Starting phenix.real_space_refine on Sun May 25 14:44:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5h_36906/05_2025/8k5h_36906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5h_36906/05_2025/8k5h_36906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k5h_36906/05_2025/8k5h_36906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5h_36906/05_2025/8k5h_36906.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5h_36906/05_2025/8k5h_36906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5h_36906/05_2025/8k5h_36906.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1744 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16255 2.51 5 N 4169 2.21 5 O 4964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.57s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25502 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 58, 'TRANS': 982} Chain breaks: 7 Chain: "A" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8226 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 58, 'TRANS': 989} Chain breaks: 7 Chain: "C" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6651 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 46, 'TRANS': 806} Chain breaks: 7 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.56, per 1000 atoms: 0.57 Number of scatterers: 25502 At special positions: 0 Unit cell: (134, 136.68, 192.96, 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 114 16.00 O 4964 8.00 N 4169 7.00 C 16255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.02 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.02 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.01 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.02 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.02 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.01 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.02 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.01 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 120 " " NAG A1303 " - " ASN A 160 " " NAG A1304 " - " ASN A 279 " " NAG A1305 " - " ASN A 328 " " NAG A1306 " - " ASN A 340 " " NAG A1307 " - " ASN A 600 " " NAG A1308 " - " ASN A 613 " " NAG A1309 " - " ASN A 706 " " NAG A1310 " - " ASN A1071 " " NAG A1311 " - " ASN A1095 " " NAG A1312 " - " ASN A1131 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 120 " " NAG B1303 " - " ASN B 160 " " NAG B1304 " - " ASN B 231 " " NAG B1305 " - " ASN B 279 " " NAG B1306 " - " ASN B 328 " " NAG B1307 " - " ASN B 340 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 706 " " NAG B1310 " - " ASN B1071 " " NAG B1311 " - " ASN B1095 " " NAG B1312 " - " ASN B1131 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 160 " " NAG C1303 " - " ASN C 279 " " NAG C1304 " - " ASN C 328 " " NAG C1305 " - " ASN C 600 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C 706 " " NAG C1308 " - " ASN C1071 " " NAG C1309 " - " ASN C1095 " " NAG C1310 " - " ASN C1131 " " NAG D 1 " - " ASN B 714 " " NAG E 1 " - " ASN B 798 " " NAG F 1 " - " ASN A 231 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN C 231 " " NAG K 1 " - " ASN C 714 " " NAG M 1 " - " ASN C 798 " Time building additional restraints: 6.42 Conformation dependent library (CDL) restraints added in 3.2 seconds 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5948 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 55 sheets defined 24.3% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.733A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.509A pdb=" N TYR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.148A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.689A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.692A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 824 through 826 No H-bonds generated for 'chain 'B' and resid 824 through 826' Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 882 through 887 removed outlier: 4.231A pdb=" N PHE B 885 " --> pdb=" O GLY B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.754A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 937 removed outlier: 4.026A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.091A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.624A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1142 removed outlier: 4.414A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.865A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.838A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.812A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 803 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.894A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 937 removed outlier: 6.522A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.448A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.067A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 removed outlier: 3.736A pdb=" N ASP A1143 " --> pdb=" O GLN A1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 613 through 617 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.605A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.614A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 846 through 853 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 4.245A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 905 through 907 No H-bonds generated for 'chain 'C' and resid 905 through 907' Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.645A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 Processing helix chain 'C' and resid 942 through 962 removed outlier: 4.348A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.900A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C1015 " --> pdb=" O ARG C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1142 removed outlier: 4.112A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.879A pdb=" N THR H 91 " --> pdb=" O PHE H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.513A pdb=" N PHE B 65 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 262 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 186 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.495A pdb=" N PHE B 43 " --> pdb=" O ARG C 564 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.901A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.803A pdb=" N GLY B 105 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 238 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 127 through 133 removed outlier: 7.583A pdb=" N VAL B 128 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS B 161 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 132 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 157 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 316 removed outlier: 3.697A pdb=" N THR B 312 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.594A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 573 " --> pdb=" O LEU B 582 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.884A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 432 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 373 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 388 through 389 removed outlier: 4.036A pdb=" N VAL B 521 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 450 Processing sheet with id=AB2, first strand: chain 'B' and resid 562 through 563 removed outlier: 7.419A pdb=" N PHE B 562 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.357A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 698 through 699 removed outlier: 6.806A pdb=" N ALA B 698 " --> pdb=" O ILE A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 710 Processing sheet with id=AB6, first strand: chain 'B' and resid 717 through 725 removed outlier: 3.530A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 717 through 725 removed outlier: 3.530A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AB9, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AC1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.809A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 264 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 260 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 91 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 183 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 182 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 188 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.743A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.289A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.601A pdb=" N SER A 167 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 130 through 133 removed outlier: 6.703A pdb=" N GLU A 130 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 158 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN A 132 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AC8, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AC9, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.788A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 394 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.091A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AD4, first strand: chain 'A' and resid 536 through 540 removed outlier: 3.601A pdb=" N THR A 550 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 670 through 672 Processing sheet with id=AD6, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.985A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.547A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A1044 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.547A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AE1, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.895A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 184 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.502A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 53 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 164 through 167 removed outlier: 3.615A pdb=" N VAL C 124 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASN C 119 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 238 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.858A pdb=" N GLU C 130 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN C 159 " --> pdb=" O GLU C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 308 through 312 Processing sheet with id=AE7, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.513A pdb=" N VAL C 536 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 545 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 583 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.966A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 688 " --> pdb=" O GLN C 672 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.668A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 718 " --> pdb=" O THR C1063 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C1053 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.668A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 718 " --> pdb=" O THR C1063 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.677A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.534A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.534A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 22 Processing sheet with id=AF7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.818A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AG1, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.807A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2520 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: 10.59 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6839 1.33 - 1.46: 6630 1.46 - 1.58: 12462 1.58 - 1.71: 0 1.71 - 1.84: 146 Bond restraints: 26077 Sorted by residual: bond pdb=" C VAL A 857 " pdb=" N LEU A 858 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.07e-02 2.33e+03 1.76e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C LEU B 458 " pdb=" N LYS B 459 " ideal model delta sigma weight residual 1.331 1.291 0.040 1.59e-02 3.96e+03 6.36e+00 bond pdb=" C1 NAG A1312 " pdb=" O5 NAG A1312 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C LYS H 12 " pdb=" N LYS H 13 " ideal model delta sigma weight residual 1.329 1.260 0.069 3.03e-02 1.09e+03 5.15e+00 ... (remaining 26072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 34320 2.44 - 4.88: 1047 4.88 - 7.32: 91 7.32 - 9.76: 15 9.76 - 12.20: 4 Bond angle restraints: 35477 Sorted by residual: angle pdb=" CB ARG B1104 " pdb=" CG ARG B1104 " pdb=" CD ARG B1104 " ideal model delta sigma weight residual 111.30 123.50 -12.20 2.30e+00 1.89e-01 2.81e+01 angle pdb=" N TYR B 377 " pdb=" CA TYR B 377 " pdb=" C TYR B 377 " ideal model delta sigma weight residual 111.17 118.16 -6.99 1.41e+00 5.03e-01 2.46e+01 angle pdb=" CG ARG B1104 " pdb=" CD ARG B1104 " pdb=" NE ARG B1104 " ideal model delta sigma weight residual 112.00 102.40 9.60 2.20e+00 2.07e-01 1.90e+01 angle pdb=" C PHE B 756 " pdb=" N CYS B 757 " pdb=" CA CYS B 757 " ideal model delta sigma weight residual 121.14 113.75 7.39 1.75e+00 3.27e-01 1.78e+01 angle pdb=" CA GLN B 560 " pdb=" CB GLN B 560 " pdb=" CG GLN B 560 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 ... (remaining 35472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.21: 14110 18.21 - 36.43: 1665 36.43 - 54.64: 335 54.64 - 72.85: 88 72.85 - 91.07: 26 Dihedral angle restraints: 16224 sinusoidal: 6994 harmonic: 9230 Sorted by residual: dihedral pdb=" CB CYS B 477 " pdb=" SG CYS B 477 " pdb=" SG CYS B 485 " pdb=" CB CYS B 485 " ideal model delta sinusoidal sigma weight residual 93.00 173.09 -80.09 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 298 " pdb=" CB CYS B 298 " ideal model delta sinusoidal sigma weight residual -86.00 -162.51 76.51 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A 477 " pdb=" SG CYS A 477 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual -86.00 -158.26 72.26 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 16221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3930 0.111 - 0.223: 231 0.223 - 0.334: 5 0.334 - 0.445: 1 0.445 - 0.556: 2 Chirality restraints: 4169 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.74e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1071 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 4166 not shown) Planarity restraints: 4561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 983 " -0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO A 984 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 340 " -0.032 2.00e-02 2.50e+03 2.81e-02 9.88e+00 pdb=" CG ASN A 340 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 340 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 340 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 883 " -0.018 2.00e-02 2.50e+03 1.84e-02 8.51e+00 pdb=" CG TRP A 883 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 883 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 883 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 883 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 883 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 883 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 883 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 883 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 883 " -0.000 2.00e-02 2.50e+03 ... (remaining 4558 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 327 2.56 - 3.15: 21767 3.15 - 3.73: 36123 3.73 - 4.32: 50189 4.32 - 4.90: 86291 Nonbonded interactions: 194697 Sorted by model distance: nonbonded pdb=" OG1 THR B 320 " pdb=" OE1 GLU B 321 " model vdw 1.977 3.040 nonbonded pdb=" NZ LYS C 808 " pdb=" OG SER C 810 " model vdw 2.033 3.120 nonbonded pdb=" NZ LYS B 41 " pdb=" O PHE C 559 " model vdw 2.063 3.120 nonbonded pdb=" O PHE C 820 " pdb=" OG1 THR C 824 " model vdw 2.080 3.040 nonbonded pdb=" O ILE B 93 " pdb=" NZ LYS B 182 " model vdw 2.081 3.120 ... (remaining 194692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 67 or resid 78 through 139 or resid 149 through \ 174 or resid 179 through 240 or resid 261 through 1144 or resid 1301 through 13 \ 12)) selection = (chain 'B' and (resid 27 through 139 or resid 149 through 1144 or resid 1301 thr \ ough 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.880 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.012 0.089 26164 Z= 0.506 Angle : 1.011 12.367 35701 Z= 0.525 Chirality : 0.061 0.556 4169 Planarity : 0.006 0.090 4519 Dihedral : 16.105 91.067 10165 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3119 helix: 0.88 (0.20), residues: 665 sheet: -1.11 (0.20), residues: 680 loop : -2.24 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP A 883 HIS 0.011 0.002 HIS A1045 PHE 0.038 0.004 PHE A 903 TYR 0.050 0.003 TYR A 901 ARG 0.019 0.002 ARG A1036 Details of bonding type rmsd link_NAG-ASN : bond 0.00872 ( 42) link_NAG-ASN : angle 3.98329 ( 126) link_BETA1-4 : bond 0.00506 ( 8) link_BETA1-4 : angle 2.46774 ( 24) hydrogen bonds : bond 0.21345 ( 884) hydrogen bonds : angle 7.79966 ( 2520) SS BOND : bond 0.00870 ( 37) SS BOND : angle 3.25414 ( 74) covalent geometry : bond 0.01212 (26077) covalent geometry : angle 0.97267 (35477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 TYR cc_start: 0.8067 (m-80) cc_final: 0.7615 (m-80) outliers start: 4 outliers final: 0 residues processed: 253 average time/residue: 0.3917 time to fit residues: 154.3504 Evaluate side-chains 155 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.7980 chunk 238 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 0.1980 chunk 183 optimal weight: 0.6980 chunk 286 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN A 66 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 202 HIS A 242 HIS ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 748 ASN A 904 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN C 748 ASN C 801 GLN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN L 39 GLN L 101 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.065104 restraints weight = 57814.735| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.97 r_work: 0.2844 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26164 Z= 0.147 Angle : 0.721 11.454 35701 Z= 0.367 Chirality : 0.048 0.272 4169 Planarity : 0.006 0.074 4519 Dihedral : 7.223 59.166 4443 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.97 % Allowed : 10.59 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3119 helix: 1.59 (0.21), residues: 652 sheet: -0.62 (0.19), residues: 726 loop : -1.98 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 97 HIS 0.010 0.001 HIS A 202 PHE 0.021 0.001 PHE A 138 TYR 0.017 0.001 TYR L 88 ARG 0.006 0.001 ARG C 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 42) link_NAG-ASN : angle 2.91347 ( 126) link_BETA1-4 : bond 0.00438 ( 8) link_BETA1-4 : angle 1.70088 ( 24) hydrogen bonds : bond 0.05852 ( 884) hydrogen bonds : angle 5.80397 ( 2520) SS BOND : bond 0.00552 ( 37) SS BOND : angle 1.65771 ( 74) covalent geometry : bond 0.00315 (26077) covalent geometry : angle 0.69636 (35477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ARG cc_start: 0.8755 (ppt170) cc_final: 0.8085 (pmt-80) REVERT: C 195 TYR cc_start: 0.8095 (m-80) cc_final: 0.7308 (m-80) REVERT: H 35 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: H 46 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8484 (tt0) REVERT: H 52 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7479 (p) REVERT: H 74 MET cc_start: 0.9203 (pmm) cc_final: 0.8435 (mmm) REVERT: H 100 TYR cc_start: 0.8467 (t80) cc_final: 0.8216 (t80) REVERT: H 109 PHE cc_start: 0.7058 (m-10) cc_final: 0.6649 (m-80) REVERT: H 117 MET cc_start: 0.7017 (tpt) cc_final: 0.6551 (tpp) REVERT: L 33 TYR cc_start: 0.7864 (m-80) cc_final: 0.7252 (m-80) REVERT: L 34 LEU cc_start: 0.7878 (pp) cc_final: 0.7560 (pp) REVERT: L 46 ARG cc_start: 0.8308 (ptt180) cc_final: 0.7986 (ptm160) REVERT: L 72 PHE cc_start: 0.6835 (m-80) cc_final: 0.6179 (m-10) REVERT: L 87 TYR cc_start: 0.7488 (m-80) cc_final: 0.7194 (m-80) REVERT: L 92 TYR cc_start: 0.8624 (p90) cc_final: 0.8217 (p90) outliers start: 27 outliers final: 10 residues processed: 192 average time/residue: 0.3838 time to fit residues: 116.9193 Evaluate side-chains 156 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 904 ASN Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain L residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 21 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS A 66 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.063437 restraints weight = 57939.009| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.30 r_work: 0.2772 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26164 Z= 0.173 Angle : 0.674 10.315 35701 Z= 0.342 Chirality : 0.047 0.245 4169 Planarity : 0.005 0.066 4519 Dihedral : 6.708 58.947 4443 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.62 % Allowed : 13.69 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3119 helix: 1.74 (0.21), residues: 649 sheet: -0.46 (0.19), residues: 741 loop : -1.85 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 97 HIS 0.016 0.001 HIS A 202 PHE 0.042 0.001 PHE C 978 TYR 0.017 0.001 TYR C1064 ARG 0.008 0.001 ARG B1036 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 42) link_NAG-ASN : angle 2.87252 ( 126) link_BETA1-4 : bond 0.00200 ( 8) link_BETA1-4 : angle 1.75775 ( 24) hydrogen bonds : bond 0.05955 ( 884) hydrogen bonds : angle 5.46019 ( 2520) SS BOND : bond 0.00380 ( 37) SS BOND : angle 1.58797 ( 74) covalent geometry : bond 0.00413 (26077) covalent geometry : angle 0.64799 (35477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1028 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: A 172 MET cc_start: 0.8159 (ppp) cc_final: 0.7380 (ppp) REVERT: A 405 ARG cc_start: 0.8740 (ppt170) cc_final: 0.8052 (pmt-80) REVERT: A 560 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6930 (mt0) REVERT: C 172 MET cc_start: 0.8136 (mmp) cc_final: 0.7532 (mmm) REVERT: C 195 TYR cc_start: 0.8122 (m-80) cc_final: 0.7226 (m-80) REVERT: H 3 GLN cc_start: 0.7590 (pm20) cc_final: 0.7108 (pm20) REVERT: H 35 GLN cc_start: 0.7707 (pm20) cc_final: 0.7401 (pm20) REVERT: H 74 MET cc_start: 0.9227 (pmm) cc_final: 0.8471 (mmm) REVERT: H 109 PHE cc_start: 0.7018 (m-10) cc_final: 0.6723 (m-80) REVERT: H 117 MET cc_start: 0.7044 (tpt) cc_final: 0.6599 (tpp) REVERT: L 34 LEU cc_start: 0.8151 (pp) cc_final: 0.7810 (pp) REVERT: L 37 TYR cc_start: 0.8284 (m-80) cc_final: 0.7560 (m-80) REVERT: L 92 TYR cc_start: 0.8543 (p90) cc_final: 0.8340 (p90) outliers start: 45 outliers final: 29 residues processed: 185 average time/residue: 0.3820 time to fit residues: 114.3293 Evaluate side-chains 173 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 112 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS B 752 GLN B1061 HIS A 66 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.102819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.062280 restraints weight = 58843.462| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.31 r_work: 0.2749 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26164 Z= 0.199 Angle : 0.668 12.222 35701 Z= 0.338 Chirality : 0.047 0.268 4169 Planarity : 0.005 0.064 4519 Dihedral : 6.423 59.660 4443 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.49 % Allowed : 14.88 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3119 helix: 1.74 (0.21), residues: 649 sheet: -0.33 (0.19), residues: 750 loop : -1.85 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 97 HIS 0.013 0.001 HIS B 622 PHE 0.025 0.002 PHE C 978 TYR 0.018 0.001 TYR C1064 ARG 0.004 0.001 ARG H 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 42) link_NAG-ASN : angle 2.68793 ( 126) link_BETA1-4 : bond 0.00175 ( 8) link_BETA1-4 : angle 1.76782 ( 24) hydrogen bonds : bond 0.06095 ( 884) hydrogen bonds : angle 5.31361 ( 2520) SS BOND : bond 0.00717 ( 37) SS BOND : angle 1.75754 ( 74) covalent geometry : bond 0.00484 (26077) covalent geometry : angle 0.64428 (35477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 146 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 PHE cc_start: 0.8241 (m-10) cc_final: 0.7955 (m-10) REVERT: B 1028 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: A 172 MET cc_start: 0.8086 (ppp) cc_final: 0.7330 (ppp) REVERT: A 405 ARG cc_start: 0.8776 (ppt170) cc_final: 0.8109 (pmt-80) REVERT: A 560 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7077 (mt0) REVERT: A 577 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.6770 (mp10) REVERT: C 172 MET cc_start: 0.8214 (mmp) cc_final: 0.7618 (mmm) REVERT: C 195 TYR cc_start: 0.8351 (m-80) cc_final: 0.7492 (m-80) REVERT: C 978 PHE cc_start: 0.7511 (p90) cc_final: 0.7045 (p90) REVERT: H 23 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8246 (tmmt) REVERT: H 35 GLN cc_start: 0.7771 (pm20) cc_final: 0.7428 (pm20) REVERT: H 117 MET cc_start: 0.7026 (tpt) cc_final: 0.6603 (tpp) REVERT: L 37 TYR cc_start: 0.8324 (m-80) cc_final: 0.7817 (m-80) outliers start: 69 outliers final: 47 residues processed: 198 average time/residue: 0.3539 time to fit residues: 113.6971 Evaluate side-chains 187 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 8 optimal weight: 9.9990 chunk 278 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 241 optimal weight: 0.0060 chunk 202 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** B 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 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 = 0.3718 r_free = 0.3718 target = 0.103741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.063363 restraints weight = 58526.296| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.32 r_work: 0.2771 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26164 Z= 0.136 Angle : 0.621 12.393 35701 Z= 0.313 Chirality : 0.046 0.254 4169 Planarity : 0.005 0.061 4519 Dihedral : 6.103 59.738 4443 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.59 % Allowed : 16.25 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3119 helix: 1.90 (0.21), residues: 648 sheet: -0.16 (0.20), residues: 721 loop : -1.78 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 97 HIS 0.007 0.001 HIS B 622 PHE 0.017 0.001 PHE C 978 TYR 0.017 0.001 TYR A 366 ARG 0.004 0.000 ARG H 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 42) link_NAG-ASN : angle 2.53800 ( 126) link_BETA1-4 : bond 0.00262 ( 8) link_BETA1-4 : angle 1.74380 ( 24) hydrogen bonds : bond 0.05309 ( 884) hydrogen bonds : angle 5.12220 ( 2520) SS BOND : bond 0.00327 ( 37) SS BOND : angle 1.74889 ( 74) covalent geometry : bond 0.00319 (26077) covalent geometry : angle 0.59779 (35477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 145 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 PHE cc_start: 0.8251 (m-80) cc_final: 0.7966 (m-10) REVERT: B 452 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9015 (tp) REVERT: B 1028 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: A 172 MET cc_start: 0.7954 (ppp) cc_final: 0.7362 (ppp) REVERT: A 405 ARG cc_start: 0.8736 (ppt170) cc_final: 0.8100 (pmt-80) REVERT: A 560 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7021 (mt0) REVERT: A 577 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: C 132 GLN cc_start: 0.8925 (mm110) cc_final: 0.8650 (mm110) REVERT: C 172 MET cc_start: 0.8179 (mmp) cc_final: 0.7558 (mmm) REVERT: C 195 TYR cc_start: 0.8331 (m-80) cc_final: 0.7426 (m-80) REVERT: C 560 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: H 23 LYS cc_start: 0.8541 (tmmt) cc_final: 0.8263 (tmmt) REVERT: H 74 MET cc_start: 0.9263 (pmm) cc_final: 0.8280 (mmt) REVERT: H 100 TYR cc_start: 0.8545 (t80) cc_final: 0.8313 (t80) REVERT: H 117 MET cc_start: 0.7171 (tpt) cc_final: 0.6744 (tpp) REVERT: L 33 TYR cc_start: 0.8355 (m-80) cc_final: 0.8075 (m-10) REVERT: L 37 TYR cc_start: 0.8266 (m-80) cc_final: 0.7972 (m-80) outliers start: 72 outliers final: 43 residues processed: 198 average time/residue: 0.3510 time to fit residues: 114.1742 Evaluate side-chains 186 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 287 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 311 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS A 66 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 904 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.102992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062631 restraints weight = 58201.180| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.29 r_work: 0.2754 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26164 Z= 0.165 Angle : 0.628 12.783 35701 Z= 0.317 Chirality : 0.046 0.249 4169 Planarity : 0.005 0.058 4519 Dihedral : 5.937 59.858 4443 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.63 % Allowed : 16.72 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3119 helix: 1.90 (0.21), residues: 649 sheet: -0.12 (0.20), residues: 733 loop : -1.76 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L 97 HIS 0.017 0.001 HIS A 202 PHE 0.024 0.001 PHE C 978 TYR 0.017 0.001 TYR C1064 ARG 0.006 0.000 ARG H 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 42) link_NAG-ASN : angle 2.49950 ( 126) link_BETA1-4 : bond 0.00216 ( 8) link_BETA1-4 : angle 1.72443 ( 24) hydrogen bonds : bond 0.05550 ( 884) hydrogen bonds : angle 5.07706 ( 2520) SS BOND : bond 0.00343 ( 37) SS BOND : angle 1.66512 ( 74) covalent geometry : bond 0.00401 (26077) covalent geometry : angle 0.60622 (35477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 140 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 PHE cc_start: 0.8277 (m-80) cc_final: 0.8001 (m-10) REVERT: B 452 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8912 (tp) REVERT: B 1028 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 172 MET cc_start: 0.8010 (ppp) cc_final: 0.7527 (ppp) REVERT: A 405 ARG cc_start: 0.8741 (ppt170) cc_final: 0.8119 (pmt-80) REVERT: A 560 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7158 (mt0) REVERT: A 577 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.6800 (mp10) REVERT: C 172 MET cc_start: 0.7949 (mmp) cc_final: 0.7319 (mmm) REVERT: C 195 TYR cc_start: 0.8357 (m-80) cc_final: 0.7429 (m-80) REVERT: C 560 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: H 23 LYS cc_start: 0.8631 (tmmt) cc_final: 0.8307 (tmmt) REVERT: H 27 PHE cc_start: 0.5903 (p90) cc_final: 0.5668 (p90) REVERT: H 74 MET cc_start: 0.9260 (pmm) cc_final: 0.8329 (mmt) REVERT: H 100 TYR cc_start: 0.8568 (t80) cc_final: 0.8308 (t80) REVERT: H 117 MET cc_start: 0.7142 (tpt) cc_final: 0.6712 (tpp) REVERT: L 33 TYR cc_start: 0.8455 (m-80) cc_final: 0.8098 (m-10) outliers start: 73 outliers final: 57 residues processed: 194 average time/residue: 0.3431 time to fit residues: 108.9371 Evaluate side-chains 201 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 139 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 97 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 182 optimal weight: 0.4980 chunk 156 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 260 optimal weight: 0.9990 chunk 312 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 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 = 0.3719 r_free = 0.3719 target = 0.103768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063434 restraints weight = 58518.944| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.35 r_work: 0.2772 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26164 Z= 0.127 Angle : 0.599 12.603 35701 Z= 0.301 Chirality : 0.045 0.253 4169 Planarity : 0.005 0.057 4519 Dihedral : 5.716 59.779 4443 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.70 % Allowed : 17.15 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3119 helix: 2.04 (0.21), residues: 644 sheet: -0.02 (0.20), residues: 719 loop : -1.72 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP L 97 HIS 0.005 0.001 HIS C 202 PHE 0.028 0.001 PHE C 978 TYR 0.016 0.001 TYR A1064 ARG 0.003 0.000 ARG H 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 42) link_NAG-ASN : angle 2.42948 ( 126) link_BETA1-4 : bond 0.00288 ( 8) link_BETA1-4 : angle 1.71117 ( 24) hydrogen bonds : bond 0.04981 ( 884) hydrogen bonds : angle 4.93509 ( 2520) SS BOND : bond 0.00311 ( 37) SS BOND : angle 1.46931 ( 74) covalent geometry : bond 0.00295 (26077) covalent geometry : angle 0.57724 (35477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 147 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 PHE cc_start: 0.8280 (m-80) cc_final: 0.8003 (m-10) REVERT: B 290 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8285 (pt) REVERT: B 452 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8974 (tp) REVERT: B 1028 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: A 172 MET cc_start: 0.7885 (ppp) cc_final: 0.7455 (ppp) REVERT: A 405 ARG cc_start: 0.8700 (ppt170) cc_final: 0.8122 (pmt-80) REVERT: A 560 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6635 (mt0) REVERT: A 577 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: A 1047 MET cc_start: 0.8955 (mtm) cc_final: 0.8665 (mtm) REVERT: C 172 MET cc_start: 0.7937 (mmp) cc_final: 0.7610 (mmm) REVERT: C 195 TYR cc_start: 0.8317 (m-80) cc_final: 0.7385 (m-80) REVERT: C 560 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8348 (mt0) REVERT: H 23 LYS cc_start: 0.8691 (tmmt) cc_final: 0.8409 (tmmt) REVERT: H 35 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: H 74 MET cc_start: 0.9255 (pmm) cc_final: 0.8348 (mmt) REVERT: H 100 TYR cc_start: 0.8580 (t80) cc_final: 0.8351 (t80) REVERT: H 117 MET cc_start: 0.7243 (tpt) cc_final: 0.6825 (tpp) REVERT: L 33 TYR cc_start: 0.8605 (m-80) cc_final: 0.8380 (m-80) outliers start: 75 outliers final: 57 residues processed: 199 average time/residue: 0.3682 time to fit residues: 119.7737 Evaluate side-chains 204 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 904 ASN Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 268 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 199 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.0040 chunk 97 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.7572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064323 restraints weight = 58061.795| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.32 r_work: 0.2789 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26164 Z= 0.114 Angle : 0.588 12.318 35701 Z= 0.295 Chirality : 0.045 0.256 4169 Planarity : 0.004 0.055 4519 Dihedral : 5.502 59.464 4443 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.56 % Allowed : 17.80 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3119 helix: 2.13 (0.21), residues: 645 sheet: 0.09 (0.20), residues: 711 loop : -1.66 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 97 HIS 0.005 0.001 HIS C 202 PHE 0.031 0.001 PHE C 978 TYR 0.017 0.001 TYR A1064 ARG 0.017 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 42) link_NAG-ASN : angle 2.36468 ( 126) link_BETA1-4 : bond 0.00301 ( 8) link_BETA1-4 : angle 1.65519 ( 24) hydrogen bonds : bond 0.04602 ( 884) hydrogen bonds : angle 4.83232 ( 2520) SS BOND : bond 0.00262 ( 37) SS BOND : angle 1.41043 ( 74) covalent geometry : bond 0.00259 (26077) covalent geometry : angle 0.56775 (35477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 145 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 PHE cc_start: 0.8291 (m-80) cc_final: 0.8019 (m-10) REVERT: B 290 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8264 (pt) REVERT: B 452 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8981 (tp) REVERT: B 1028 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: A 172 MET cc_start: 0.7830 (ppp) cc_final: 0.7484 (ppp) REVERT: A 391 ASN cc_start: 0.7254 (t0) cc_final: 0.6881 (t0) REVERT: A 405 ARG cc_start: 0.8678 (ppt170) cc_final: 0.8124 (pmt-80) REVERT: A 560 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7090 (mt0) REVERT: A 577 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.6806 (mp10) REVERT: A 1047 MET cc_start: 0.8906 (mtm) cc_final: 0.8671 (mtm) REVERT: C 172 MET cc_start: 0.7830 (mmp) cc_final: 0.7566 (mmm) REVERT: C 195 TYR cc_start: 0.8255 (m-80) cc_final: 0.7439 (m-80) REVERT: C 560 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: H 23 LYS cc_start: 0.8861 (tmmt) cc_final: 0.8594 (tmmt) REVERT: H 35 GLN cc_start: 0.7209 (pm20) cc_final: 0.6927 (pm20) REVERT: H 74 MET cc_start: 0.9194 (pmm) cc_final: 0.8335 (mmt) REVERT: H 100 TYR cc_start: 0.8568 (t80) cc_final: 0.8322 (t80) REVERT: L 33 TYR cc_start: 0.8634 (m-80) cc_final: 0.8376 (m-80) REVERT: L 92 TYR cc_start: 0.8317 (p90) cc_final: 0.8095 (p90) outliers start: 71 outliers final: 51 residues processed: 195 average time/residue: 0.3557 time to fit residues: 112.5935 Evaluate side-chains 195 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain L residue 97 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 182 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 290 optimal weight: 0.5980 chunk 272 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.104546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064508 restraints weight = 58709.855| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.34 r_work: 0.2797 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26164 Z= 0.113 Angle : 0.594 15.038 35701 Z= 0.295 Chirality : 0.045 0.254 4169 Planarity : 0.004 0.055 4519 Dihedral : 5.335 58.994 4443 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.45 % Allowed : 18.05 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3119 helix: 2.20 (0.21), residues: 645 sheet: 0.14 (0.20), residues: 711 loop : -1.62 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 97 HIS 0.008 0.001 HIS A 202 PHE 0.030 0.001 PHE C 978 TYR 0.017 0.001 TYR A1064 ARG 0.007 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 42) link_NAG-ASN : angle 2.30888 ( 126) link_BETA1-4 : bond 0.00306 ( 8) link_BETA1-4 : angle 1.64145 ( 24) hydrogen bonds : bond 0.04455 ( 884) hydrogen bonds : angle 4.77345 ( 2520) SS BOND : bond 0.00260 ( 37) SS BOND : angle 1.33344 ( 74) covalent geometry : bond 0.00259 (26077) covalent geometry : angle 0.57508 (35477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 144 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 PHE cc_start: 0.8300 (m-80) cc_final: 0.8030 (m-10) REVERT: B 290 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8267 (pt) REVERT: B 452 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 1028 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: A 172 MET cc_start: 0.7805 (ppp) cc_final: 0.7570 (ppp) REVERT: A 391 ASN cc_start: 0.7230 (t0) cc_final: 0.6820 (t0) REVERT: A 405 ARG cc_start: 0.8670 (ppt170) cc_final: 0.8151 (pmt-80) REVERT: A 560 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6880 (mt0) REVERT: A 577 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6795 (mp10) REVERT: A 1047 MET cc_start: 0.8885 (mtm) cc_final: 0.8672 (mtm) REVERT: C 132 GLN cc_start: 0.9029 (mm110) cc_final: 0.8766 (mm110) REVERT: C 195 TYR cc_start: 0.8254 (m-80) cc_final: 0.7442 (m-80) REVERT: C 1089 GLU cc_start: 0.8298 (pm20) cc_final: 0.8037 (mp0) REVERT: H 23 LYS cc_start: 0.8919 (tmmt) cc_final: 0.8653 (tmmt) REVERT: H 35 GLN cc_start: 0.7212 (pm20) cc_final: 0.6926 (pm20) REVERT: H 74 MET cc_start: 0.9201 (pmm) cc_final: 0.8395 (mmt) REVERT: H 100 TYR cc_start: 0.8538 (t80) cc_final: 0.8329 (t80) REVERT: H 117 MET cc_start: 0.6898 (tpp) cc_final: 0.5597 (tmm) REVERT: L 36 TRP cc_start: 0.8460 (m100) cc_final: 0.7893 (m100) outliers start: 68 outliers final: 58 residues processed: 192 average time/residue: 0.3479 time to fit residues: 108.7679 Evaluate side-chains 202 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 139 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 904 ASN Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 294 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 39 optimal weight: 0.0770 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.104279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064362 restraints weight = 58454.071| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.32 r_work: 0.2791 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 26164 Z= 0.162 Angle : 0.718 59.195 35701 Z= 0.390 Chirality : 0.046 0.252 4169 Planarity : 0.005 0.055 4519 Dihedral : 5.338 58.967 4443 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.38 % Allowed : 18.05 % Favored : 79.57 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3119 helix: 2.14 (0.21), residues: 645 sheet: 0.15 (0.20), residues: 713 loop : -1.62 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 97 HIS 0.009 0.001 HIS A 202 PHE 0.029 0.001 PHE A 903 TYR 0.017 0.001 TYR A1064 ARG 0.010 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 42) link_NAG-ASN : angle 2.30246 ( 126) link_BETA1-4 : bond 0.00305 ( 8) link_BETA1-4 : angle 1.64829 ( 24) hydrogen bonds : bond 0.04621 ( 884) hydrogen bonds : angle 4.77921 ( 2520) SS BOND : bond 0.00303 ( 37) SS BOND : angle 1.33240 ( 74) covalent geometry : bond 0.00381 (26077) covalent geometry : angle 0.70328 (35477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6238 Ramachandran restraints generated. 3119 Oldfield, 0 Emsley, 3119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 PHE cc_start: 0.8298 (m-80) cc_final: 0.8028 (m-10) REVERT: B 290 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8286 (pt) REVERT: B 452 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8982 (tp) REVERT: B 1028 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: A 172 MET cc_start: 0.7790 (ppp) cc_final: 0.7558 (ppp) REVERT: A 391 ASN cc_start: 0.7240 (t0) cc_final: 0.6827 (t0) REVERT: A 405 ARG cc_start: 0.8672 (ppt170) cc_final: 0.8161 (pmt-80) REVERT: A 560 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6912 (mt0) REVERT: A 577 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.6795 (mp10) REVERT: A 1047 MET cc_start: 0.8890 (mtm) cc_final: 0.8650 (mtm) REVERT: C 132 GLN cc_start: 0.9027 (mm110) cc_final: 0.8754 (mm110) REVERT: C 172 MET cc_start: 0.7161 (mmm) cc_final: 0.6889 (mmm) REVERT: C 195 TYR cc_start: 0.8259 (m-80) cc_final: 0.7451 (m-80) REVERT: C 1046 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8973 (tp) REVERT: H 23 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8654 (tmmt) REVERT: H 35 GLN cc_start: 0.7219 (pm20) cc_final: 0.6925 (pm20) REVERT: H 74 MET cc_start: 0.9205 (pmm) cc_final: 0.8402 (mmt) REVERT: H 100 TYR cc_start: 0.8568 (t80) cc_final: 0.8335 (t80) REVERT: H 117 MET cc_start: 0.6905 (tpp) cc_final: 0.5589 (tmm) outliers start: 66 outliers final: 60 residues processed: 186 average time/residue: 0.3588 time to fit residues: 109.1432 Evaluate side-chains 204 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 138 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 119 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 85 optimal weight: 0.0980 chunk 132 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.104256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064350 restraints weight = 58489.479| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.32 r_work: 0.2791 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 26164 Z= 0.162 Angle : 0.718 59.195 35701 Z= 0.390 Chirality : 0.046 0.252 4169 Planarity : 0.005 0.055 4519 Dihedral : 5.338 58.967 4443 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.38 % Allowed : 18.02 % Favored : 79.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3119 helix: 2.14 (0.21), residues: 645 sheet: 0.15 (0.20), residues: 713 loop : -1.62 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 97 HIS 0.009 0.001 HIS A 202 PHE 0.029 0.001 PHE A 903 TYR 0.017 0.001 TYR A1064 ARG 0.010 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 42) link_NAG-ASN : angle 2.30246 ( 126) link_BETA1-4 : bond 0.00305 ( 8) link_BETA1-4 : angle 1.64829 ( 24) hydrogen bonds : bond 0.04621 ( 884) hydrogen bonds : angle 4.77921 ( 2520) SS BOND : bond 0.00303 ( 37) SS BOND : angle 1.33240 ( 74) covalent geometry : bond 0.00381 (26077) covalent geometry : angle 0.70328 (35477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12483.03 seconds wall clock time: 216 minutes 51.40 seconds (13011.40 seconds total)