Starting phenix.real_space_refine on Mon Jul 6 05:55:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.cif" model { file = "/net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0x_26267/07_2026/7u0x_26267.map" } resolution = 3.82 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= -0.003 sd= 0.058 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 144 5.16 5 C 20954 2.51 5 N 5461 2.21 5 O 6515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33074 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8494 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 4 Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "C" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 59, 'TRANS': 1027} Chain breaks: 4 Chain: "F" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1738 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "H" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1745 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "L" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.87, per 1000 atoms: 0.21 Number of scatterers: 33074 At special positions: 0 Unit cell: (163.572, 165.711, 210.613, 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 144 16.00 O 6515 8.00 N 5461 7.00 C 20954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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 B 15 " - pdb=" SG CYS B 136 " 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 C 15 " - pdb=" SG CYS C 136 " 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 F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 110 " distance=2.02 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 343 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 17 " " NAG C1311 " - " ASN C 343 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 709 " " NAG M 1 " - " ASN A 17 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 79 sheets defined 20.8% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.589A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.535A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.673A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.115A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.558A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.928A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.625A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.987A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.606A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.821A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.904A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.550A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.934A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.774A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.409A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.528A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.739A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.650A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.575A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.676A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.506A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 4.113A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.563A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.968A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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: 4.161A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.726A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.352A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 4.541A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.555A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.816A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) 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 756 No H-bonds generated for 'chain 'C' and resid 755 through 756' Processing helix chain 'C' and resid 757 through 760 removed outlier: 3.722A pdb=" N CYS C 760 " --> pdb=" O GLY C 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 757 through 760' Processing helix chain 'C' and resid 761 through 782 removed outlier: 3.887A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.573A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.901A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.530A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.513A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.341A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.909A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 127 through 132 removed outlier: 3.609A pdb=" N GLN G 130 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 192 removed outlier: 3.504A pdb=" N HIS G 192 " --> pdb=" O GLN G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 removed outlier: 3.731A pdb=" N GLU G 214 " --> pdb=" O ALA G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.889A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 removed outlier: 4.251A pdb=" N GLN L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 192 removed outlier: 3.775A pdb=" N SER L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS L 192 " --> pdb=" O GLN L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.241A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TRP A 64 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL A 267 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS A 66 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR A 265 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 5.538A pdb=" N TRP A 64 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL A 267 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS A 66 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR A 265 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.516A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.684A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 155 removed outlier: 3.581A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.591A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.591A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.564A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 359 removed outlier: 4.509A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.030A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.122A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.294A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.294A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.800A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.611A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.595A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.023A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.807A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.490A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.935A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.575A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.693A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.276A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.276A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.607A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.733A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.733A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.727A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.088A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 151 through 155 removed outlier: 3.783A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.714A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.445A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.484A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.709A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.097A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 714 Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.872A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.250A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.601A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.854A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 58 through 59 removed outlier: 6.968A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.889A pdb=" N SER F 136 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 159 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU F 154 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL F 198 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS F 156 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER F 196 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 158 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR F 192 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 197 " --> pdb=" O HIS F 180 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.889A pdb=" N SER F 136 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 159 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU F 154 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL F 198 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS F 156 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER F 196 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 158 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR F 192 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 166 through 167 Processing sheet with id=AG5, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.741A pdb=" N THR G 23 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AG7, first strand: chain 'G' and resid 33 through 34 removed outlier: 4.096A pdb=" N TYR G 33 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR G 94 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER G 93 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 100 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AG9, first strand: chain 'G' and resid 118 through 122 removed outlier: 4.194A pdb=" N SER G 118 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER G 141 " --> pdb=" O SER G 118 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 120 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 139 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL G 137 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA G 134 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR G 176 " --> pdb=" O ASP G 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 181 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU G 164 " --> pdb=" O TYR G 181 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 118 through 122 removed outlier: 4.194A pdb=" N SER G 118 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER G 141 " --> pdb=" O SER G 118 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 120 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 139 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL G 137 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA G 134 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR G 176 " --> pdb=" O ASP G 142 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 157 through 159 removed outlier: 4.483A pdb=" N TRP G 152 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.194A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.194A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AH6, first strand: chain 'H' and resid 34 through 37 Processing sheet with id=AH7, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.523A pdb=" N TYR H 59 " --> pdb=" O PHE H 50 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 139 through 140 removed outlier: 3.530A pdb=" N LEU H 140 " --> pdb=" O GLY H 155 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL H 200 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU H 154 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 198 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER H 196 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 158 through 161 removed outlier: 3.661A pdb=" N VAL H 158 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 167 through 170 Processing sheet with id=AI2, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.193A pdb=" N THR L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU L 76 " --> pdb=" O ILE L 20 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.197A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR L 89 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.197A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR L 89 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS L 92 " --> pdb=" O GLN L 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER L 93 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 119 through 122 removed outlier: 4.084A pdb=" N THR L 120 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L 139 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 119 through 122 removed outlier: 4.084A pdb=" N THR L 120 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L 139 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.188A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA L 151 " --> pdb=" O GLN L 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN L 198 " --> pdb=" O ALA L 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS L 153 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER L 196 " --> pdb=" O LYS L 153 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3036 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.75 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5357 1.28 - 1.41: 8467 1.41 - 1.55: 19797 1.55 - 1.68: 43 1.68 - 1.82: 180 Bond restraints: 33844 Sorted by residual: bond pdb=" C GLU L 51 " pdb=" O GLU L 51 " ideal model delta sigma weight residual 1.235 1.141 0.095 1.26e-02 6.30e+03 5.64e+01 bond pdb=" N GLU L 51 " pdb=" CA GLU L 51 " ideal model delta sigma weight residual 1.457 1.367 0.091 1.29e-02 6.01e+03 4.92e+01 bond pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta sigma weight residual 1.527 1.592 -0.066 1.75e-02 3.27e+03 1.40e+01 bond pdb=" N ASP A 427 " pdb=" CA ASP A 427 " ideal model delta sigma weight residual 1.459 1.415 0.043 1.16e-02 7.43e+03 1.39e+01 bond pdb=" C PRO L 7 " pdb=" N HIS L 8 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.43e-02 4.89e+03 7.45e+00 ... (remaining 33839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 45497 2.26 - 4.51: 527 4.51 - 6.77: 52 6.77 - 9.03: 12 9.03 - 11.29: 3 Bond angle restraints: 46091 Sorted by residual: angle pdb=" O TYR L 50 " pdb=" C TYR L 50 " pdb=" N GLU L 51 " ideal model delta sigma weight residual 123.44 130.92 -7.48 1.23e+00 6.61e-01 3.70e+01 angle pdb=" C GLU L 51 " pdb=" N ASP L 52 " pdb=" CA ASP L 52 " ideal model delta sigma weight residual 121.54 132.83 -11.29 1.91e+00 2.74e-01 3.49e+01 angle pdb=" N ASP A 427 " pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 111.02 103.91 7.11 1.22e+00 6.72e-01 3.40e+01 angle pdb=" CA TYR L 50 " pdb=" C TYR L 50 " pdb=" N GLU L 51 " ideal model delta sigma weight residual 116.29 108.41 7.88 1.45e+00 4.76e-01 2.95e+01 angle pdb=" CA PRO L 7 " pdb=" C PRO L 7 " pdb=" O PRO L 7 " ideal model delta sigma weight residual 120.60 129.57 -8.97 1.82e+00 3.02e-01 2.43e+01 ... (remaining 46086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17194 17.96 - 35.92: 1884 35.92 - 53.88: 423 53.88 - 71.84: 81 71.84 - 89.80: 38 Dihedral angle restraints: 19620 sinusoidal: 7538 harmonic: 12082 Sorted by residual: dihedral pdb=" CB CYS H 105 " pdb=" SG CYS H 105 " pdb=" SG CYS H 110 " pdb=" CB CYS H 110 " ideal model delta sinusoidal sigma weight residual 93.00 20.35 72.65 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 33.41 59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 148.02 -55.02 1 1.00e+01 1.00e-02 4.10e+01 ... (remaining 19617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4538 0.060 - 0.120: 782 0.120 - 0.180: 45 0.180 - 0.239: 7 0.239 - 0.299: 1 Chirality restraints: 5373 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 5370 not shown) Planarity restraints: 5938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 51 " 0.034 2.00e-02 2.50e+03 7.14e-02 5.09e+01 pdb=" C GLU L 51 " -0.123 2.00e-02 2.50e+03 pdb=" O GLU L 51 " 0.048 2.00e-02 2.50e+03 pdb=" N ASP L 52 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 56 " 0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO C 57 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 55 " -0.054 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO L 56 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO L 56 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 56 " -0.045 5.00e-02 4.00e+02 ... (remaining 5935 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2539 2.74 - 3.28: 32458 3.28 - 3.82: 53386 3.82 - 4.36: 58925 4.36 - 4.90: 103607 Nonbonded interactions: 250915 Sorted by model distance: nonbonded pdb=" OG SER H 219 " pdb=" OG1 THR H 221 " model vdw 2.198 3.040 nonbonded pdb=" O ILE C 569 " pdb=" OG1 THR C 572 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OG1 THR B 998 " model vdw 2.203 3.040 nonbonded pdb=" O THR B 747 " pdb=" OG SER B 750 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG L 62 " pdb=" OD2 ASP L 85 " model vdw 2.234 3.120 ... (remaining 250910 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 14 through 178 or resid 185 through 1308)) selection = (chain 'B' and (resid 14 through 178 or resid 185 through 623 or resid 633 throu \ gh 1308)) selection = (chain 'C' and (resid 14 through 70 or resid 76 through 623 or resid 633 through \ 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'F' selection = (chain 'H' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 234)) } ncs_group { reference = chain 'G' selection = chain 'L' } 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: 4.600 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 30.910 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 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 : 0.004 0.282 33923 Z= 0.228 Angle : 0.597 11.286 46306 Z= 0.303 Chirality : 0.045 0.299 5373 Planarity : 0.004 0.092 5894 Dihedral : 15.970 89.795 11809 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 0.39 % Allowed : 23.07 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.35 (0.13), residues: 4122 helix: 1.63 (0.21), residues: 672 sheet: -0.26 (0.17), residues: 998 loop : -0.74 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 98 TYR 0.024 0.001 TYR C 904 PHE 0.020 0.001 PHE H 29 TRP 0.047 0.001 TRP A 886 HIS 0.009 0.001 HIS H 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (33844) covalent geometry : angle 0.58734 / 0.30 (46091) SS BOND : bond 0.00326 / 0.24 ( 19) SS BOND : angle 0.90241 / 0.61 ( 38) hydrogen bonds : bond 0.24261 / 16.04 ( 1085) hydrogen bonds : angle 9.38453 / 6.39 ( 3036) Misc. bond : bond 0.28160 / 14.82 ( 1) link_BETA1-4 : bond 0.00452 / 0.29 ( 15) link_BETA1-4 : angle 1.84234 / 1.44 ( 45) link_NAG-ASN : bond 0.00393 / 0.30 ( 44) link_NAG-ASN : angle 1.73956 / 1.63 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 409 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7752 (mttt) cc_final: 0.7490 (tttp) REVERT: A 544 ASN cc_start: 0.7782 (t0) cc_final: 0.7016 (p0) REVERT: A 950 ASP cc_start: 0.8389 (t0) cc_final: 0.8053 (t0) REVERT: A 978 ASN cc_start: 0.7028 (m-40) cc_final: 0.6740 (t0) REVERT: A 990 GLU cc_start: 0.7311 (tt0) cc_final: 0.6912 (pp20) REVERT: B 65 PHE cc_start: 0.7092 (m-80) cc_final: 0.6266 (m-10) REVERT: B 208 THR cc_start: 0.8500 (m) cc_final: 0.8131 (p) REVERT: B 553 THR cc_start: 0.7389 (p) cc_final: 0.7141 (p) REVERT: B 869 MET cc_start: 0.7681 (mtm) cc_final: 0.7434 (mtm) REVERT: C 580 GLN cc_start: 0.6737 (tp40) cc_final: 0.6250 (mt0) REVERT: H 83 MET cc_start: 0.4136 (ptp) cc_final: 0.3767 (ptm) REVERT: H 119 TRP cc_start: -0.0985 (m100) cc_final: -0.1461 (m100) REVERT: H 230 LYS cc_start: -0.0559 (tttt) cc_final: -0.1853 (tppt) outliers start: 14 outliers final: 3 residues processed: 419 average time/residue: 0.2132 time to fit residues: 147.4928 Evaluate side-chains 257 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 437 ASN A 580 GLN A 751 ASN A 949 GLN A1142 GLN B 164 ASN B 954 GLN C 30 ASN C 164 ASN C1088 HIS F 35 HIS ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 74 ASN H 104 HIS ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS L 198 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.237379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.194509 restraints weight = 56548.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.189011 restraints weight = 74356.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.186379 restraints weight = 52668.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.186392 restraints weight = 40522.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.186215 restraints weight = 38763.535| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33923 Z= 0.228 Angle : 0.665 10.886 46306 Z= 0.342 Chirality : 0.047 0.359 5373 Planarity : 0.005 0.064 5894 Dihedral : 4.505 31.599 4473 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 4.67 % Allowed : 20.59 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.57 (0.13), residues: 4122 helix: 1.06 (0.20), residues: 701 sheet: -0.36 (0.16), residues: 1051 loop : -0.81 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 38 TYR 0.024 0.002 TYR B 917 PHE 0.024 0.002 PHE B 92 TRP 0.036 0.002 TRP A 886 HIS 0.013 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (33844) covalent geometry : angle 0.65440 / 0.34 (46091) SS BOND : bond 0.00757 / 0.41 ( 19) SS BOND : angle 1.69997 / 1.34 ( 38) hydrogen bonds : bond 0.05036 / 3.34 ( 1085) hydrogen bonds : angle 6.94533 / 4.68 ( 3036) Misc. bond : bond 0.00513 / 0.27 ( 1) link_BETA1-4 : bond 0.00376 / 0.20 ( 15) link_BETA1-4 : angle 1.75127 / 1.31 ( 45) link_NAG-ASN : bond 0.00503 / 0.35 ( 44) link_NAG-ASN : angle 1.97852 / 1.80 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 259 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7045 (mm) REVERT: A 275 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8603 (m-10) REVERT: A 514 SER cc_start: 0.6807 (OUTLIER) cc_final: 0.6527 (p) REVERT: A 544 ASN cc_start: 0.7519 (t0) cc_final: 0.7172 (p0) REVERT: B 51 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8896 (p) REVERT: B 83 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7481 (p) REVERT: B 208 THR cc_start: 0.8337 (m) cc_final: 0.7962 (p) REVERT: C 36 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7360 (p) REVERT: C 580 GLN cc_start: 0.6792 (tp40) cc_final: 0.6561 (mt0) REVERT: H 80 TYR cc_start: 0.6453 (m-80) cc_final: 0.6205 (m-80) REVERT: H 83 MET cc_start: 0.3683 (ptp) cc_final: 0.2775 (ptm) REVERT: H 104 HIS cc_start: 0.5956 (p90) cc_final: 0.5041 (p90) REVERT: H 119 TRP cc_start: -0.0697 (m100) cc_final: -0.1333 (m100) REVERT: H 230 LYS cc_start: -0.1528 (tttt) cc_final: -0.2418 (tppt) outliers start: 169 outliers final: 100 residues processed: 412 average time/residue: 0.1937 time to fit residues: 135.5005 Evaluate side-chains 319 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 213 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 337 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 355 optimal weight: 40.0000 chunk 197 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 chunk 303 optimal weight: 0.7980 chunk 253 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 271 GLN A 751 ASN B 751 ASN B 787 GLN B 954 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS F 77 ASN H 3 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.239095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.192094 restraints weight = 56644.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.188269 restraints weight = 63178.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.177901 restraints weight = 36387.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.178479 restraints weight = 46516.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.179046 restraints weight = 35637.780| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33923 Z= 0.130 Angle : 0.573 9.759 46306 Z= 0.293 Chirality : 0.045 0.349 5373 Planarity : 0.004 0.074 5894 Dihedral : 4.284 32.578 4473 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % Rotamer: Outliers : 3.84 % Allowed : 21.22 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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 (0.13), residues: 4122 helix: 1.31 (0.20), residues: 687 sheet: -0.25 (0.16), residues: 1048 loop : -0.79 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 30 TYR 0.036 0.001 TYR L 37 PHE 0.028 0.001 PHE C 65 TRP 0.041 0.001 TRP A 886 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (33844) covalent geometry : angle 0.56387 / 0.29 (46091) SS BOND : bond 0.00255 / 0.20 ( 19) SS BOND : angle 1.22282 / 0.89 ( 38) hydrogen bonds : bond 0.04298 / 2.87 ( 1085) hydrogen bonds : angle 6.38091 / 4.30 ( 3036) Misc. bond : bond 0.00195 / 0.10 ( 1) link_BETA1-4 : bond 0.00411 / 0.25 ( 15) link_BETA1-4 : angle 1.69974 / 1.25 ( 45) link_NAG-ASN : bond 0.00378 / 0.28 ( 44) link_NAG-ASN : angle 1.68481 / 1.55 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 242 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8615 (p) cc_final: 0.8403 (p) REVERT: A 514 SER cc_start: 0.7317 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 544 ASN cc_start: 0.7475 (t0) cc_final: 0.7141 (p0) REVERT: A 740 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: B 83 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7480 (p) REVERT: B 190 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6007 (mtt180) REVERT: B 238 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6474 (p90) REVERT: C 580 GLN cc_start: 0.6604 (tp40) cc_final: 0.6319 (mt0) REVERT: C 987 PRO cc_start: 0.8737 (OUTLIER) cc_final: 0.8534 (Cg_endo) REVERT: H 58 LYS cc_start: 0.2786 (mmtm) cc_final: 0.2537 (tppt) REVERT: H 83 MET cc_start: 0.2581 (ptp) cc_final: 0.1898 (ptm) REVERT: H 230 LYS cc_start: -0.2406 (tttt) cc_final: -0.2903 (tppt) REVERT: L 51 GLU cc_start: 0.6621 (mm-30) cc_final: 0.5796 (tm-30) outliers start: 139 outliers final: 91 residues processed: 357 average time/residue: 0.1740 time to fit residues: 106.3421 Evaluate side-chains 310 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 213 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 212 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 167 optimal weight: 0.6980 chunk 225 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 330 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 GLN ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.239749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.195619 restraints weight = 56647.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.186413 restraints weight = 69998.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.181505 restraints weight = 50888.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.183178 restraints weight = 46643.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.183137 restraints weight = 36932.343| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33923 Z= 0.113 Angle : 0.544 10.004 46306 Z= 0.276 Chirality : 0.044 0.348 5373 Planarity : 0.004 0.074 5894 Dihedral : 4.127 32.629 4471 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 4.26 % Allowed : 20.81 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.40 (0.13), residues: 4122 helix: 1.37 (0.21), residues: 685 sheet: -0.19 (0.16), residues: 1046 loop : -0.77 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 55 TYR 0.023 0.001 TYR A 904 PHE 0.027 0.001 PHE A 135 TRP 0.020 0.001 TRP F 47 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (33844) covalent geometry : angle 0.53510 / 0.27 (46091) SS BOND : bond 0.00196 / 0.15 ( 19) SS BOND : angle 1.08868 / 0.82 ( 38) hydrogen bonds : bond 0.03752 / 2.52 ( 1085) hydrogen bonds : angle 5.94818 / 4.02 ( 3036) Misc. bond : bond 0.00142 / 0.07 ( 1) link_BETA1-4 : bond 0.00506 / 0.32 ( 15) link_BETA1-4 : angle 1.65367 / 1.21 ( 45) link_NAG-ASN : bond 0.00345 / 0.25 ( 44) link_NAG-ASN : angle 1.64177 / 1.48 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 238 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8582 (p) cc_final: 0.8367 (p) REVERT: A 514 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6993 (p) REVERT: A 544 ASN cc_start: 0.7434 (t0) cc_final: 0.7156 (p0) REVERT: A 740 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8067 (tmm) REVERT: B 51 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8851 (p) REVERT: B 190 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.5888 (mtt180) REVERT: B 238 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6621 (p90) REVERT: B 611 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 1002 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7745 (tp40) REVERT: C 118 LEU cc_start: 0.8960 (tp) cc_final: 0.8672 (mm) REVERT: C 306 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: C 580 GLN cc_start: 0.6534 (tp40) cc_final: 0.6290 (mt0) REVERT: C 1072 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: H 34 MET cc_start: 0.6239 (ptt) cc_final: 0.5935 (ptm) REVERT: H 83 MET cc_start: 0.2609 (ptp) cc_final: 0.1911 (ptm) REVERT: H 230 LYS cc_start: -0.2257 (tttt) cc_final: -0.2814 (tppt) REVERT: L 51 GLU cc_start: 0.6371 (mm-30) cc_final: 0.5875 (tm-30) outliers start: 154 outliers final: 104 residues processed: 370 average time/residue: 0.1698 time to fit residues: 107.1802 Evaluate side-chains 328 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 215 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 49 optimal weight: 10.0000 chunk 388 optimal weight: 30.0000 chunk 289 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 214 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.232708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.190167 restraints weight = 56522.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.181936 restraints weight = 70611.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.178673 restraints weight = 58415.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.180304 restraints weight = 49196.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.180345 restraints weight = 36397.314| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33923 Z= 0.159 Angle : 0.574 11.826 46306 Z= 0.291 Chirality : 0.045 0.349 5373 Planarity : 0.004 0.054 5894 Dihedral : 4.187 33.415 4471 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 4.73 % Allowed : 20.83 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.44 (0.13), residues: 4122 helix: 1.15 (0.20), residues: 698 sheet: -0.15 (0.16), residues: 1031 loop : -0.77 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 55 TYR 0.024 0.001 TYR A 904 PHE 0.031 0.001 PHE A 135 TRP 0.017 0.001 TRP A 886 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (33844) covalent geometry : angle 0.56364 / 0.29 (46091) SS BOND : bond 0.00231 / 0.18 ( 19) SS BOND : angle 1.53237 / 1.19 ( 38) hydrogen bonds : bond 0.03977 / 2.67 ( 1085) hydrogen bonds : angle 5.84995 / 3.95 ( 3036) Misc. bond : bond 0.00094 / 0.05 ( 1) link_BETA1-4 : bond 0.00390 / 0.23 ( 15) link_BETA1-4 : angle 1.66380 / 1.21 ( 45) link_NAG-ASN : bond 0.00400 / 0.29 ( 44) link_NAG-ASN : angle 1.77719 / 1.56 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 211 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 SER cc_start: 0.6974 (OUTLIER) cc_final: 0.6738 (p) REVERT: A 544 ASN cc_start: 0.7579 (t0) cc_final: 0.7207 (p0) REVERT: A 740 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8072 (tmm) REVERT: B 51 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8811 (p) REVERT: B 190 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.5911 (mtt180) REVERT: B 238 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6311 (p90) REVERT: B 611 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8488 (tp) REVERT: C 118 LEU cc_start: 0.8976 (tp) cc_final: 0.8705 (mm) REVERT: C 306 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: C 580 GLN cc_start: 0.6644 (tp40) cc_final: 0.6224 (mt0) REVERT: C 1072 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: H 34 MET cc_start: 0.6323 (ptt) cc_final: 0.6015 (ptm) REVERT: H 43 LYS cc_start: 0.1947 (tptp) cc_final: 0.1502 (tptm) REVERT: H 83 MET cc_start: 0.3165 (ptp) cc_final: 0.2322 (ptm) REVERT: H 230 LYS cc_start: -0.2166 (tttt) cc_final: -0.2844 (tppt) REVERT: L 4 LEU cc_start: -0.2073 (OUTLIER) cc_final: -0.2418 (mt) REVERT: L 51 GLU cc_start: 0.6001 (mm-30) cc_final: 0.5791 (tm-30) outliers start: 171 outliers final: 132 residues processed: 357 average time/residue: 0.1794 time to fit residues: 110.8021 Evaluate side-chains 345 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 204 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 235 optimal weight: 6.9990 chunk 333 optimal weight: 30.0000 chunk 268 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 406 optimal weight: 9.9990 chunk 363 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.231661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.188764 restraints weight = 56368.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.182739 restraints weight = 76789.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.179003 restraints weight = 53368.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.178835 restraints weight = 48931.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.179528 restraints weight = 37760.082| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33923 Z= 0.170 Angle : 0.582 11.391 46306 Z= 0.293 Chirality : 0.045 0.351 5373 Planarity : 0.004 0.053 5894 Dihedral : 4.229 33.746 4471 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 5.22 % Allowed : 20.83 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.44 (0.13), residues: 4122 helix: 1.08 (0.20), residues: 690 sheet: -0.13 (0.16), residues: 1040 loop : -0.76 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 55 TYR 0.028 0.001 TYR A 904 PHE 0.026 0.001 PHE A 135 TRP 0.013 0.001 TRP L 36 HIS 0.016 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (33844) covalent geometry : angle 0.57158 / 0.29 (46091) SS BOND : bond 0.00239 / 0.18 ( 19) SS BOND : angle 1.25499 / 0.96 ( 38) hydrogen bonds : bond 0.03997 / 2.69 ( 1085) hydrogen bonds : angle 5.76951 / 3.90 ( 3036) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.00402 / 0.25 ( 15) link_BETA1-4 : angle 1.68393 / 1.22 ( 45) link_NAG-ASN : bond 0.00421 / 0.31 ( 44) link_NAG-ASN : angle 1.82926 / 1.59 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 216 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 SER cc_start: 0.6876 (OUTLIER) cc_final: 0.6648 (p) REVERT: A 544 ASN cc_start: 0.7699 (t0) cc_final: 0.7228 (p0) REVERT: A 740 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8051 (tmm) REVERT: A 820 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: B 51 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8811 (p) REVERT: B 81 ASN cc_start: 0.7590 (p0) cc_final: 0.7285 (p0) REVERT: B 190 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.5773 (mtt180) REVERT: B 238 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6400 (p90) REVERT: B 611 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8554 (tp) REVERT: B 966 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8535 (mp) REVERT: B 1002 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: C 118 LEU cc_start: 0.8998 (tp) cc_final: 0.8699 (mm) REVERT: C 306 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8605 (m-80) REVERT: C 580 GLN cc_start: 0.6578 (tp40) cc_final: 0.6147 (mt0) REVERT: C 959 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8520 (mp) REVERT: C 1072 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: H 34 MET cc_start: 0.6260 (ptt) cc_final: 0.6020 (ptm) REVERT: H 43 LYS cc_start: 0.2084 (tptp) cc_final: 0.1669 (tptm) REVERT: H 83 MET cc_start: 0.3253 (ptp) cc_final: 0.2364 (ptm) REVERT: H 230 LYS cc_start: -0.2098 (tttt) cc_final: -0.2805 (tppt) REVERT: L 51 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5743 (tm-30) outliers start: 189 outliers final: 142 residues processed: 382 average time/residue: 0.1871 time to fit residues: 123.0732 Evaluate side-chains 349 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 195 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 276 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 405 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 356 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 751 ASN B 787 GLN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.228187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.184636 restraints weight = 56309.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.177810 restraints weight = 72393.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.172996 restraints weight = 60457.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.174082 restraints weight = 51864.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.174034 restraints weight = 38974.294| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 33923 Z= 0.252 Angle : 0.662 10.261 46306 Z= 0.333 Chirality : 0.047 0.477 5373 Planarity : 0.005 0.053 5894 Dihedral : 4.529 34.382 4471 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.25 % Allowed : 21.22 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.64 (0.13), residues: 4122 helix: 0.69 (0.20), residues: 698 sheet: -0.19 (0.16), residues: 1057 loop : -0.86 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 646 TYR 0.036 0.002 TYR A 904 PHE 0.043 0.002 PHE A 135 TRP 0.022 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (33844) covalent geometry : angle 0.64742 / 0.33 (46091) SS BOND : bond 0.00280 / 0.21 ( 19) SS BOND : angle 1.52888 / 1.19 ( 38) hydrogen bonds : bond 0.04506 / 3.02 ( 1085) hydrogen bonds : angle 5.92889 / 4.00 ( 3036) Misc. bond : bond 0.00081 / 0.04 ( 1) link_BETA1-4 : bond 0.00449 / 0.26 ( 15) link_BETA1-4 : angle 1.62357 / 1.19 ( 45) link_NAG-ASN : bond 0.00552 / 0.38 ( 44) link_NAG-ASN : angle 2.43503 / 2.26 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 204 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: A 544 ASN cc_start: 0.7830 (t0) cc_final: 0.7338 (p0) REVERT: A 740 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8048 (tmm) REVERT: A 786 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7981 (pttm) REVERT: A 820 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: A 1034 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 51 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8839 (p) REVERT: B 81 ASN cc_start: 0.7334 (p0) cc_final: 0.6944 (p0) REVERT: B 190 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5862 (mtt180) REVERT: B 238 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6445 (p90) REVERT: B 611 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8674 (tp) REVERT: B 966 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8690 (mp) REVERT: C 118 LEU cc_start: 0.9010 (tp) cc_final: 0.8672 (mm) REVERT: C 189 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5158 (tp) REVERT: C 306 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: C 580 GLN cc_start: 0.6493 (tp40) cc_final: 0.6033 (tm-30) REVERT: C 959 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8640 (mp) REVERT: C 1072 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: H 34 MET cc_start: 0.6245 (ptt) cc_final: 0.5890 (ptm) REVERT: H 43 LYS cc_start: 0.2209 (tptp) cc_final: 0.1757 (tptm) REVERT: H 83 MET cc_start: 0.3186 (ptp) cc_final: 0.2528 (ptm) REVERT: H 230 LYS cc_start: -0.1973 (tttt) cc_final: -0.2709 (tppt) REVERT: L 51 GLU cc_start: 0.5900 (mm-30) cc_final: 0.5551 (tm-30) outliers start: 190 outliers final: 146 residues processed: 373 average time/residue: 0.1919 time to fit residues: 123.6291 Evaluate side-chains 351 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 192 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 387 optimal weight: 9.9990 chunk 280 optimal weight: 0.7980 chunk 351 optimal weight: 2.9990 chunk 304 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 359 optimal weight: 30.0000 chunk 87 optimal weight: 0.0010 chunk 33 optimal weight: 10.0000 chunk 284 optimal weight: 0.5980 chunk 307 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN B 641 ASN B1083 HIS C 360 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.232794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.192053 restraints weight = 56311.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.185871 restraints weight = 74776.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.181959 restraints weight = 58317.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.182698 restraints weight = 51892.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.183150 restraints weight = 37524.326| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33923 Z= 0.111 Angle : 0.567 10.739 46306 Z= 0.283 Chirality : 0.044 0.351 5373 Planarity : 0.004 0.061 5894 Dihedral : 4.186 27.263 4469 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.79 % Allowed : 22.55 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.42 (0.13), residues: 4122 helix: 1.06 (0.20), residues: 697 sheet: -0.04 (0.16), residues: 1053 loop : -0.78 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.034 0.001 TYR A 904 PHE 0.048 0.001 PHE A 135 TRP 0.017 0.001 TRP L 36 HIS 0.030 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (33844) covalent geometry : angle 0.55209 / 0.28 (46091) SS BOND : bond 0.00372 / 0.23 ( 19) SS BOND : angle 0.97369 / 0.64 ( 38) hydrogen bonds : bond 0.03700 / 2.50 ( 1085) hydrogen bonds : angle 5.57622 / 3.77 ( 3036) Misc. bond : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : bond 0.00452 / 0.29 ( 15) link_BETA1-4 : angle 1.53441 / 1.17 ( 45) link_NAG-ASN : bond 0.00425 / 0.33 ( 44) link_NAG-ASN : angle 2.33280 / 2.18 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 206 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.7633 (t0) cc_final: 0.7307 (p0) REVERT: A 740 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7978 (tmm) REVERT: B 51 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 190 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.5797 (mtt180) REVERT: B 238 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6583 (p90) REVERT: C 102 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7355 (mpp-170) REVERT: C 118 LEU cc_start: 0.8926 (tp) cc_final: 0.8712 (mm) REVERT: C 189 LEU cc_start: 0.5183 (OUTLIER) cc_final: 0.4920 (tp) REVERT: C 306 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: C 580 GLN cc_start: 0.6407 (tp40) cc_final: 0.6036 (mt0) REVERT: C 904 TYR cc_start: 0.6896 (t80) cc_final: 0.6636 (t80) REVERT: C 1072 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: H 34 MET cc_start: 0.6031 (ptt) cc_final: 0.5823 (ptm) REVERT: H 43 LYS cc_start: 0.2046 (tptp) cc_final: 0.1650 (tptm) REVERT: H 83 MET cc_start: 0.3398 (ptp) cc_final: 0.2647 (ptm) REVERT: H 98 ARG cc_start: 0.5503 (ttm-80) cc_final: 0.5175 (ttm-80) REVERT: H 230 LYS cc_start: -0.1857 (tttt) cc_final: -0.2631 (tppt) outliers start: 137 outliers final: 109 residues processed: 325 average time/residue: 0.1968 time to fit residues: 109.0392 Evaluate side-chains 312 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 196 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 295 optimal weight: 3.9990 chunk 371 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 391 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 346 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 275 optimal weight: 0.3980 chunk 319 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 chunk 323 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1088 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.231286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.187580 restraints weight = 55941.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.179997 restraints weight = 71797.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.175496 restraints weight = 58664.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.177120 restraints weight = 45092.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.176733 restraints weight = 37983.753| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33923 Z= 0.150 Angle : 0.582 10.640 46306 Z= 0.291 Chirality : 0.045 0.351 5373 Planarity : 0.004 0.053 5894 Dihedral : 4.172 27.980 4469 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.87 % Allowed : 22.60 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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 (0.13), residues: 4122 helix: 1.02 (0.20), residues: 703 sheet: -0.08 (0.17), residues: 1049 loop : -0.79 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.040 0.001 TYR A 505 PHE 0.054 0.001 PHE A 135 TRP 0.013 0.001 TRP L 36 HIS 0.009 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (33844) covalent geometry : angle 0.56898 / 0.29 (46091) SS BOND : bond 0.00505 / 0.27 ( 19) SS BOND : angle 0.84704 / 0.57 ( 38) hydrogen bonds : bond 0.03811 / 2.58 ( 1085) hydrogen bonds : angle 5.57899 / 3.76 ( 3036) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00413 / 0.24 ( 15) link_BETA1-4 : angle 1.54673 / 1.16 ( 45) link_NAG-ASN : bond 0.00437 / 0.34 ( 44) link_NAG-ASN : angle 2.22077 / 2.09 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 196 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.7709 (t0) cc_final: 0.7350 (p0) REVERT: A 740 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8010 (tmm) REVERT: A 820 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: B 51 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8794 (p) REVERT: B 190 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5883 (mtt180) REVERT: B 238 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6494 (p90) REVERT: C 102 ARG cc_start: 0.8216 (mmt-90) cc_final: 0.7405 (mpp-170) REVERT: C 118 LEU cc_start: 0.9006 (tp) cc_final: 0.8698 (mm) REVERT: C 189 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.5070 (tp) REVERT: C 306 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: C 580 GLN cc_start: 0.6496 (tp40) cc_final: 0.5985 (mt0) REVERT: C 904 TYR cc_start: 0.6936 (t80) cc_final: 0.6636 (t80) REVERT: C 1072 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: H 43 LYS cc_start: 0.2373 (tptp) cc_final: 0.1890 (tptm) REVERT: H 83 MET cc_start: 0.3277 (ptp) cc_final: 0.2528 (ptm) REVERT: H 230 LYS cc_start: -0.1985 (tttt) cc_final: -0.2695 (tppt) outliers start: 140 outliers final: 116 residues processed: 322 average time/residue: 0.1927 time to fit residues: 106.8922 Evaluate side-chains 315 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 191 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 155 optimal weight: 20.0000 chunk 110 optimal weight: 0.3980 chunk 382 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 chunk 399 optimal weight: 30.0000 chunk 150 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 292 optimal weight: 0.7980 chunk 384 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 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 = 0.4865 r_free = 0.4865 target = 0.227546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.183711 restraints weight = 56305.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.176028 restraints weight = 72169.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.172274 restraints weight = 62809.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.173816 restraints weight = 50581.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.173289 restraints weight = 40112.764| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 33923 Z= 0.248 Angle : 0.664 10.941 46306 Z= 0.334 Chirality : 0.047 0.366 5373 Planarity : 0.005 0.063 5894 Dihedral : 4.470 28.420 4469 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.84 % Allowed : 22.69 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.70 (0.13), residues: 4122 helix: 0.61 (0.20), residues: 710 sheet: -0.24 (0.16), residues: 1097 loop : -0.90 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.046 0.002 TYR A 904 PHE 0.033 0.002 PHE A 135 TRP 0.017 0.001 TRP A 104 HIS 0.007 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (33844) covalent geometry : angle 0.65035 / 0.33 (46091) SS BOND : bond 0.00532 / 0.30 ( 19) SS BOND : angle 1.03150 / 0.73 ( 38) hydrogen bonds : bond 0.04482 / 3.01 ( 1085) hydrogen bonds : angle 5.79045 / 3.90 ( 3036) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.00428 / 0.25 ( 15) link_BETA1-4 : angle 1.64546 / 1.20 ( 45) link_NAG-ASN : bond 0.00581 / 0.43 ( 44) link_NAG-ASN : angle 2.42759 / 2.23 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 197 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.7902 (t0) cc_final: 0.7420 (p0) REVERT: A 740 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: A 820 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: B 51 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8862 (p) REVERT: B 178 ASP cc_start: 0.3105 (OUTLIER) cc_final: 0.2828 (m-30) REVERT: B 190 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.5934 (mtt180) REVERT: B 238 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6363 (p90) REVERT: C 102 ARG cc_start: 0.8369 (mmt-90) cc_final: 0.7552 (mpp-170) REVERT: C 118 LEU cc_start: 0.9027 (tp) cc_final: 0.8610 (mm) REVERT: C 189 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.5149 (tp) REVERT: C 238 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5466 (p90) REVERT: C 306 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: C 580 GLN cc_start: 0.6496 (tp40) cc_final: 0.5908 (mt0) REVERT: C 904 TYR cc_start: 0.6990 (t80) cc_final: 0.6659 (t80) REVERT: C 1072 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: H 34 MET cc_start: 0.6193 (ptt) cc_final: 0.5987 (ptt) REVERT: H 43 LYS cc_start: 0.2600 (tptp) cc_final: 0.2176 (tptm) REVERT: H 83 MET cc_start: 0.3580 (ptp) cc_final: 0.2741 (ptm) REVERT: H 230 LYS cc_start: -0.2115 (tttt) cc_final: -0.2853 (tppt) REVERT: L 51 GLU cc_start: 0.5879 (mm-30) cc_final: 0.5408 (tm-30) outliers start: 139 outliers final: 114 residues processed: 326 average time/residue: 0.1959 time to fit residues: 109.6220 Evaluate side-chains 317 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 193 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 232 optimal weight: 0.6980 chunk 376 optimal weight: 2.9990 chunk 188 optimal weight: 0.0040 chunk 362 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 366 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 349 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 393 optimal weight: 8.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN B1088 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.229673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.187378 restraints weight = 56315.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.182519 restraints weight = 76270.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.178560 restraints weight = 58489.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.178738 restraints weight = 50677.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.179062 restraints weight = 40087.887| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33923 Z= 0.155 Angle : 0.590 10.948 46306 Z= 0.293 Chirality : 0.045 0.352 5373 Planarity : 0.004 0.059 5894 Dihedral : 4.275 28.165 4469 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.45 % Allowed : 23.13 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.52 (0.13), residues: 4122 helix: 0.88 (0.20), residues: 703 sheet: -0.14 (0.16), residues: 1123 loop : -0.82 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 72 TYR 0.045 0.001 TYR A 505 PHE 0.039 0.001 PHE A 135 TRP 0.013 0.001 TRP L 36 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (33844) covalent geometry : angle 0.57723 / 0.29 (46091) SS BOND : bond 0.00499 / 0.27 ( 19) SS BOND : angle 0.89856 / 0.61 ( 38) hydrogen bonds : bond 0.03897 / 2.63 ( 1085) hydrogen bonds : angle 5.57115 / 3.75 ( 3036) Misc. bond : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : bond 0.00445 / 0.27 ( 15) link_BETA1-4 : angle 1.59450 / 1.18 ( 45) link_NAG-ASN : bond 0.00452 / 0.34 ( 44) link_NAG-ASN : angle 2.15149 / 2.07 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5549.99 seconds wall clock time: 97 minutes 20.32 seconds (5840.32 seconds total)