B 896 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8050 (tp) REVERT: B 990 GLU cc_start: 0.8702 (pp20) cc_final: 0.8400 (pp20) REVERT: C 495 TYR cc_start: 0.5844 (OUTLIER) cc_final: 0.2941 (t80) REVERT: C 559 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: C 585 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8537 (mt) REVERT: C 780 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8625 (mt-10) REVERT: C 887 THR cc_start: 0.8964 (p) cc_final: 0.8519 (t) REVERT: C 1123 SER cc_start: 0.8379 (p) cc_final: 0.8050 (p) REVERT: H 50 TYR cc_start: 0.8076 (p90) cc_final: 0.7570 (p90) REVERT: G 48 MET cc_start: 0.8522 (mtp) cc_final: 0.8034 (mpp) REVERT: G 65 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8608 (tp40) REVERT: G 67 GLN cc_start: 0.7851 (mp10) cc_final: 0.7363 (mp10) REVERT: G 81 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5904 (mp) REVERT: G 103 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.6807 (t80) REVERT: I 48 MET cc_start: 0.8288 (mtp) cc_final: 0.8014 (mtp) REVERT: I 65 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8176 (tp40) REVERT: I 67 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8041 (mp10) REVERT: I 110 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7047 (t80) outliers start: 115 outliers final: 76 residues processed: 325 average time/residue: 0.1365 time to fit residues: 75.9199 Evaluate side-chains 307 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 217 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 359 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 54 optimal weight: 0.0010 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1088 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.098930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074810 restraints weight = 78930.555| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.89 r_work: 0.3081 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28719 Z= 0.103 Angle : 0.566 11.886 39201 Z= 0.285 Chirality : 0.044 0.300 4542 Planarity : 0.004 0.069 5001 Dihedral : 4.969 36.845 3888 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.55 % Favored : 96.28 % Rotamer: Outliers : 3.38 % Allowed : 23.94 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3573 helix: 0.74 (0.21), residues: 633 sheet: -0.42 (0.17), residues: 930 loop : -1.26 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 38 TYR 0.021 0.001 TYR D 50 PHE 0.015 0.001 PHE B 817 TRP 0.018 0.001 TRP E 47 HIS 0.004 0.001 HIS I 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (28650) covalent geometry : angle 0.55673 / 0.28 (39051) SS BOND : bond 0.00263 / 0.17 ( 39) SS BOND : angle 1.08553 / 0.71 ( 78) hydrogen bonds : bond 0.03107 / 2.08 ( 958) hydrogen bonds : angle 4.85995 / 3.33 ( 2595) Misc. bond : bond 0.00046 / 0.03 ( 6) link_NAG-ASN : bond 0.00275 / 0.18 ( 24) link_NAG-ASN : angle 2.24554 / 1.41 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 247 time to evaluate : 1.084 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 559 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: A 585 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 887 THR cc_start: 0.8821 (p) cc_final: 0.8338 (t) REVERT: D 52 ASN cc_start: 0.8108 (m-40) cc_final: 0.7745 (m-40) REVERT: D 92 TRP cc_start: 0.8721 (t-100) cc_final: 0.8024 (t-100) REVERT: D 110 LEU cc_start: 0.6938 (mt) cc_final: 0.6280 (pp) REVERT: E 48 MET cc_start: 0.8122 (mtp) cc_final: 0.7889 (mpp) REVERT: E 57 ASP cc_start: 0.8862 (t0) cc_final: 0.8429 (t0) REVERT: E 65 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8396 (tp40) REVERT: E 67 GLN cc_start: 0.8294 (mm110) cc_final: 0.7956 (mp10) REVERT: E 78 THR cc_start: 0.7963 (p) cc_final: 0.7757 (p) REVERT: B 488 CYS cc_start: 0.4878 (OUTLIER) cc_final: 0.4544 (m) REVERT: B 559 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: B 780 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: B 896 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7735 (tp) REVERT: B 990 GLU cc_start: 0.8638 (pp20) cc_final: 0.8377 (pp20) REVERT: C 320 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8812 (m) REVERT: C 346 ARG cc_start: 0.8253 (mtm110) cc_final: 0.8020 (mtt90) REVERT: C 488 CYS cc_start: 0.5019 (OUTLIER) cc_final: 0.4562 (m) REVERT: C 559 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: C 585 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8476 (mt) REVERT: C 780 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8341 (mp0) REVERT: C 887 THR cc_start: 0.8785 (p) cc_final: 0.8384 (t) REVERT: C 1123 SER cc_start: 0.8370 (p) cc_final: 0.8013 (p) REVERT: F 110 LEU cc_start: 0.7034 (mt) cc_final: 0.6381 (pp) REVERT: H 50 TYR cc_start: 0.7699 (p90) cc_final: 0.7221 (p90) REVERT: G 48 MET cc_start: 0.8305 (mtp) cc_final: 0.7917 (mpp) REVERT: G 65 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (tp40) REVERT: G 67 GLN cc_start: 0.7937 (mp10) cc_final: 0.7653 (mp10) REVERT: I 48 MET cc_start: 0.8165 (mtp) cc_final: 0.7870 (mpp) REVERT: I 65 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8441 (tp40) REVERT: I 67 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8231 (mp10) REVERT: I 78 THR cc_start: 0.7729 (p) cc_final: 0.7405 (p) REVERT: I 110 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7122 (t80) outliers start: 100 outliers final: 61 residues processed: 329 average time/residue: 0.1353 time to fit residues: 75.8933 Evaluate side-chains 301 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 226 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 115 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 151 optimal weight: 0.2980 chunk 266 optimal weight: 8.9990 chunk 92 optimal weight: 0.0050 chunk 119 optimal weight: 0.0670 chunk 118 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 219 optimal weight: 10.0000 chunk 351 optimal weight: 4.9990 overall best weight: 0.5734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.099581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075483 restraints weight = 78449.215| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.93 r_work: 0.3092 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28719 Z= 0.099 Angle : 0.550 12.094 39201 Z= 0.277 Chirality : 0.043 0.300 4542 Planarity : 0.004 0.068 5001 Dihedral : 4.694 35.142 3887 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 3.17 % Allowed : 24.59 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.79 (0.14), residues: 3573 helix: 1.01 (0.21), residues: 654 sheet: -0.30 (0.17), residues: 915 loop : -1.16 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1091 TYR 0.018 0.001 TYR D 50 PHE 0.012 0.001 PHE F 63 TRP 0.017 0.001 TRP E 47 HIS 0.003 0.000 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (28650) covalent geometry : angle 0.54132 / 0.27 (39051) SS BOND : bond 0.00222 / 0.15 ( 39) SS BOND : angle 0.99743 / 0.64 ( 78) hydrogen bonds : bond 0.02940 / 1.97 ( 958) hydrogen bonds : angle 4.66361 / 3.21 ( 2595) Misc. bond : bond 0.00034 / 0.02 ( 6) link_NAG-ASN : bond 0.00241 / 0.16 ( 24) link_NAG-ASN : angle 2.11606 / 1.33 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 246 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 CYS cc_start: 0.4812 (OUTLIER) cc_final: 0.4285 (m) REVERT: A 559 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: A 585 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8356 (mt) REVERT: A 887 THR cc_start: 0.8757 (p) cc_final: 0.8274 (t) REVERT: D 92 TRP cc_start: 0.8622 (t-100) cc_final: 0.7691 (t-100) REVERT: D 110 LEU cc_start: 0.7021 (mt) cc_final: 0.6332 (pp) REVERT: E 48 MET cc_start: 0.8146 (mtp) cc_final: 0.7832 (mpp) REVERT: E 57 ASP cc_start: 0.8938 (t0) cc_final: 0.8495 (t0) REVERT: E 65 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8426 (tp40) REVERT: E 78 THR cc_start: 0.7954 (p) cc_final: 0.7679 (p) REVERT: B 191 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: B 495 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.3735 (t80) REVERT: B 559 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: B 780 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: B 896 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7668 (tp) REVERT: B 981 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9062 (mm) REVERT: C 320 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8780 (m) REVERT: C 488 CYS cc_start: 0.4683 (OUTLIER) cc_final: 0.4242 (m) REVERT: C 559 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: C 585 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8411 (mt) REVERT: C 887 THR cc_start: 0.8754 (p) cc_final: 0.8362 (t) REVERT: C 1123 SER cc_start: 0.8370 (p) cc_final: 0.8005 (p) REVERT: F 110 LEU cc_start: 0.7067 (mt) cc_final: 0.6298 (pp) REVERT: H 17 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8132 (mmpt) REVERT: H 50 TYR cc_start: 0.7772 (p90) cc_final: 0.7223 (p90) REVERT: H 55 ARG cc_start: 0.8513 (ptp90) cc_final: 0.8303 (ptp90) REVERT: G 48 MET cc_start: 0.8231 (mtp) cc_final: 0.7855 (mpp) REVERT: G 67 GLN cc_start: 0.7840 (mp10) cc_final: 0.7573 (mp10) REVERT: G 78 THR cc_start: 0.7806 (p) cc_final: 0.7536 (p) REVERT: G 103 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6508 (t80) REVERT: I 48 MET cc_start: 0.8074 (mtp) cc_final: 0.7793 (mpp) REVERT: I 65 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8650 (tp40) REVERT: I 67 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8176 (mp10) REVERT: I 78 THR cc_start: 0.7707 (p) cc_final: 0.7409 (p) outliers start: 94 outliers final: 55 residues processed: 324 average time/residue: 0.1332 time to fit residues: 73.8159 Evaluate side-chains 298 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 227 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 234 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 258 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.099454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075333 restraints weight = 79052.560| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.89 r_work: 0.3091 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28719 Z= 0.108 Angle : 0.549 13.432 39201 Z= 0.276 Chirality : 0.043 0.299 4542 Planarity : 0.004 0.067 5001 Dihedral : 4.603 36.252 3885 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 2.94 % Allowed : 24.62 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.69 (0.14), residues: 3573 helix: 1.12 (0.21), residues: 654 sheet: -0.24 (0.17), residues: 915 loop : -1.10 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 38 TYR 0.021 0.001 TYR D 50 PHE 0.018 0.001 PHE B 817 TRP 0.015 0.001 TRP E 47 HIS 0.004 0.000 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (28650) covalent geometry : angle 0.54085 / 0.27 (39051) SS BOND : bond 0.00246 / 0.16 ( 39) SS BOND : angle 1.03631 / 0.67 ( 78) hydrogen bonds : bond 0.02937 / 1.96 ( 958) hydrogen bonds : angle 4.62181 / 3.19 ( 2595) Misc. bond : bond 0.00028 / 0.02 ( 6) link_NAG-ASN : bond 0.00228 / 0.15 ( 24) link_NAG-ASN : angle 2.06942 / 1.30 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 236 time to evaluate : 1.102 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 488 CYS cc_start: 0.4824 (OUTLIER) cc_final: 0.4294 (m) REVERT: A 559 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: A 585 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 780 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: A 887 THR cc_start: 0.8783 (p) cc_final: 0.8315 (t) REVERT: D 92 TRP cc_start: 0.8586 (t-100) cc_final: 0.7571 (t-100) REVERT: D 110 LEU cc_start: 0.6939 (mt) cc_final: 0.6225 (pp) REVERT: E 48 MET cc_start: 0.8156 (mtp) cc_final: 0.7850 (mpp) REVERT: E 57 ASP cc_start: 0.8872 (t0) cc_final: 0.8423 (t0) REVERT: E 65 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8420 (tp40) REVERT: E 78 THR cc_start: 0.8005 (p) cc_final: 0.7739 (p) REVERT: B 191 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 495 TYR cc_start: 0.5445 (OUTLIER) cc_final: 0.3474 (t80) REVERT: B 559 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: B 780 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: B 896 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7745 (tp) REVERT: B 990 GLU cc_start: 0.8576 (pp20) cc_final: 0.8335 (pp20) REVERT: C 320 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8829 (m) REVERT: C 488 CYS cc_start: 0.4761 (OUTLIER) cc_final: 0.4298 (m) REVERT: C 559 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: C 585 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8346 (mt) REVERT: C 1123 SER cc_start: 0.8438 (p) cc_final: 0.8072 (p) REVERT: F 110 LEU cc_start: 0.7081 (mt) cc_final: 0.6315 (pp) REVERT: H 50 TYR cc_start: 0.7736 (p90) cc_final: 0.7258 (p90) REVERT: G 48 MET cc_start: 0.8324 (mtp) cc_final: 0.7929 (mpp) REVERT: G 57 ASP cc_start: 0.8664 (t0) cc_final: 0.8351 (t0) REVERT: G 78 THR cc_start: 0.7785 (p) cc_final: 0.7519 (p) REVERT: G 103 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6519 (t80) REVERT: I 48 MET cc_start: 0.8041 (mtp) cc_final: 0.7767 (mpp) REVERT: I 65 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8378 (tp40) REVERT: I 67 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8174 (mp10) REVERT: I 78 THR cc_start: 0.7694 (p) cc_final: 0.7399 (p) outliers start: 87 outliers final: 61 residues processed: 309 average time/residue: 0.1439 time to fit residues: 75.8348 Evaluate side-chains 304 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 103 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 88 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 303 optimal weight: 0.9980 chunk 343 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 318 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 295 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.098666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074505 restraints weight = 79105.255| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.88 r_work: 0.3074 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28719 Z= 0.136 Angle : 0.559 9.621 39201 Z= 0.282 Chirality : 0.044 0.296 4542 Planarity : 0.004 0.067 5001 Dihedral : 4.629 36.767 3882 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 2.84 % Allowed : 24.79 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.62 (0.14), residues: 3573 helix: 1.12 (0.20), residues: 654 sheet: -0.11 (0.17), residues: 918 loop : -1.09 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1091 TYR 0.018 0.001 TYR D 50 PHE 0.015 0.001 PHE F 63 TRP 0.014 0.001 TRP E 47 HIS 0.010 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (28650) covalent geometry : angle 0.55047 / 0.28 (39051) SS BOND : bond 0.00270 / 0.18 ( 39) SS BOND : angle 1.09637 / 0.71 ( 78) hydrogen bonds : bond 0.03093 / 2.06 ( 958) hydrogen bonds : angle 4.67136 / 3.23 ( 2595) Misc. bond : bond 0.00019 / 0.01 ( 6) link_NAG-ASN : bond 0.00197 / 0.13 ( 24) link_NAG-ASN : angle 2.08029 / 1.31 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 225 time to evaluate : 1.027 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 559 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: A 585 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8324 (mt) REVERT: A 887 THR cc_start: 0.8843 (p) cc_final: 0.8380 (t) REVERT: D 92 TRP cc_start: 0.8645 (t-100) cc_final: 0.7582 (t-100) REVERT: E 48 MET cc_start: 0.8197 (mtp) cc_final: 0.7902 (mpp) REVERT: E 57 ASP cc_start: 0.8890 (t0) cc_final: 0.8444 (t0) REVERT: E 65 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: E 78 THR cc_start: 0.8007 (p) cc_final: 0.7740 (p) REVERT: B 191 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 495 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.3264 (t80) REVERT: B 559 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: B 780 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: B 896 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7874 (tp) REVERT: B 990 GLU cc_start: 0.8584 (pp20) cc_final: 0.8334 (pp20) REVERT: C 421 TYR cc_start: 0.8818 (m-80) cc_final: 0.8606 (m-80) REVERT: C 559 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: C 585 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8339 (mt) REVERT: C 780 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8289 (mp0) REVERT: C 887 THR cc_start: 0.8826 (p) cc_final: 0.8451 (t) REVERT: C 1123 SER cc_start: 0.8450 (p) cc_final: 0.8076 (p) REVERT: H 17 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8143 (mmpt) REVERT: H 50 TYR cc_start: 0.7823 (p90) cc_final: 0.7293 (p90) REVERT: H 55 ARG cc_start: 0.8524 (ptp90) cc_final: 0.8284 (ptp90) REVERT: H 63 PHE cc_start: 0.6728 (m-80) cc_final: 0.6527 (m-80) REVERT: G 48 MET cc_start: 0.8269 (mtp) cc_final: 0.7871 (mpp) REVERT: G 57 ASP cc_start: 0.8655 (t0) cc_final: 0.8355 (t0) REVERT: G 78 THR cc_start: 0.7701 (p) cc_final: 0.7438 (p) REVERT: G 103 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6551 (t80) REVERT: I 48 MET cc_start: 0.8195 (mtp) cc_final: 0.7847 (mpp) REVERT: I 65 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8553 (tp40) REVERT: I 67 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8155 (mp10) REVERT: I 78 THR cc_start: 0.7706 (p) cc_final: 0.7414 (p) outliers start: 84 outliers final: 66 residues processed: 292 average time/residue: 0.1392 time to fit residues: 70.1141 Evaluate side-chains 295 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 218 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 272 optimal weight: 0.1980 chunk 203 optimal weight: 0.8980 chunk 161 optimal weight: 0.0470 chunk 303 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 151 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 784 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.099622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075658 restraints weight = 78190.307| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.88 r_work: 0.3096 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 28719 Z= 0.098 Angle : 0.547 10.017 39201 Z= 0.274 Chirality : 0.043 0.289 4542 Planarity : 0.004 0.067 5001 Dihedral : 4.509 35.139 3882 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 2.57 % Allowed : 24.79 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.59 (0.14), residues: 3573 helix: 1.25 (0.21), residues: 654 sheet: -0.16 (0.17), residues: 888 loop : -1.06 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1091 TYR 0.021 0.001 TYR D 50 PHE 0.015 0.001 PHE B 817 TRP 0.017 0.001 TRP I 47 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (28650) covalent geometry : angle 0.53894 / 0.27 (39051) SS BOND : bond 0.00242 / 0.16 ( 39) SS BOND : angle 0.99719 / 0.64 ( 78) hydrogen bonds : bond 0.02889 / 1.93 ( 958) hydrogen bonds : angle 4.56323 / 3.15 ( 2595) Misc. bond : bond 0.00035 / 0.02 ( 6) link_NAG-ASN : bond 0.00254 / 0.16 ( 24) link_NAG-ASN : angle 2.00537 / 1.27 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 231 time to evaluate : 0.849 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 559 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: A 585 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 780 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: A 887 THR cc_start: 0.8766 (p) cc_final: 0.8294 (t) REVERT: D 92 TRP cc_start: 0.8576 (t-100) cc_final: 0.7528 (t-100) REVERT: D 110 LEU cc_start: 0.6775 (mt) cc_final: 0.6077 (pp) REVERT: E 48 MET cc_start: 0.8128 (mtp) cc_final: 0.7864 (mpp) REVERT: E 57 ASP cc_start: 0.8933 (t0) cc_final: 0.8471 (t0) REVERT: E 65 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8408 (tp40) REVERT: E 78 THR cc_start: 0.7949 (p) cc_final: 0.7691 (p) REVERT: B 191 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7798 (mt-10) REVERT: B 559 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: B 780 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: B 896 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 990 GLU cc_start: 0.8567 (pp20) cc_final: 0.8336 (pp20) REVERT: C 559 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: C 585 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8352 (mt) REVERT: C 780 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8314 (mp0) REVERT: C 1123 SER cc_start: 0.8422 (p) cc_final: 0.8050 (p) REVERT: F 50 TYR cc_start: 0.7597 (p90) cc_final: 0.7062 (p90) REVERT: F 110 LEU cc_start: 0.7030 (mt) cc_final: 0.6262 (pp) REVERT: H 50 TYR cc_start: 0.7736 (p90) cc_final: 0.7290 (p90) REVERT: G 48 MET cc_start: 0.8202 (mtp) cc_final: 0.7838 (mpp) REVERT: G 57 ASP cc_start: 0.8608 (t0) cc_final: 0.8297 (t0) REVERT: G 78 THR cc_start: 0.7737 (p) cc_final: 0.7420 (p) REVERT: G 103 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6527 (t80) REVERT: I 48 MET cc_start: 0.8060 (mtp) cc_final: 0.7747 (mpp) REVERT: I 65 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8538 (tp40) REVERT: I 67 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8184 (mp10) REVERT: I 78 THR cc_start: 0.7894 (p) cc_final: 0.7634 (p) outliers start: 76 outliers final: 59 residues processed: 296 average time/residue: 0.1475 time to fit residues: 75.0164 Evaluate side-chains 291 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1011 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.097632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073302 restraints weight = 79821.523| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.93 r_work: 0.3045 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28719 Z= 0.194 Angle : 0.598 14.881 39201 Z= 0.301 Chirality : 0.045 0.293 4542 Planarity : 0.004 0.066 5001 Dihedral : 4.748 38.385 3882 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 2.84 % Allowed : 24.89 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.58 (0.14), residues: 3573 helix: 1.11 (0.21), residues: 636 sheet: -0.10 (0.17), residues: 918 loop : -1.01 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1091 TYR 0.020 0.001 TYR D 50 PHE 0.027 0.001 PHE B 168 TRP 0.013 0.002 TRP I 47 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (28650) covalent geometry : angle 0.58917 / 0.30 (39051) SS BOND : bond 0.00334 / 0.23 ( 39) SS BOND : angle 1.23147 / 0.81 ( 78) hydrogen bonds : bond 0.03311 / 2.20 ( 958) hydrogen bonds : angle 4.75343 / 3.28 ( 2595) Misc. bond : bond 0.00018 / 0.01 ( 6) link_NAG-ASN : bond 0.00177 / 0.12 ( 24) link_NAG-ASN : angle 2.12777 / 1.33 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5656.06 seconds wall clock time: 98 minutes 0.14 seconds (5880.14 seconds total)