Starting phenix.real_space_refine on Thu Mar 5 14:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xf6_22162/03_2026/6xf6_22162.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xf6_22162/03_2026/6xf6_22162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xf6_22162/03_2026/6xf6_22162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xf6_22162/03_2026/6xf6_22162.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xf6_22162/03_2026/6xf6_22162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xf6_22162/03_2026/6xf6_22162.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 14604 2.51 5 N 3767 2.21 5 O 4467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22938 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7630 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 6862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 6862 Classifications: {'peptide': 945} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 46, 'TRANS': 898} Chain breaks: 11 Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 698 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 16, 'GLU:plan': 11, 'GLN:plan1': 9, 'ARG:plan': 8, 'PHE:plan': 8, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 364 Chain: "C" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7620 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 87 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: "H" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 4.75, per 1000 atoms: 0.21 Number of scatterers: 22938 At special positions: 0 Unit cell: (127.33, 130.54, 179.76, 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 100 16.00 O 4467 8.00 N 3767 7.00 C 14604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1315 " - " ASN A1074 " " NAG A1320 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1315 " - " ASN C1074 " " NAG C1320 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 783.8 milliseconds 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5488 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 43 sheets defined 26.4% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.659A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.819A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.586A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.571A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.245A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.566A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.807A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.017A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.658A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.223A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.593A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.987A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.891A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.865A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.670A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.156A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.923A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.878A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.643A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.248A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.994A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.207A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.519A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.022A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.624A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.218A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.540A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.666A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.603A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.335A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.449A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.235A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.893A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.591A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.591A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.333A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.111A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.605A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.794A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.509A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.541A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.895A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.719A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.296A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.004A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.509A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.509A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.213A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.290A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 956 hydrogen bonds defined for protein. 2667 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: 4.58 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7212 1.34 - 1.46: 5689 1.46 - 1.59: 10393 1.59 - 1.71: 0 1.71 - 1.84: 124 Bond restraints: 23418 Sorted by residual: bond pdb=" N VAL C 608 " pdb=" CA VAL C 608 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N VAL B 608 " pdb=" CA VAL B 608 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N ILE C 742 " pdb=" CA ILE C 742 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.68e+00 bond pdb=" N VAL B 610 " pdb=" CA VAL B 610 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.35e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.26e+00 ... (remaining 23413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 31303 2.51 - 5.01: 554 5.01 - 7.52: 45 7.52 - 10.03: 13 10.03 - 12.53: 5 Bond angle restraints: 31920 Sorted by residual: angle pdb=" N ASN A 87 " pdb=" CA ASN A 87 " pdb=" C ASN A 87 " ideal model delta sigma weight residual 111.07 115.67 -4.60 1.07e+00 8.73e-01 1.85e+01 angle pdb=" N GLU A1017 " pdb=" CA GLU A1017 " pdb=" CB GLU A1017 " ideal model delta sigma weight residual 110.39 117.46 -7.07 1.66e+00 3.63e-01 1.81e+01 angle pdb=" N PHE B 338 " pdb=" CA PHE B 338 " pdb=" C PHE B 338 " ideal model delta sigma weight residual 112.89 107.61 5.28 1.24e+00 6.50e-01 1.81e+01 angle pdb=" CB MET C 740 " pdb=" CG MET C 740 " pdb=" SD MET C 740 " ideal model delta sigma weight residual 112.70 125.23 -12.53 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CA GLU A1017 " pdb=" CB GLU A1017 " pdb=" CG GLU A1017 " ideal model delta sigma weight residual 114.10 122.13 -8.03 2.00e+00 2.50e-01 1.61e+01 ... (remaining 31915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13817 17.98 - 35.96: 681 35.96 - 53.94: 133 53.94 - 71.93: 23 71.93 - 89.91: 28 Dihedral angle restraints: 14682 sinusoidal: 6181 harmonic: 8501 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.78 89.78 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.47 -84.47 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 176.80 -83.80 1 1.00e+01 1.00e-02 8.56e+01 ... (remaining 14679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3552 0.100 - 0.200: 307 0.200 - 0.299: 17 0.299 - 0.399: 5 0.399 - 0.499: 5 Chirality restraints: 3886 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.53e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.40e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.86e+01 ... (remaining 3883 not shown) Planarity restraints: 4096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG K 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.049 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.504 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.328 2.00e-02 2.50e+03 2.78e-01 9.65e+02 pdb=" C7 NAG C1306 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.186 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1320 " 0.271 2.00e-02 2.50e+03 2.32e-01 6.74e+02 pdb=" C7 NAG A1320 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A1320 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG A1320 " -0.403 2.00e-02 2.50e+03 pdb=" O7 NAG A1320 " 0.031 2.00e-02 2.50e+03 ... (remaining 4093 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4024 2.78 - 3.31: 20219 3.31 - 3.84: 38692 3.84 - 4.37: 42884 4.37 - 4.90: 75471 Nonbonded interactions: 181290 Sorted by model distance: nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.249 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.251 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASN A 360 " pdb=" OG1 THR A 523 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN C 360 " pdb=" OG1 THR C 523 " model vdw 2.283 3.040 ... (remaining 181285 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) \ or resid 341 through 344 or (resid 345 through 360 and (name N or name CA or nam \ e C or name O or name CB )) or resid 361 or (resid 362 through 378 and (name N o \ r name CA or name C or name O or name CB )) or resid 379 or (resid 380 and (name \ N or name CA or name C or name O or name CB )) or resid 381 or (resid 382 throu \ gh 383 and (name N or name CA or name C or name O or name CB )) or resid 384 or \ (resid 385 through 390 and (name N or name CA or name C or name O or name CB )) \ or resid 391 or (resid 392 through 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 or (resid 405 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 4 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 416 or (res \ id 417 through 425 and (name N or name CA or name C or name O or name CB )) or r \ esid 426 or (resid 427 through 430 and (name N or name CA or name C or name O or \ name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N or na \ me CA or name C or name O or name CB )) or resid 446 through 447 or (resid 448 t \ hrough 454 and (name N or name CA or name C or name O or name CB )) or resid 491 \ or (resid 492 through 495 and (name N or name CA or name C or name O or name CB \ )) or resid 496 or (resid 497 through 498 and (name N or name CA or name C or n \ ame O or name CB )) or resid 499 or (resid 500 through 501 and (name N or name C \ A or name C or name O or name CB )) or resid 502 or (resid 503 and (name N or na \ me CA or name C or name O or name CB )) or resid 504 or (resid 505 through 506 a \ nd (name N or name CA or name C or name O or name CB )) or resid 507 or (resid 5 \ 08 through 515 and (name N or name CA or name C or name O or name CB )) or (resi \ d 522 through 524 and (name N or name CA or name C or name O or name CB )) or re \ sid 525 through 553 or (resid 554 and (name N or name CA or name C or name O or \ name CB )) or resid 555 through 793 or (resid 794 and (name N or name CA or name \ C or name O or name CB )) or resid 795 or (resid 796 and (name N or name CA or \ name C or name O or name CB )) or resid 797 through 827 or resid 856 through 866 \ or (resid 867 through 868 and (name N or name CA or name C or name O or name CB \ )) or resid 869 through 939 or (resid 940 and (name N or name CA or name C or n \ ame O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name C \ A or name C or name O or name CB )) or resid 986 through 987 or (resid 988 throu \ gh 989 and (name N or name CA or name C or name O or name CB )) or resid 990 thr \ ough 1141 or (resid 1142 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 through 1320)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 527 or (resid 528 and (name N or name CA or name C or \ name O or name CB )) or resid 529 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 o \ r (resid 582 through 583 and (name N or name CA or name C or name O or name CB ) \ ) or resid 584 through 585 or (resid 586 and (name N or name CA or name C or nam \ e O or name CB )) or resid 587 through 613 or (resid 614 and (name N or name CA \ or name C or name O or name CB )) or resid 615 through 618 or (resid 619 and (na \ me N or name CA or name C or name O or name CB )) or resid 620 through 676 or re \ sid 690 through 744 or (resid 745 and (name N or name CA or name C or name O or \ name CB )) or resid 746 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 939 or (resid 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 339 or (resid 340 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 344 or \ (resid 345 through 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 or (resid 362 through 378 and (name N or name CA or name C or name \ O or name CB )) or resid 379 or (resid 380 and (name N or name CA or name C or \ name O or name CB )) or resid 381 or (resid 382 through 383 and (name N or name \ CA or name C or name O or name CB )) or resid 384 or (resid 385 through 390 and \ (name N or name CA or name C or name O or name CB )) or resid 391 or (resid 392 \ through 403 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 4 or (resid 405 through 411 and (name N or name CA or name C or name O or name C \ B )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA o \ r name C or name O or name CB )) or resid 416 or (resid 417 through 425 and (nam \ e N or name CA or name C or name O or name CB )) or resid 426 or (resid 427 thro \ ugh 430 and (name N or name CA or name C or name O or name CB )) or resid 431 th \ rough 432 or (resid 433 through 445 and (name N or name CA or name C or name O o \ r name CB )) or resid 446 through 447 or (resid 448 through 454 and (name N or n \ ame CA or name C or name O or name CB )) or resid 491 or (resid 492 through 495 \ and (name N or name CA or name C or name O or name CB )) or resid 496 or (resid \ 497 through 498 and (name N or name CA or name C or name O or name CB )) or resi \ d 499 or (resid 500 through 501 and (name N or name CA or name C or name O or na \ me CB )) or resid 502 or (resid 503 and (name N or name CA or name C or name O o \ r name CB )) or resid 504 or (resid 505 through 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name N \ or name CA or name C or name O or name CB )) or (resid 522 through 524 and (name \ N or name CA or name C or name O or name CB )) or resid 525 through 527 or (res \ id 528 and (name N or name CA or name C or name O or name CB )) or resid 529 thr \ ough 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) \ or resid 555 through 567 or (resid 568 and (name N or name CA or name C or name \ O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name CA or \ name C or name O or name CB )) or resid 572 through 581 or (resid 582 through 5 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) or r \ esid 587 through 618 or (resid 619 and (name N or name CA or name C or name O or \ name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N or na \ me CA or name C or name O or name CB )) or resid 648 through 793 or (resid 794 a \ nd (name N or name CA or name C or name O or name CB )) or resid 795 or (resid 7 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 797 through \ 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) or r \ esid 922 through 1072 or (resid 1073 and (name N or name CA or name C or name O \ or name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA o \ r name C or name O or name CB )) or resid 1119 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 or (resid 1144 \ through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.005 0.065 23515 Z= 0.297 Angle : 0.849 14.158 32173 Z= 0.484 Chirality : 0.058 0.499 3886 Planarity : 0.012 0.287 4049 Dihedral : 11.194 89.908 9080 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.21 % Allowed : 0.47 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 2870 helix: 0.86 (0.19), residues: 688 sheet: 0.70 (0.20), residues: 585 loop : -0.59 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1019 TYR 0.013 0.001 TYR C1067 PHE 0.021 0.001 PHE A 559 TRP 0.015 0.001 TRP A 104 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00478 (23418) covalent geometry : angle 0.79654 (31920) SS BOND : bond 0.00411 ( 38) SS BOND : angle 1.49234 ( 76) hydrogen bonds : bond 0.18467 ( 949) hydrogen bonds : angle 7.57157 ( 2667) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.15097 ( 36) link_NAG-ASN : bond 0.01240 ( 47) link_NAG-ASN : angle 4.40952 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.7285 (t80) cc_final: 0.6875 (t80) REVERT: A 742 ILE cc_start: 0.9670 (mt) cc_final: 0.9121 (tp) REVERT: A 869 MET cc_start: 0.9312 (mtm) cc_final: 0.9028 (mtm) REVERT: A 900 MET cc_start: 0.7950 (mmt) cc_final: 0.7683 (mmt) REVERT: A 1001 LEU cc_start: 0.9657 (pp) cc_final: 0.9419 (pp) REVERT: A 1002 GLN cc_start: 0.9677 (mt0) cc_final: 0.9246 (mt0) REVERT: A 1010 GLN cc_start: 0.9377 (mp10) cc_final: 0.9158 (mp10) REVERT: B 731 MET cc_start: 0.8738 (ttm) cc_final: 0.8398 (ttm) REVERT: B 759 PHE cc_start: 0.9206 (m-80) cc_final: 0.8922 (m-80) REVERT: B 763 LEU cc_start: 0.9587 (mt) cc_final: 0.8789 (pp) REVERT: B 869 MET cc_start: 0.8985 (ptp) cc_final: 0.8692 (ptp) REVERT: B 1029 MET cc_start: 0.9279 (tmm) cc_final: 0.9077 (tmm) REVERT: C 427 ASP cc_start: 0.9514 (m-30) cc_final: 0.9236 (p0) REVERT: C 742 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9165 (tt) REVERT: C 950 ASP cc_start: 0.9500 (t70) cc_final: 0.9233 (t0) outliers start: 5 outliers final: 0 residues processed: 131 average time/residue: 0.1523 time to fit residues: 31.9170 Evaluate side-chains 80 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 742 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 613 GLN A 762 GLN A 804 GLN A 935 GLN A 955 ASN A1005 GLN A1011 GLN B 207 HIS B 804 GLN B 935 GLN B1010 GLN B1135 ASN C 613 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.042359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.030707 restraints weight = 196864.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.031775 restraints weight = 111761.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.032509 restraints weight = 75350.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.033030 restraints weight = 56633.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.033372 restraints weight = 45725.022| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23515 Z= 0.173 Angle : 0.597 10.910 32173 Z= 0.299 Chirality : 0.043 0.338 3886 Planarity : 0.004 0.051 4049 Dihedral : 5.133 59.199 4338 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.55 % Allowed : 4.38 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 2870 helix: 1.43 (0.20), residues: 713 sheet: 0.61 (0.20), residues: 638 loop : -0.23 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1019 TYR 0.010 0.001 TYR B1007 PHE 0.016 0.001 PHE C 464 TRP 0.007 0.001 TRP B1102 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00350 (23418) covalent geometry : angle 0.57506 (31920) SS BOND : bond 0.00315 ( 38) SS BOND : angle 0.78722 ( 76) hydrogen bonds : bond 0.04107 ( 949) hydrogen bonds : angle 5.93808 ( 2667) link_BETA1-4 : bond 0.00440 ( 12) link_BETA1-4 : angle 1.20288 ( 36) link_NAG-ASN : bond 0.00491 ( 47) link_NAG-ASN : angle 2.38734 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.9127 (ppp) cc_final: 0.8679 (pmm) REVERT: A 900 MET cc_start: 0.8507 (mmt) cc_final: 0.8260 (mmt) REVERT: A 1002 GLN cc_start: 0.9604 (mt0) cc_final: 0.9215 (mt0) REVERT: B 731 MET cc_start: 0.8579 (ttm) cc_final: 0.8164 (ttm) REVERT: B 763 LEU cc_start: 0.9662 (mt) cc_final: 0.9170 (pp) REVERT: B 773 GLU cc_start: 0.8809 (tt0) cc_final: 0.8496 (tp30) REVERT: B 1129 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8645 (m) REVERT: C 427 ASP cc_start: 0.9504 (m-30) cc_final: 0.9162 (p0) REVERT: C 950 ASP cc_start: 0.9429 (t70) cc_final: 0.9196 (t0) outliers start: 13 outliers final: 2 residues processed: 83 average time/residue: 0.1266 time to fit residues: 18.6408 Evaluate side-chains 66 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 211 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN B 901 GLN C 949 GLN C 953 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.039181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.028270 restraints weight = 207715.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.029252 restraints weight = 116487.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.029922 restraints weight = 78044.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.030357 restraints weight = 58510.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.030680 restraints weight = 47813.889| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 23515 Z= 0.270 Angle : 0.691 10.978 32173 Z= 0.351 Chirality : 0.044 0.287 3886 Planarity : 0.004 0.062 4049 Dihedral : 5.156 51.542 4336 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 1.02 % Allowed : 6.16 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2870 helix: 1.20 (0.20), residues: 708 sheet: 0.35 (0.20), residues: 646 loop : -0.22 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.024 0.002 TYR A 789 PHE 0.029 0.002 PHE B 906 TRP 0.013 0.002 TRP B1102 HIS 0.006 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00543 (23418) covalent geometry : angle 0.66712 (31920) SS BOND : bond 0.00390 ( 38) SS BOND : angle 2.20754 ( 76) hydrogen bonds : bond 0.04497 ( 949) hydrogen bonds : angle 5.89459 ( 2667) link_BETA1-4 : bond 0.00445 ( 12) link_BETA1-4 : angle 1.35286 ( 36) link_NAG-ASN : bond 0.00510 ( 47) link_NAG-ASN : angle 2.26355 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8830 (m-30) cc_final: 0.8383 (p0) REVERT: A 731 MET cc_start: 0.7446 (tmm) cc_final: 0.7244 (tmm) REVERT: A 740 MET cc_start: 0.8828 (tpp) cc_final: 0.8389 (tpp) REVERT: A 900 MET cc_start: 0.8917 (mmt) cc_final: 0.8588 (mmt) REVERT: A 1002 GLN cc_start: 0.9536 (mt0) cc_final: 0.9242 (mt0) REVERT: A 1029 MET cc_start: 0.9174 (tmm) cc_final: 0.8863 (tmm) REVERT: B 697 MET cc_start: 0.9065 (ppp) cc_final: 0.8539 (ppp) REVERT: B 731 MET cc_start: 0.8587 (ttm) cc_final: 0.8239 (ttp) REVERT: B 740 MET cc_start: 0.9082 (tpp) cc_final: 0.8679 (tpp) REVERT: B 742 ILE cc_start: 0.9756 (mt) cc_final: 0.9455 (tp) REVERT: B 869 MET cc_start: 0.9402 (ptp) cc_final: 0.8942 (ptp) REVERT: C 697 MET cc_start: 0.8781 (ppp) cc_final: 0.8462 (pmm) REVERT: C 763 LEU cc_start: 0.9813 (mt) cc_final: 0.9569 (pp) REVERT: C 900 MET cc_start: 0.9189 (mpp) cc_final: 0.8695 (mpp) REVERT: C 1029 MET cc_start: 0.9331 (ttm) cc_final: 0.8957 (ptm) outliers start: 24 outliers final: 7 residues processed: 81 average time/residue: 0.1361 time to fit residues: 19.2968 Evaluate side-chains 59 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 158 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 262 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1048 HIS B 762 GLN C 953 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.039155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.028221 restraints weight = 206630.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.029214 restraints weight = 115343.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.029892 restraints weight = 77149.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.030348 restraints weight = 57816.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030666 restraints weight = 47090.205| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23515 Z= 0.186 Angle : 0.569 10.086 32173 Z= 0.286 Chirality : 0.043 0.294 3886 Planarity : 0.004 0.046 4049 Dihedral : 4.830 47.248 4336 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.72 % Allowed : 7.27 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2870 helix: 1.52 (0.20), residues: 711 sheet: 0.29 (0.19), residues: 652 loop : -0.23 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1019 TYR 0.012 0.001 TYR A 707 PHE 0.015 0.001 PHE A 906 TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00377 (23418) covalent geometry : angle 0.54805 (31920) SS BOND : bond 0.00250 ( 38) SS BOND : angle 1.41083 ( 76) hydrogen bonds : bond 0.03866 ( 949) hydrogen bonds : angle 5.63868 ( 2667) link_BETA1-4 : bond 0.00199 ( 12) link_BETA1-4 : angle 1.12958 ( 36) link_NAG-ASN : bond 0.00433 ( 47) link_NAG-ASN : angle 2.09664 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8763 (m-30) cc_final: 0.8455 (p0) REVERT: A 740 MET cc_start: 0.8773 (tpp) cc_final: 0.8339 (tpp) REVERT: A 900 MET cc_start: 0.8948 (mmt) cc_final: 0.8692 (mmt) REVERT: A 1002 GLN cc_start: 0.9534 (mt0) cc_final: 0.9201 (mt0) REVERT: A 1050 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8000 (ptp) REVERT: B 697 MET cc_start: 0.9091 (ppp) cc_final: 0.8700 (ppp) REVERT: B 731 MET cc_start: 0.8618 (ttm) cc_final: 0.8208 (ttp) REVERT: B 742 ILE cc_start: 0.9790 (mt) cc_final: 0.9459 (tp) REVERT: B 869 MET cc_start: 0.9372 (ptp) cc_final: 0.9094 (ptp) REVERT: B 1050 MET cc_start: 0.8350 (tmm) cc_final: 0.7927 (tmm) REVERT: C 763 LEU cc_start: 0.9803 (mt) cc_final: 0.9540 (pp) REVERT: C 900 MET cc_start: 0.9107 (mpp) cc_final: 0.8462 (mpp) outliers start: 17 outliers final: 9 residues processed: 72 average time/residue: 0.1345 time to fit residues: 17.0106 Evaluate side-chains 59 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.028413 restraints weight = 204988.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.029412 restraints weight = 114159.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.030099 restraints weight = 76231.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.030548 restraints weight = 57106.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.030871 restraints weight = 46489.990| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23515 Z= 0.127 Angle : 0.525 10.146 32173 Z= 0.263 Chirality : 0.043 0.295 3886 Planarity : 0.004 0.039 4049 Dihedral : 4.512 47.433 4336 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.72 % Allowed : 7.87 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2870 helix: 1.66 (0.20), residues: 716 sheet: 0.31 (0.19), residues: 650 loop : -0.20 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.009 0.001 TYR C 396 PHE 0.012 0.001 PHE B1052 TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00258 (23418) covalent geometry : angle 0.50597 (31920) SS BOND : bond 0.00251 ( 38) SS BOND : angle 1.08373 ( 76) hydrogen bonds : bond 0.03644 ( 949) hydrogen bonds : angle 5.36173 ( 2667) link_BETA1-4 : bond 0.00202 ( 12) link_BETA1-4 : angle 1.06365 ( 36) link_NAG-ASN : bond 0.00410 ( 47) link_NAG-ASN : angle 2.01925 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8777 (m-30) cc_final: 0.8453 (p0) REVERT: A 697 MET cc_start: 0.9259 (ppp) cc_final: 0.9012 (ppp) REVERT: A 740 MET cc_start: 0.8680 (tpp) cc_final: 0.8176 (tpp) REVERT: A 774 GLN cc_start: 0.9456 (OUTLIER) cc_final: 0.9226 (mm-40) REVERT: A 900 MET cc_start: 0.8887 (mmt) cc_final: 0.8636 (mmt) REVERT: A 1002 GLN cc_start: 0.9531 (mt0) cc_final: 0.9178 (mt0) REVERT: B 697 MET cc_start: 0.9100 (ppp) cc_final: 0.8794 (ppp) REVERT: B 731 MET cc_start: 0.8622 (ttm) cc_final: 0.8196 (ttp) REVERT: B 742 ILE cc_start: 0.9781 (mt) cc_final: 0.9467 (tp) REVERT: B 759 PHE cc_start: 0.9041 (m-80) cc_final: 0.8746 (m-80) REVERT: B 869 MET cc_start: 0.9379 (ptp) cc_final: 0.8839 (ptp) REVERT: B 1050 MET cc_start: 0.8343 (tmm) cc_final: 0.7850 (tmm) REVERT: C 763 LEU cc_start: 0.9805 (mt) cc_final: 0.9585 (pp) REVERT: C 900 MET cc_start: 0.9057 (mpp) cc_final: 0.8438 (mpp) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 0.1309 time to fit residues: 16.5481 Evaluate side-chains 63 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 133 optimal weight: 40.0000 chunk 100 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 196 ASN B 762 GLN B1071 GLN C 450 ASN C 953 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.038042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.027314 restraints weight = 209843.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.028265 restraints weight = 116954.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.028910 restraints weight = 78400.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.029344 restraints weight = 59013.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029618 restraints weight = 48220.514| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 23515 Z= 0.238 Angle : 0.624 11.398 32173 Z= 0.313 Chirality : 0.043 0.302 3886 Planarity : 0.004 0.051 4049 Dihedral : 4.788 47.882 4336 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.06 % Allowed : 8.63 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2870 helix: 1.44 (0.20), residues: 714 sheet: 0.10 (0.19), residues: 663 loop : -0.33 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1014 TYR 0.017 0.002 TYR A 789 PHE 0.024 0.002 PHE B1095 TRP 0.007 0.001 TRP B1102 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00483 (23418) covalent geometry : angle 0.60622 (31920) SS BOND : bond 0.00321 ( 38) SS BOND : angle 1.14623 ( 76) hydrogen bonds : bond 0.03964 ( 949) hydrogen bonds : angle 5.59277 ( 2667) link_BETA1-4 : bond 0.00265 ( 12) link_BETA1-4 : angle 1.34271 ( 36) link_NAG-ASN : bond 0.00474 ( 47) link_NAG-ASN : angle 2.12558 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.679 Fit side-chains REVERT: A 408 ARG cc_start: 0.9537 (OUTLIER) cc_final: 0.9258 (ppt90) REVERT: A 427 ASP cc_start: 0.8789 (m-30) cc_final: 0.8506 (p0) REVERT: A 740 MET cc_start: 0.8765 (tpp) cc_final: 0.8315 (tpp) REVERT: A 864 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8803 (mm) REVERT: A 900 MET cc_start: 0.8988 (mmt) cc_final: 0.8740 (mmt) REVERT: A 1002 GLN cc_start: 0.9531 (mt0) cc_final: 0.9258 (mt0) REVERT: B 697 MET cc_start: 0.9145 (ppp) cc_final: 0.8845 (ppp) REVERT: B 731 MET cc_start: 0.8723 (ttm) cc_final: 0.8310 (ttp) REVERT: B 742 ILE cc_start: 0.9773 (mt) cc_final: 0.9507 (tp) REVERT: B 756 TYR cc_start: 0.9152 (m-10) cc_final: 0.8908 (m-10) REVERT: B 759 PHE cc_start: 0.9189 (m-80) cc_final: 0.8947 (m-80) REVERT: B 869 MET cc_start: 0.9409 (ptp) cc_final: 0.8984 (ptp) REVERT: B 1050 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7949 (tmm) REVERT: C 763 LEU cc_start: 0.9827 (mt) cc_final: 0.9615 (pp) REVERT: C 900 MET cc_start: 0.9168 (mpp) cc_final: 0.8667 (mpp) outliers start: 25 outliers final: 13 residues processed: 71 average time/residue: 0.1301 time to fit residues: 16.5548 Evaluate side-chains 64 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 263 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 50 optimal weight: 0.3980 chunk 120 optimal weight: 7.9990 chunk 208 optimal weight: 0.4980 chunk 285 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1005 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 = 0.3148 r_free = 0.3148 target = 0.038071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027366 restraints weight = 208315.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.028329 restraints weight = 115105.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.028981 restraints weight = 76844.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029441 restraints weight = 57662.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.029735 restraints weight = 46744.841| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23515 Z= 0.207 Angle : 0.586 9.998 32173 Z= 0.294 Chirality : 0.043 0.286 3886 Planarity : 0.004 0.035 4049 Dihedral : 4.847 51.727 4336 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.15 % Allowed : 9.01 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 2870 helix: 1.51 (0.20), residues: 715 sheet: 0.04 (0.19), residues: 669 loop : -0.36 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1014 TYR 0.013 0.001 TYR C 396 PHE 0.017 0.001 PHE A 906 TRP 0.012 0.001 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00419 (23418) covalent geometry : angle 0.56891 (31920) SS BOND : bond 0.00284 ( 38) SS BOND : angle 1.06973 ( 76) hydrogen bonds : bond 0.03797 ( 949) hydrogen bonds : angle 5.52983 ( 2667) link_BETA1-4 : bond 0.00143 ( 12) link_BETA1-4 : angle 1.13785 ( 36) link_NAG-ASN : bond 0.00431 ( 47) link_NAG-ASN : angle 2.05292 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.9586 (OUTLIER) cc_final: 0.9272 (ppt90) REVERT: A 427 ASP cc_start: 0.8866 (m-30) cc_final: 0.8660 (p0) REVERT: A 740 MET cc_start: 0.8772 (tpp) cc_final: 0.8288 (tpp) REVERT: A 864 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8749 (mm) REVERT: A 900 MET cc_start: 0.8919 (mmt) cc_final: 0.8690 (mmt) REVERT: A 1002 GLN cc_start: 0.9564 (mt0) cc_final: 0.9280 (mt0) REVERT: B 697 MET cc_start: 0.9211 (ppp) cc_final: 0.8947 (ppp) REVERT: B 731 MET cc_start: 0.8746 (ttm) cc_final: 0.8280 (ttp) REVERT: B 742 ILE cc_start: 0.9768 (mt) cc_final: 0.9472 (tp) REVERT: B 869 MET cc_start: 0.9409 (ptp) cc_final: 0.8976 (ptp) REVERT: B 1050 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8050 (tmm) REVERT: C 740 MET cc_start: 0.9337 (tpp) cc_final: 0.8983 (tpp) REVERT: C 763 LEU cc_start: 0.9834 (mt) cc_final: 0.9593 (pp) REVERT: C 900 MET cc_start: 0.9155 (mpp) cc_final: 0.8829 (mpp) outliers start: 27 outliers final: 18 residues processed: 75 average time/residue: 0.1325 time to fit residues: 17.7317 Evaluate side-chains 67 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 269 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.038989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.028098 restraints weight = 202677.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.029114 restraints weight = 111205.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.029814 restraints weight = 73823.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.030310 restraints weight = 54881.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.030641 restraints weight = 44108.947| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23515 Z= 0.097 Angle : 0.526 9.955 32173 Z= 0.258 Chirality : 0.043 0.294 3886 Planarity : 0.003 0.036 4049 Dihedral : 4.361 52.636 4336 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.72 % Allowed : 9.35 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2870 helix: 1.88 (0.20), residues: 711 sheet: 0.15 (0.19), residues: 674 loop : -0.29 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.019 0.001 TYR C 351 PHE 0.012 0.001 PHE A1089 TRP 0.009 0.001 TRP B 886 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00200 (23418) covalent geometry : angle 0.50876 (31920) SS BOND : bond 0.00223 ( 38) SS BOND : angle 0.92714 ( 76) hydrogen bonds : bond 0.03427 ( 949) hydrogen bonds : angle 5.15517 ( 2667) link_BETA1-4 : bond 0.00247 ( 12) link_BETA1-4 : angle 0.99258 ( 36) link_NAG-ASN : bond 0.00427 ( 47) link_NAG-ASN : angle 1.94380 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.9615 (OUTLIER) cc_final: 0.9313 (ppt90) REVERT: A 427 ASP cc_start: 0.8903 (m-30) cc_final: 0.8650 (p0) REVERT: A 740 MET cc_start: 0.8754 (tpp) cc_final: 0.8256 (tpp) REVERT: A 864 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8902 (mm) REVERT: A 1002 GLN cc_start: 0.9568 (mt0) cc_final: 0.9252 (mt0) REVERT: B 697 MET cc_start: 0.9208 (ppp) cc_final: 0.8945 (ppp) REVERT: B 742 ILE cc_start: 0.9734 (mt) cc_final: 0.9425 (tp) REVERT: B 759 PHE cc_start: 0.9166 (m-80) cc_final: 0.8835 (m-80) REVERT: B 869 MET cc_start: 0.9373 (ptp) cc_final: 0.8898 (ptp) REVERT: B 1050 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7961 (tmm) REVERT: C 740 MET cc_start: 0.9339 (tpp) cc_final: 0.8918 (tpp) REVERT: C 763 LEU cc_start: 0.9825 (mt) cc_final: 0.9611 (pp) REVERT: C 900 MET cc_start: 0.9050 (mpp) cc_final: 0.8787 (mpp) outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.1340 time to fit residues: 16.3820 Evaluate side-chains 63 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 245 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 955 ASN C 953 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.037772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.027161 restraints weight = 209957.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.028126 restraints weight = 115683.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.028782 restraints weight = 76929.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.029228 restraints weight = 57411.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029545 restraints weight = 46665.116| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23515 Z= 0.200 Angle : 0.592 10.698 32173 Z= 0.293 Chirality : 0.043 0.286 3886 Planarity : 0.004 0.043 4049 Dihedral : 4.615 49.408 4336 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.85 % Allowed : 9.44 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2870 helix: 1.59 (0.20), residues: 718 sheet: 0.02 (0.19), residues: 666 loop : -0.31 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1014 TYR 0.013 0.001 TYR A 707 PHE 0.017 0.001 PHE B1095 TRP 0.008 0.001 TRP B1102 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00408 (23418) covalent geometry : angle 0.57388 (31920) SS BOND : bond 0.00302 ( 38) SS BOND : angle 1.13490 ( 76) hydrogen bonds : bond 0.03705 ( 949) hydrogen bonds : angle 5.37819 ( 2667) link_BETA1-4 : bond 0.00184 ( 12) link_BETA1-4 : angle 1.25242 ( 36) link_NAG-ASN : bond 0.00437 ( 47) link_NAG-ASN : angle 2.06691 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.829 Fit side-chains REVERT: A 740 MET cc_start: 0.8774 (tpp) cc_final: 0.8307 (tpp) REVERT: A 864 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8898 (mm) REVERT: A 1002 GLN cc_start: 0.9572 (mt0) cc_final: 0.9261 (mt0) REVERT: B 697 MET cc_start: 0.9198 (ppp) cc_final: 0.8961 (ppp) REVERT: B 742 ILE cc_start: 0.9743 (mt) cc_final: 0.9484 (tp) REVERT: B 869 MET cc_start: 0.9378 (ptp) cc_final: 0.9128 (ptp) REVERT: B 1050 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8039 (tmm) REVERT: C 406 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: C 738 CYS cc_start: 0.7758 (OUTLIER) cc_final: 0.6619 (p) REVERT: C 740 MET cc_start: 0.9343 (tpp) cc_final: 0.9006 (tpp) REVERT: C 763 LEU cc_start: 0.9835 (mt) cc_final: 0.9633 (pp) REVERT: C 900 MET cc_start: 0.9150 (mpp) cc_final: 0.8791 (mpp) outliers start: 20 outliers final: 14 residues processed: 64 average time/residue: 0.1372 time to fit residues: 15.8082 Evaluate side-chains 63 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 214 optimal weight: 0.9980 chunk 266 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 232 optimal weight: 0.2980 chunk 129 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 274 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 953 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.027739 restraints weight = 206054.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.028723 restraints weight = 113617.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.029391 restraints weight = 75538.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.029846 restraints weight = 56449.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.030170 restraints weight = 45772.524| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23515 Z= 0.115 Angle : 0.533 11.457 32173 Z= 0.260 Chirality : 0.043 0.288 3886 Planarity : 0.004 0.052 4049 Dihedral : 4.369 51.213 4336 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.81 % Allowed : 9.48 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2870 helix: 1.78 (0.20), residues: 720 sheet: 0.15 (0.19), residues: 664 loop : -0.30 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 408 TYR 0.010 0.001 TYR B 265 PHE 0.013 0.001 PHE B1095 TRP 0.007 0.001 TRP B 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00241 (23418) covalent geometry : angle 0.51562 (31920) SS BOND : bond 0.00225 ( 38) SS BOND : angle 0.94259 ( 76) hydrogen bonds : bond 0.03421 ( 949) hydrogen bonds : angle 5.15642 ( 2667) link_BETA1-4 : bond 0.00204 ( 12) link_BETA1-4 : angle 1.02022 ( 36) link_NAG-ASN : bond 0.00410 ( 47) link_NAG-ASN : angle 1.95249 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.9468 (OUTLIER) cc_final: 0.9203 (ppt90) REVERT: A 740 MET cc_start: 0.8695 (tpp) cc_final: 0.8222 (tpp) REVERT: A 864 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8887 (mm) REVERT: A 1002 GLN cc_start: 0.9544 (mt0) cc_final: 0.9238 (mt0) REVERT: B 742 ILE cc_start: 0.9726 (mt) cc_final: 0.9454 (tp) REVERT: B 759 PHE cc_start: 0.9117 (m-80) cc_final: 0.8797 (m-80) REVERT: B 869 MET cc_start: 0.9364 (ptp) cc_final: 0.8905 (ptp) REVERT: B 1050 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7984 (tmm) REVERT: C 406 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: C 740 MET cc_start: 0.9330 (tpp) cc_final: 0.8958 (tpp) REVERT: C 763 LEU cc_start: 0.9825 (mt) cc_final: 0.9617 (pp) REVERT: C 900 MET cc_start: 0.9141 (mpp) cc_final: 0.8837 (mpp) outliers start: 19 outliers final: 15 residues processed: 66 average time/residue: 0.1247 time to fit residues: 14.9813 Evaluate side-chains 67 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 124 optimal weight: 0.5980 chunk 278 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 chunk 35 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 202 optimal weight: 0.0370 chunk 281 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.038232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.027620 restraints weight = 207162.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.028585 restraints weight = 114744.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.029259 restraints weight = 76348.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.029718 restraints weight = 57156.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.030010 restraints weight = 46300.705| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23515 Z= 0.118 Angle : 0.528 11.466 32173 Z= 0.258 Chirality : 0.043 0.291 3886 Planarity : 0.003 0.040 4049 Dihedral : 4.182 50.042 4336 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.81 % Allowed : 9.57 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2870 helix: 1.83 (0.20), residues: 719 sheet: 0.17 (0.19), residues: 664 loop : -0.26 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 408 TYR 0.008 0.001 TYR B 265 PHE 0.013 0.001 PHE B1095 TRP 0.005 0.001 TRP B 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00244 (23418) covalent geometry : angle 0.51147 (31920) SS BOND : bond 0.00200 ( 38) SS BOND : angle 0.89480 ( 76) hydrogen bonds : bond 0.03361 ( 949) hydrogen bonds : angle 5.04322 ( 2667) link_BETA1-4 : bond 0.00188 ( 12) link_BETA1-4 : angle 1.06097 ( 36) link_NAG-ASN : bond 0.00398 ( 47) link_NAG-ASN : angle 1.94614 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3328.18 seconds wall clock time: 58 minutes 42.61 seconds (3522.61 seconds total)