Starting phenix.real_space_refine on Sat Dec 28 01:46:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usp_42510/12_2024/8usp_42510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usp_42510/12_2024/8usp_42510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8usp_42510/12_2024/8usp_42510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usp_42510/12_2024/8usp_42510.map" model { file = "/net/cci-nas-00/data/ceres_data/8usp_42510/12_2024/8usp_42510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usp_42510/12_2024/8usp_42510.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3426 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 30732 2.51 5 N 7608 2.21 5 O 8886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 47406 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7901 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 27, 'TRANS': 954} Chain breaks: 2 Chain: "B" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7901 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 27, 'TRANS': 954} Chain breaks: 2 Chain: "C" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7901 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 27, 'TRANS': 954} Chain breaks: 2 Chain: "D" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7901 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 27, 'TRANS': 954} Chain breaks: 2 Chain: "E" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7901 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 27, 'TRANS': 954} Chain breaks: 2 Chain: "F" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7901 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 27, 'TRANS': 954} Chain breaks: 2 Time building chain proxies: 19.78, per 1000 atoms: 0.42 Number of scatterers: 47406 At special positions: 0 Unit cell: (163.086, 176.853, 162.027, 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 180 16.00 O 8886 8.00 N 7608 7.00 C 30732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.79 Conformation dependent library (CDL) restraints added in 4.4 seconds 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11520 Finding SS restraints... Secondary structure from input PDB file: 325 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.901A pdb=" N ALA A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 removed outlier: 4.210A pdb=" N GLU A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 75 removed outlier: 3.817A pdb=" N ARG A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 98 removed outlier: 3.798A pdb=" N ILE A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.921A pdb=" N VAL A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.535A pdb=" N ALA A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 Proline residue: A 147 - end of helix removed outlier: 3.600A pdb=" N PHE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.819A pdb=" N ASN A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 206 removed outlier: 3.609A pdb=" N LEU A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.574A pdb=" N ASN A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 4.097A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 269 removed outlier: 3.922A pdb=" N SER A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASP A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 293 through 314 removed outlier: 5.873A pdb=" N THR A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.656A pdb=" N ALA A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 380 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 398 through 414 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 419 through 442 removed outlier: 3.751A pdb=" N PHE A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 removed outlier: 4.237A pdb=" N GLU A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 461' Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.720A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 556 removed outlier: 3.745A pdb=" N VAL A 544 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 549 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.866A pdb=" N ILE A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 Processing helix chain 'A' and resid 613 through 632 removed outlier: 3.552A pdb=" N ASN A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 659 Proline residue: A 651 - end of helix removed outlier: 4.092A pdb=" N ILE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 683 removed outlier: 3.988A pdb=" N LYS A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 715 through 724 removed outlier: 3.558A pdb=" N TYR A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 749 Processing helix chain 'A' and resid 754 through 772 Processing helix chain 'A' and resid 774 through 782 Processing helix chain 'A' and resid 788 through 805 removed outlier: 3.906A pdb=" N GLY A 801 " --> pdb=" O TRP A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 822 removed outlier: 3.655A pdb=" N ALA A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 834 removed outlier: 4.756A pdb=" N SER A 828 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 838 Processing helix chain 'A' and resid 859 through 877 removed outlier: 4.220A pdb=" N GLN A 870 " --> pdb=" O GLY A 866 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 899 removed outlier: 4.351A pdb=" N HIS A 898 " --> pdb=" O LEU A 894 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 904 removed outlier: 3.889A pdb=" N VAL A 904 " --> pdb=" O SER A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 918 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 923 through 941 Processing helix chain 'A' and resid 942 through 960 removed outlier: 5.360A pdb=" N SER A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR A 951 " --> pdb=" O GLU A 947 " (cutoff:3.500A) Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 967 through 985 Processing helix chain 'A' and resid 986 through 992 removed outlier: 3.744A pdb=" N SER A 992 " --> pdb=" O ASN A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 Processing helix chain 'A' and resid 1010 through 1029 removed outlier: 3.525A pdb=" N GLY A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A1028 " --> pdb=" O TYR A1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 20 removed outlier: 3.947A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 removed outlier: 3.944A pdb=" N ALA B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 51 removed outlier: 4.019A pdb=" N GLU B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 removed outlier: 4.291A pdb=" N SER B 55 " --> pdb=" O TYR B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 57 through 75 removed outlier: 3.724A pdb=" N ARG B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 98 removed outlier: 3.996A pdb=" N ILE B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 removed outlier: 4.068A pdb=" N VAL B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 removed outlier: 4.026A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 removed outlier: 3.947A pdb=" N TRP B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix removed outlier: 3.649A pdb=" N ARG B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 4.122A pdb=" N ASP B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 182 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 206 removed outlier: 3.522A pdb=" N LEU B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.696A pdb=" N ASN B 211 " --> pdb=" O ASN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 4.057A pdb=" N PHE B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 269 removed outlier: 4.327A pdb=" N SER B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 293 through 314 removed outlier: 6.004A pdb=" N THR B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.675A pdb=" N ALA B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 380 Proline residue: B 376 - end of helix Processing helix chain 'B' and resid 383 through 396 Processing helix chain 'B' and resid 398 through 414 Proline residue: B 411 - end of helix Processing helix chain 'B' and resid 419 through 442 removed outlier: 3.790A pdb=" N PHE B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 removed outlier: 4.280A pdb=" N GLU B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 480 through 497 removed outlier: 3.608A pdb=" N ARG B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 520 Processing helix chain 'B' and resid 522 through 540 Processing helix chain 'B' and resid 540 through 556 removed outlier: 3.855A pdb=" N VAL B 544 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 549 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 551 " --> pdb=" O ILE B 547 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.876A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 610 Processing helix chain 'B' and resid 613 through 631 Processing helix chain 'B' and resid 638 through 659 Proline residue: B 651 - end of helix removed outlier: 4.101A pdb=" N ILE B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 683 removed outlier: 3.998A pdb=" N LYS B 683 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 688 through 701 Processing helix chain 'B' and resid 714 through 724 removed outlier: 4.330A pdb=" N SER B 718 " --> pdb=" O VAL B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 749 Processing helix chain 'B' and resid 754 through 772 Processing helix chain 'B' and resid 774 through 781 Processing helix chain 'B' and resid 788 through 805 removed outlier: 3.505A pdb=" N GLY B 801 " --> pdb=" O TRP B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 822 removed outlier: 4.138A pdb=" N LYS B 815 " --> pdb=" O SER B 811 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 834 removed outlier: 4.717A pdb=" N SER B 828 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU B 829 " --> pdb=" O GLU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 838 Processing helix chain 'B' and resid 859 through 877 removed outlier: 4.205A pdb=" N GLN B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 899 removed outlier: 4.262A pdb=" N HIS B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 904 removed outlier: 3.966A pdb=" N VAL B 904 " --> pdb=" O SER B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 918 Proline residue: B 913 - end of helix Processing helix chain 'B' and resid 923 through 941 Processing helix chain 'B' and resid 942 through 960 removed outlier: 3.593A pdb=" N THR B 946 " --> pdb=" O HIS B 942 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER B 950 " --> pdb=" O THR B 946 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR B 951 " --> pdb=" O GLU B 947 " (cutoff:3.500A) Proline residue: B 954 - end of helix Processing helix chain 'B' and resid 967 through 985 Processing helix chain 'B' and resid 986 through 993 removed outlier: 3.703A pdb=" N SER B 992 " --> pdb=" O ASN B 988 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 Processing helix chain 'B' and resid 1010 through 1029 removed outlier: 3.544A pdb=" N GLY B1027 " --> pdb=" O TYR B1023 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B1028 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 24 through 39 removed outlier: 3.854A pdb=" N ALA C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 4.205A pdb=" N GLU C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 55 removed outlier: 4.236A pdb=" N SER C 55 " --> pdb=" O TYR C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 57 through 75 removed outlier: 3.839A pdb=" N ARG C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 98 removed outlier: 4.220A pdb=" N ILE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.930A pdb=" N VAL C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 removed outlier: 3.897A pdb=" N LEU C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 158 removed outlier: 3.927A pdb=" N TRP C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Proline residue: C 147 - end of helix removed outlier: 3.630A pdb=" N PHE C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 182 removed outlier: 4.745A pdb=" N ASP C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.621A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 224 removed outlier: 4.352A pdb=" N VAL C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 269 removed outlier: 4.827A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 290 Processing helix chain 'C' and resid 293 through 314 removed outlier: 6.024A pdb=" N THR C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 359 Processing helix chain 'C' and resid 359 through 380 Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 383 through 396 Processing helix chain 'C' and resid 398 through 414 Proline residue: C 411 - end of helix Processing helix chain 'C' and resid 419 through 442 removed outlier: 3.778A pdb=" N PHE C 432 " --> pdb=" O MET C 428 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 433 " --> pdb=" O ASN C 429 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 480 through 497 removed outlier: 3.695A pdb=" N ARG C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 520 Processing helix chain 'C' and resid 522 through 540 Processing helix chain 'C' and resid 540 through 556 removed outlier: 3.526A pdb=" N VAL C 544 " --> pdb=" O TYR C 540 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 551 " --> pdb=" O ILE C 547 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 4.231A pdb=" N ILE C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 584 " --> pdb=" O ILE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 610 Processing helix chain 'C' and resid 613 through 632 removed outlier: 3.564A pdb=" N ASN C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 632 " --> pdb=" O ASN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 659 Proline residue: C 651 - end of helix removed outlier: 4.141A pdb=" N ILE C 656 " --> pdb=" O LYS C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 683 removed outlier: 3.966A pdb=" N LYS C 683 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 687 No H-bonds generated for 'chain 'C' and resid 685 through 687' Processing helix chain 'C' and resid 688 through 701 Processing helix chain 'C' and resid 715 through 724 removed outlier: 3.521A pdb=" N TYR C 719 " --> pdb=" O LEU C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 749 Processing helix chain 'C' and resid 754 through 772 Processing helix chain 'C' and resid 774 through 781 Processing helix chain 'C' and resid 788 through 805 removed outlier: 3.889A pdb=" N GLY C 801 " --> pdb=" O TRP C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 822 removed outlier: 4.195A pdb=" N LYS C 815 " --> pdb=" O SER C 811 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 834 Processing helix chain 'C' and resid 835 through 838 Processing helix chain 'C' and resid 859 through 878 removed outlier: 4.228A pdb=" N GLN C 870 " --> pdb=" O GLY C 866 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 897 Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.911A pdb=" N VAL C 904 " --> pdb=" O SER C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 918 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 923 through 941 Processing helix chain 'C' and resid 942 through 960 removed outlier: 5.363A pdb=" N SER C 950 " --> pdb=" O THR C 946 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR C 951 " --> pdb=" O GLU C 947 " (cutoff:3.500A) Proline residue: C 954 - end of helix Processing helix chain 'C' and resid 967 through 985 Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.759A pdb=" N SER C 992 " --> pdb=" O ASN C 988 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 993 " --> pdb=" O TYR C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1001 Processing helix chain 'C' and resid 1010 through 1029 removed outlier: 3.564A pdb=" N GLY C1027 " --> pdb=" O TYR C1023 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C1028 " --> pdb=" O TYR C1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 24 through 39 removed outlier: 3.920A pdb=" N ALA D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 removed outlier: 4.201A pdb=" N GLU D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 55 removed outlier: 4.322A pdb=" N SER D 55 " --> pdb=" O TYR D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 55' Processing helix chain 'D' and resid 57 through 75 removed outlier: 4.071A pdb=" N ARG D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 98 removed outlier: 3.838A pdb=" N ILE D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE D 89 " --> pdb=" O CYS D 85 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.805A pdb=" N VAL D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.755A pdb=" N LEU D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.610A pdb=" N ILE D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.628A pdb=" N GLU D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 206 removed outlier: 3.886A pdb=" N SER D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.506A pdb=" N ASN D 211 " --> pdb=" O ASN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.654A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.541A pdb=" N THR D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 6.948A pdb=" N LEU D 256 " --> pdb=" O ALA D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 257 through 269 removed outlier: 4.173A pdb=" N SER D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 290 Processing helix chain 'D' and resid 293 through 314 removed outlier: 6.017A pdb=" N THR D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 359 removed outlier: 3.703A pdb=" N ALA D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 380 Proline residue: D 376 - end of helix Processing helix chain 'D' and resid 383 through 396 Processing helix chain 'D' and resid 398 through 414 Proline residue: D 411 - end of helix Processing helix chain 'D' and resid 419 through 442 removed outlier: 3.717A pdb=" N PHE D 432 " --> pdb=" O MET D 428 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 433 " --> pdb=" O ASN D 429 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 480 through 497 removed outlier: 3.860A pdb=" N ARG D 484 " --> pdb=" O GLU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 520 Processing helix chain 'D' and resid 522 through 540 Processing helix chain 'D' and resid 540 through 556 removed outlier: 3.863A pdb=" N VAL D 544 " --> pdb=" O TYR D 540 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE D 545 " --> pdb=" O GLU D 541 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 549 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 551 " --> pdb=" O ILE D 547 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.875A pdb=" N ILE D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 610 Processing helix chain 'D' and resid 613 through 632 removed outlier: 3.502A pdb=" N ASN D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 632 " --> pdb=" O ASN D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 659 Proline residue: D 651 - end of helix removed outlier: 4.176A pdb=" N ILE D 656 " --> pdb=" O LYS D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 683 removed outlier: 3.950A pdb=" N LYS D 683 " --> pdb=" O PHE D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 687 No H-bonds generated for 'chain 'D' and resid 685 through 687' Processing helix chain 'D' and resid 688 through 701 Processing helix chain 'D' and resid 714 through 724 removed outlier: 4.333A pdb=" N SER D 718 " --> pdb=" O VAL D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 749 Processing helix chain 'D' and resid 754 through 772 Processing helix chain 'D' and resid 774 through 781 Processing helix chain 'D' and resid 788 through 805 removed outlier: 3.871A pdb=" N GLY D 801 " --> pdb=" O TRP D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 822 removed outlier: 4.214A pdb=" N LYS D 815 " --> pdb=" O SER D 811 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 822 " --> pdb=" O ILE D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 834 removed outlier: 4.709A pdb=" N SER D 828 " --> pdb=" O GLU D 824 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU D 829 " --> pdb=" O GLU D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 838 Processing helix chain 'D' and resid 859 through 878 removed outlier: 4.239A pdb=" N GLN D 870 " --> pdb=" O GLY D 866 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR D 871 " --> pdb=" O ASP D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 899 removed outlier: 4.369A pdb=" N HIS D 898 " --> pdb=" O LEU D 894 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR D 899 " --> pdb=" O VAL D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 904 removed outlier: 4.042A pdb=" N VAL D 904 " --> pdb=" O SER D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 918 Proline residue: D 913 - end of helix Processing helix chain 'D' and resid 923 through 941 Processing helix chain 'D' and resid 942 through 960 removed outlier: 5.364A pdb=" N SER D 950 " --> pdb=" O THR D 946 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR D 951 " --> pdb=" O GLU D 947 " (cutoff:3.500A) Proline residue: D 954 - end of helix Processing helix chain 'D' and resid 967 through 985 Processing helix chain 'D' and resid 986 through 992 removed outlier: 3.748A pdb=" N SER D 992 " --> pdb=" O ASN D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1001 Processing helix chain 'D' and resid 1010 through 1029 removed outlier: 3.806A pdb=" N GLN D1028 " --> pdb=" O TYR D1024 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 24 through 39 removed outlier: 3.950A pdb=" N ALA E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 removed outlier: 4.165A pdb=" N GLU E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.321A pdb=" N SER E 55 " --> pdb=" O TYR E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 57 through 75 removed outlier: 3.817A pdb=" N ARG E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 98 removed outlier: 4.003A pdb=" N ILE E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE E 89 " --> pdb=" O CYS E 85 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 removed outlier: 4.017A pdb=" N VAL E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.559A pdb=" N LEU E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 158 removed outlier: 3.689A pdb=" N LYS E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 182 removed outlier: 3.573A pdb=" N ASN E 172 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 182 " --> pdb=" O THR E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 206 removed outlier: 3.551A pdb=" N LEU E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 204 " --> pdb=" O LYS E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 removed outlier: 3.502A pdb=" N ASN E 211 " --> pdb=" O ASN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 257 through 269 removed outlier: 4.253A pdb=" N SER E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 290 Processing helix chain 'E' and resid 293 through 314 removed outlier: 6.056A pdb=" N THR E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 359 removed outlier: 3.691A pdb=" N ALA E 343 " --> pdb=" O THR E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 380 Proline residue: E 376 - end of helix Processing helix chain 'E' and resid 383 through 396 Processing helix chain 'E' and resid 398 through 414 Proline residue: E 411 - end of helix Processing helix chain 'E' and resid 419 through 442 removed outlier: 3.880A pdb=" N PHE E 432 " --> pdb=" O MET E 428 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE E 433 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 435 " --> pdb=" O SER E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 removed outlier: 4.213A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 474 Processing helix chain 'E' and resid 480 through 497 removed outlier: 3.620A pdb=" N ARG E 484 " --> pdb=" O GLU E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 520 Processing helix chain 'E' and resid 522 through 540 Processing helix chain 'E' and resid 540 through 556 removed outlier: 3.542A pdb=" N VAL E 544 " --> pdb=" O TYR E 540 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 549 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS E 551 " --> pdb=" O ILE E 547 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU E 556 " --> pdb=" O LEU E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 584 removed outlier: 3.897A pdb=" N ILE E 577 " --> pdb=" O HIS E 573 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE E 584 " --> pdb=" O ILE E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 610 Processing helix chain 'E' and resid 613 through 632 removed outlier: 3.573A pdb=" N GLN E 632 " --> pdb=" O ASN E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 659 Proline residue: E 651 - end of helix removed outlier: 4.147A pdb=" N ILE E 656 " --> pdb=" O LYS E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 683 removed outlier: 3.992A pdb=" N LYS E 683 " --> pdb=" O PHE E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 687 No H-bonds generated for 'chain 'E' and resid 685 through 687' Processing helix chain 'E' and resid 688 through 701 Processing helix chain 'E' and resid 715 through 724 removed outlier: 3.502A pdb=" N TYR E 719 " --> pdb=" O LEU E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 749 Processing helix chain 'E' and resid 754 through 772 Processing helix chain 'E' and resid 774 through 781 Processing helix chain 'E' and resid 788 through 805 removed outlier: 3.516A pdb=" N GLY E 801 " --> pdb=" O TRP E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 822 removed outlier: 4.193A pdb=" N LYS E 815 " --> pdb=" O SER E 811 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 822 " --> pdb=" O ILE E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 834 removed outlier: 4.689A pdb=" N SER E 828 " --> pdb=" O GLU E 824 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU E 829 " --> pdb=" O GLU E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 838 Processing helix chain 'E' and resid 859 through 877 removed outlier: 4.274A pdb=" N GLN E 870 " --> pdb=" O GLY E 866 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR E 871 " --> pdb=" O ASP E 867 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 897 Processing helix chain 'E' and resid 900 through 904 removed outlier: 3.638A pdb=" N VAL E 904 " --> pdb=" O SER E 901 " (cutoff:3.500A) Processing helix chain 'E' and resid 907 through 918 Proline residue: E 913 - end of helix Processing helix chain 'E' and resid 923 through 941 Processing helix chain 'E' and resid 942 through 961 removed outlier: 5.365A pdb=" N SER E 950 " --> pdb=" O THR E 946 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR E 951 " --> pdb=" O GLU E 947 " (cutoff:3.500A) Proline residue: E 954 - end of helix removed outlier: 4.011A pdb=" N LEU E 961 " --> pdb=" O LEU E 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 967 through 985 Processing helix chain 'E' and resid 986 through 993 removed outlier: 3.736A pdb=" N SER E 992 " --> pdb=" O ASN E 988 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR E 993 " --> pdb=" O TYR E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1001 Processing helix chain 'E' and resid 1010 through 1029 removed outlier: 3.831A pdb=" N GLN E1028 " --> pdb=" O TYR E1024 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 20 removed outlier: 4.031A pdb=" N ASP F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 39 removed outlier: 3.874A pdb=" N ALA F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR F 30 " --> pdb=" O GLU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 51 removed outlier: 4.211A pdb=" N GLU F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 55 removed outlier: 4.170A pdb=" N SER F 55 " --> pdb=" O TYR F 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 52 through 55' Processing helix chain 'F' and resid 57 through 75 removed outlier: 3.839A pdb=" N ARG F 61 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 98 removed outlier: 4.160A pdb=" N ILE F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE F 89 " --> pdb=" O CYS F 85 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.764A pdb=" N VAL F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 133 removed outlier: 3.908A pdb=" N LEU F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 158 removed outlier: 3.932A pdb=" N TRP F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Proline residue: F 147 - end of helix Processing helix chain 'F' and resid 168 through 182 removed outlier: 4.669A pdb=" N ASP F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL F 182 " --> pdb=" O THR F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 206 removed outlier: 3.603A pdb=" N LEU F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER F 204 " --> pdb=" O LYS F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 213 Processing helix chain 'F' and resid 214 through 224 removed outlier: 4.431A pdb=" N ASP F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 269 removed outlier: 4.817A pdb=" N SER F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP F 267 " --> pdb=" O SER F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 290 Processing helix chain 'F' and resid 293 through 314 removed outlier: 6.034A pdb=" N THR F 301 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU F 302 " --> pdb=" O GLU F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 359 Processing helix chain 'F' and resid 359 through 380 Proline residue: F 376 - end of helix Processing helix chain 'F' and resid 383 through 396 Processing helix chain 'F' and resid 398 through 414 Proline residue: F 411 - end of helix Processing helix chain 'F' and resid 419 through 442 removed outlier: 3.773A pdb=" N PHE F 432 " --> pdb=" O MET F 428 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE F 433 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP F 435 " --> pdb=" O SER F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 474 Processing helix chain 'F' and resid 480 through 497 removed outlier: 3.751A pdb=" N ARG F 484 " --> pdb=" O GLU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 520 Processing helix chain 'F' and resid 522 through 540 Processing helix chain 'F' and resid 540 through 556 removed outlier: 3.549A pdb=" N VAL F 544 " --> pdb=" O TYR F 540 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 549 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS F 551 " --> pdb=" O ILE F 547 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU F 556 " --> pdb=" O LEU F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 584 removed outlier: 4.211A pdb=" N ILE F 577 " --> pdb=" O HIS F 573 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE F 584 " --> pdb=" O ILE F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 610 Processing helix chain 'F' and resid 613 through 632 removed outlier: 3.547A pdb=" N ASN F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F 632 " --> pdb=" O ASN F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 659 Proline residue: F 651 - end of helix removed outlier: 4.159A pdb=" N ILE F 656 " --> pdb=" O LYS F 652 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 659 " --> pdb=" O GLU F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 683 removed outlier: 3.965A pdb=" N LYS F 683 " --> pdb=" O PHE F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 687 No H-bonds generated for 'chain 'F' and resid 685 through 687' Processing helix chain 'F' and resid 688 through 701 Processing helix chain 'F' and resid 714 through 724 removed outlier: 4.348A pdb=" N SER F 718 " --> pdb=" O VAL F 714 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR F 719 " --> pdb=" O LEU F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 749 Processing helix chain 'F' and resid 754 through 772 Processing helix chain 'F' and resid 774 through 781 Processing helix chain 'F' and resid 788 through 805 removed outlier: 3.925A pdb=" N GLY F 801 " --> pdb=" O TRP F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 822 removed outlier: 4.209A pdb=" N LYS F 815 " --> pdb=" O SER F 811 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER F 822 " --> pdb=" O ILE F 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 826 through 834 Processing helix chain 'F' and resid 835 through 838 Processing helix chain 'F' and resid 859 through 877 removed outlier: 4.353A pdb=" N GLN F 870 " --> pdb=" O GLY F 866 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR F 871 " --> pdb=" O ASP F 867 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 897 Processing helix chain 'F' and resid 900 through 904 removed outlier: 3.883A pdb=" N VAL F 904 " --> pdb=" O SER F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 907 through 918 Proline residue: F 913 - end of helix Processing helix chain 'F' and resid 923 through 941 Processing helix chain 'F' and resid 942 through 960 removed outlier: 5.354A pdb=" N SER F 950 " --> pdb=" O THR F 946 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR F 951 " --> pdb=" O GLU F 947 " (cutoff:3.500A) Proline residue: F 954 - end of helix Processing helix chain 'F' and resid 967 through 985 Processing helix chain 'F' and resid 986 through 992 removed outlier: 3.726A pdb=" N SER F 992 " --> pdb=" O ASN F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 994 through 1001 Processing helix chain 'F' and resid 1010 through 1029 2984 hydrogen bonds defined for protein. 8880 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: 15.39 Time building geometry restraints manager: 10.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14816 1.34 - 1.46: 7312 1.46 - 1.58: 25824 1.58 - 1.70: 0 1.70 - 1.82: 282 Bond restraints: 48234 Sorted by residual: bond pdb=" N ASP B 242 " pdb=" CA ASP B 242 " ideal model delta sigma weight residual 1.458 1.347 0.111 1.90e-02 2.77e+03 3.39e+01 bond pdb=" N ASP E 242 " pdb=" CA ASP E 242 " ideal model delta sigma weight residual 1.458 1.349 0.109 1.90e-02 2.77e+03 3.32e+01 bond pdb=" N ASP D 242 " pdb=" CA ASP D 242 " ideal model delta sigma weight residual 1.458 1.369 0.089 1.90e-02 2.77e+03 2.17e+01 bond pdb=" N PRO C 225 " pdb=" CD PRO C 225 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" N PRO F 225 " pdb=" CD PRO F 225 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.05e+01 ... (remaining 48229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 64871 3.24 - 6.47: 360 6.47 - 9.71: 43 9.71 - 12.94: 8 12.94 - 16.18: 10 Bond angle restraints: 65292 Sorted by residual: angle pdb=" N LEU B 243 " pdb=" CA LEU B 243 " pdb=" CB LEU B 243 " ideal model delta sigma weight residual 110.49 125.38 -14.89 1.47e+00 4.63e-01 1.03e+02 angle pdb=" N LEU E 243 " pdb=" CA LEU E 243 " pdb=" CB LEU E 243 " ideal model delta sigma weight residual 110.49 125.07 -14.58 1.47e+00 4.63e-01 9.84e+01 angle pdb=" N LEU D 243 " pdb=" CA LEU D 243 " pdb=" CB LEU D 243 " ideal model delta sigma weight residual 110.49 124.69 -14.20 1.47e+00 4.63e-01 9.33e+01 angle pdb=" N ASP B 242 " pdb=" CA ASP B 242 " pdb=" CB ASP B 242 " ideal model delta sigma weight residual 110.50 122.39 -11.89 1.70e+00 3.46e-01 4.89e+01 angle pdb=" N ASP E 242 " pdb=" CA ASP E 242 " pdb=" CB ASP E 242 " ideal model delta sigma weight residual 110.50 122.15 -11.65 1.70e+00 3.46e-01 4.70e+01 ... (remaining 65287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 26097 17.36 - 34.71: 2788 34.71 - 52.07: 495 52.07 - 69.42: 56 69.42 - 86.78: 48 Dihedral angle restraints: 29484 sinusoidal: 11910 harmonic: 17574 Sorted by residual: dihedral pdb=" N LEU F 243 " pdb=" C LEU F 243 " pdb=" CA LEU F 243 " pdb=" CB LEU F 243 " ideal model delta harmonic sigma weight residual 122.80 138.15 -15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" N LEU A 243 " pdb=" C LEU A 243 " pdb=" CA LEU A 243 " pdb=" CB LEU A 243 " ideal model delta harmonic sigma weight residual 122.80 138.13 -15.33 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" N LEU C 243 " pdb=" C LEU C 243 " pdb=" CA LEU C 243 " pdb=" CB LEU C 243 " ideal model delta harmonic sigma weight residual 122.80 137.97 -15.17 0 2.50e+00 1.60e-01 3.68e+01 ... (remaining 29481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 7701 0.097 - 0.193: 157 0.193 - 0.290: 1 0.290 - 0.387: 1 0.387 - 0.484: 6 Chirality restraints: 7866 Sorted by residual: chirality pdb=" CA LEU A 243 " pdb=" N LEU A 243 " pdb=" C LEU A 243 " pdb=" CB LEU A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA LEU F 243 " pdb=" N LEU F 243 " pdb=" C LEU F 243 " pdb=" CB LEU F 243 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA LEU C 243 " pdb=" N LEU C 243 " pdb=" C LEU C 243 " pdb=" CB LEU C 243 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 7863 not shown) Planarity restraints: 8112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 146 " 0.024 2.00e-02 2.50e+03 2.61e-02 1.70e+01 pdb=" CG TRP E 146 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP E 146 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP E 146 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 146 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 146 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 146 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 146 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 146 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 146 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 214 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C GLU D 214 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU D 214 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP D 215 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 905 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO E 906 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 906 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 906 " 0.028 5.00e-02 4.00e+02 ... (remaining 8109 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 179 2.48 - 3.09: 34870 3.09 - 3.69: 73809 3.69 - 4.30: 102970 4.30 - 4.90: 168078 Nonbonded interactions: 379906 Sorted by model distance: nonbonded pdb=" OD1 ASP D 242 " pdb=" N LEU D 243 " model vdw 1.875 3.120 nonbonded pdb=" OD1 ASP E 242 " pdb=" N LEU E 243 " model vdw 1.911 3.120 nonbonded pdb=" OD1 ASP C 242 " pdb=" N LEU C 243 " model vdw 1.914 3.120 nonbonded pdb=" OD1 ASP B 242 " pdb=" N LEU B 243 " model vdw 1.941 3.120 nonbonded pdb=" OD1 ASP A 242 " pdb=" N LEU A 243 " model vdw 1.950 3.120 ... (remaining 379901 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.030 Extract box with map and model: 1.440 Check model and map are aligned: 0.300 Set scattering table: 0.320 Process input model: 78.200 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.003 0.111 48234 Z= 0.175 Angle : 0.657 16.177 65292 Z= 0.352 Chirality : 0.040 0.484 7866 Planarity : 0.004 0.050 8112 Dihedral : 14.457 86.779 17964 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 0.15 % Allowed : 0.48 % Favored : 99.38 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 5856 helix: 1.44 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -1.07 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP E 146 HIS 0.005 0.000 HIS F 941 PHE 0.028 0.001 PHE F 837 TYR 0.022 0.001 TYR F 512 ARG 0.008 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 676 time to evaluate : 4.635 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 158 PHE cc_start: 0.8563 (t80) cc_final: 0.8043 (t80) REVERT: A 279 ASP cc_start: 0.9460 (m-30) cc_final: 0.9253 (m-30) REVERT: A 299 ASN cc_start: 0.9335 (m-40) cc_final: 0.9106 (m110) REVERT: A 372 ASP cc_start: 0.9127 (m-30) cc_final: 0.8853 (m-30) REVERT: A 467 MET cc_start: 0.8295 (tmm) cc_final: 0.7948 (tmm) REVERT: A 804 MET cc_start: 0.7580 (mmt) cc_final: 0.7311 (mmt) REVERT: A 819 ASP cc_start: 0.9329 (m-30) cc_final: 0.9125 (m-30) REVERT: B 91 PHE cc_start: 0.9516 (m-80) cc_final: 0.9225 (m-80) REVERT: B 158 PHE cc_start: 0.8693 (t80) cc_final: 0.8189 (t80) REVERT: B 193 LEU cc_start: 0.8986 (tt) cc_final: 0.8657 (mm) REVERT: B 243 LEU cc_start: 0.6138 (tp) cc_final: 0.5742 (tp) REVERT: B 260 ASP cc_start: 0.9315 (m-30) cc_final: 0.9072 (t0) REVERT: B 279 ASP cc_start: 0.9353 (m-30) cc_final: 0.9108 (m-30) REVERT: B 310 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8315 (tm-30) REVERT: B 632 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: B 804 MET cc_start: 0.7065 (mmt) cc_final: 0.6834 (mmt) REVERT: B 848 LYS cc_start: 0.8904 (pttp) cc_final: 0.7938 (pttp) REVERT: B 1021 GLN cc_start: 0.8721 (tp40) cc_final: 0.8478 (pp30) REVERT: C 109 PHE cc_start: 0.9093 (m-10) cc_final: 0.8738 (m-80) REVERT: C 158 PHE cc_start: 0.8679 (t80) cc_final: 0.8219 (t80) REVERT: C 198 LEU cc_start: 0.9190 (mm) cc_final: 0.8901 (mm) REVERT: C 279 ASP cc_start: 0.9351 (m-30) cc_final: 0.9136 (m-30) REVERT: C 299 ASN cc_start: 0.9286 (m-40) cc_final: 0.8973 (m110) REVERT: C 310 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8433 (tm-30) REVERT: C 471 MET cc_start: 0.8599 (mmm) cc_final: 0.8347 (mmm) REVERT: C 475 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8420 (ttm110) REVERT: C 531 GLU cc_start: 0.9359 (tp30) cc_final: 0.9082 (tp30) REVERT: C 799 THR cc_start: 0.9319 (p) cc_final: 0.9105 (p) REVERT: C 804 MET cc_start: 0.7207 (mmt) cc_final: 0.7002 (mmt) REVERT: C 867 ASP cc_start: 0.8500 (t70) cc_final: 0.8278 (t0) REVERT: D 92 TYR cc_start: 0.9363 (p90) cc_final: 0.9092 (p90) REVERT: D 193 LEU cc_start: 0.8747 (tt) cc_final: 0.8414 (mm) REVERT: D 257 PHE cc_start: 0.9258 (m-80) cc_final: 0.8866 (m-80) REVERT: D 259 GLU cc_start: 0.8188 (pm20) cc_final: 0.7861 (pm20) REVERT: D 260 ASP cc_start: 0.9408 (m-30) cc_final: 0.9007 (m-30) REVERT: D 456 ASN cc_start: 0.8241 (p0) cc_final: 0.7995 (p0) REVERT: D 467 MET cc_start: 0.8306 (tmm) cc_final: 0.7932 (tmm) REVERT: D 804 MET cc_start: 0.7593 (mmt) cc_final: 0.7314 (mmt) REVERT: D 921 MET cc_start: 0.7571 (mmm) cc_final: 0.7035 (mmm) REVERT: D 980 MET cc_start: 0.8100 (mmm) cc_final: 0.7896 (mmp) REVERT: E 91 PHE cc_start: 0.9727 (m-80) cc_final: 0.9394 (m-80) REVERT: E 158 PHE cc_start: 0.8821 (t80) cc_final: 0.8609 (t80) REVERT: E 198 LEU cc_start: 0.9202 (mm) cc_final: 0.8988 (mm) REVERT: E 279 ASP cc_start: 0.9343 (m-30) cc_final: 0.9100 (m-30) REVERT: E 310 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8329 (tm-30) REVERT: E 520 ASP cc_start: 0.8452 (t0) cc_final: 0.8007 (p0) REVERT: E 921 MET cc_start: 0.7389 (mmt) cc_final: 0.7119 (mmt) REVERT: F 109 PHE cc_start: 0.8933 (m-10) cc_final: 0.8510 (m-80) REVERT: F 158 PHE cc_start: 0.8696 (t80) cc_final: 0.8276 (t80) REVERT: F 198 LEU cc_start: 0.9171 (mm) cc_final: 0.8876 (mm) REVERT: F 214 GLU cc_start: 0.8451 (tp30) cc_final: 0.8177 (tp30) REVERT: F 279 ASP cc_start: 0.9364 (m-30) cc_final: 0.9154 (m-30) REVERT: F 299 ASN cc_start: 0.9291 (m-40) cc_final: 0.9058 (m110) REVERT: F 531 GLU cc_start: 0.9329 (tp30) cc_final: 0.9049 (tp30) REVERT: F 867 ASP cc_start: 0.8939 (m-30) cc_final: 0.8712 (t0) outliers start: 8 outliers final: 0 residues processed: 682 average time/residue: 0.4375 time to fit residues: 518.3967 Evaluate side-chains 488 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 487 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 632 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 0.9990 chunk 445 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 300 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 460 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 343 optimal weight: 0.9990 chunk 533 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN B 16 ASN B 264 ASN B 994 GLN C 211 ASN C 994 GLN D 264 ASN D 994 GLN E 93 GLN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 48234 Z= 0.243 Angle : 0.605 8.207 65292 Z= 0.315 Chirality : 0.040 0.181 7866 Planarity : 0.004 0.049 8112 Dihedral : 4.100 71.270 6207 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.97 % Allowed : 9.62 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.11), residues: 5856 helix: 1.51 (0.08), residues: 4248 sheet: None (None), residues: 0 loop : -1.16 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 146 HIS 0.003 0.001 HIS E 942 PHE 0.036 0.002 PHE A 89 TYR 0.036 0.001 TYR A 92 ARG 0.011 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 521 time to evaluate : 4.266 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 158 PHE cc_start: 0.8584 (t80) cc_final: 0.8105 (t80) REVERT: A 279 ASP cc_start: 0.9485 (m-30) cc_final: 0.9261 (m-30) REVERT: A 299 ASN cc_start: 0.9442 (m-40) cc_final: 0.9198 (m110) REVERT: A 467 MET cc_start: 0.8364 (tmm) cc_final: 0.7948 (tmm) REVERT: A 520 ASP cc_start: 0.8656 (t0) cc_final: 0.8308 (p0) REVERT: A 804 MET cc_start: 0.7848 (mmt) cc_final: 0.7547 (mmt) REVERT: B 91 PHE cc_start: 0.9544 (m-80) cc_final: 0.9326 (m-80) REVERT: B 158 PHE cc_start: 0.8767 (t80) cc_final: 0.8207 (t80) REVERT: B 193 LEU cc_start: 0.9012 (tt) cc_final: 0.8739 (mm) REVERT: B 279 ASP cc_start: 0.9376 (m-30) cc_final: 0.9123 (m-30) REVERT: B 520 ASP cc_start: 0.8366 (t0) cc_final: 0.7962 (p0) REVERT: B 804 MET cc_start: 0.7080 (mmt) cc_final: 0.6756 (mmt) REVERT: B 819 ASP cc_start: 0.9111 (m-30) cc_final: 0.8820 (m-30) REVERT: C 109 PHE cc_start: 0.9203 (m-10) cc_final: 0.8826 (m-80) REVERT: C 158 PHE cc_start: 0.8747 (t80) cc_final: 0.8308 (t80) REVERT: C 276 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9256 (m) REVERT: C 279 ASP cc_start: 0.9387 (m-30) cc_final: 0.9150 (m-30) REVERT: C 299 ASN cc_start: 0.9318 (m-40) cc_final: 0.9032 (m110) REVERT: C 310 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8416 (tm-30) REVERT: C 475 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8514 (ttm110) REVERT: C 531 GLU cc_start: 0.9365 (tp30) cc_final: 0.9114 (tp30) REVERT: C 804 MET cc_start: 0.7468 (mmt) cc_final: 0.7258 (mmt) REVERT: C 867 ASP cc_start: 0.8568 (t70) cc_final: 0.8350 (t0) REVERT: D 92 TYR cc_start: 0.9302 (p90) cc_final: 0.9018 (p90) REVERT: D 158 PHE cc_start: 0.8929 (t80) cc_final: 0.8722 (t80) REVERT: D 177 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8934 (pm20) REVERT: D 193 LEU cc_start: 0.8759 (tt) cc_final: 0.8439 (mm) REVERT: D 456 ASN cc_start: 0.8325 (p0) cc_final: 0.8104 (p0) REVERT: D 467 MET cc_start: 0.8349 (tmm) cc_final: 0.7940 (tmm) REVERT: D 520 ASP cc_start: 0.8651 (t0) cc_final: 0.8315 (p0) REVERT: D 804 MET cc_start: 0.7777 (mmt) cc_final: 0.7517 (mmt) REVERT: D 921 MET cc_start: 0.8092 (mmm) cc_final: 0.7654 (mmm) REVERT: D 980 MET cc_start: 0.8142 (mmm) cc_final: 0.7905 (mmp) REVERT: E 158 PHE cc_start: 0.8862 (t80) cc_final: 0.8594 (t80) REVERT: E 180 LEU cc_start: 0.9348 (mm) cc_final: 0.9106 (mm) REVERT: E 215 ASP cc_start: 0.8987 (m-30) cc_final: 0.8744 (p0) REVERT: E 279 ASP cc_start: 0.9366 (m-30) cc_final: 0.9112 (m-30) REVERT: E 520 ASP cc_start: 0.8399 (t0) cc_final: 0.8006 (p0) REVERT: E 632 GLN cc_start: 0.8480 (mt0) cc_final: 0.8093 (tm-30) REVERT: E 795 MET cc_start: 0.8802 (mmt) cc_final: 0.8540 (mmt) REVERT: E 819 ASP cc_start: 0.9053 (m-30) cc_final: 0.8798 (m-30) REVERT: E 921 MET cc_start: 0.7861 (mmt) cc_final: 0.7601 (mmt) REVERT: F 109 PHE cc_start: 0.9001 (m-10) cc_final: 0.8618 (m-80) REVERT: F 158 PHE cc_start: 0.8773 (t80) cc_final: 0.8337 (t80) REVERT: F 276 VAL cc_start: 0.9474 (OUTLIER) cc_final: 0.9208 (m) REVERT: F 279 ASP cc_start: 0.9358 (m-30) cc_final: 0.9078 (m-30) REVERT: F 299 ASN cc_start: 0.9314 (m-40) cc_final: 0.9017 (m110) REVERT: F 475 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8521 (ttm110) REVERT: F 531 GLU cc_start: 0.9345 (tp30) cc_final: 0.9097 (tp30) outliers start: 53 outliers final: 37 residues processed: 550 average time/residue: 0.4225 time to fit residues: 405.0997 Evaluate side-chains 502 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 462 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 983 THR Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 983 THR Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 723 LEU Chi-restraints excluded: chain F residue 753 MET Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 444 optimal weight: 7.9990 chunk 363 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 534 optimal weight: 0.7980 chunk 577 optimal weight: 0.8980 chunk 476 optimal weight: 1.9990 chunk 530 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 429 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN F 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48234 Z= 0.173 Angle : 0.541 7.675 65292 Z= 0.281 Chirality : 0.038 0.215 7866 Planarity : 0.003 0.051 8112 Dihedral : 3.945 22.333 6204 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.41 % Allowed : 13.12 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 5856 helix: 1.56 (0.08), residues: 4248 sheet: None (None), residues: 0 loop : -1.15 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 146 HIS 0.003 0.000 HIS B 749 PHE 0.017 0.001 PHE D 584 TYR 0.048 0.001 TYR E 92 ARG 0.008 0.000 ARG D 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 537 time to evaluate : 4.272 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 146 TRP cc_start: 0.9191 (m100) cc_final: 0.8780 (m100) REVERT: A 158 PHE cc_start: 0.8585 (t80) cc_final: 0.8089 (t80) REVERT: A 170 ARG cc_start: 0.9437 (mpp-170) cc_final: 0.9220 (mpp-170) REVERT: A 260 ASP cc_start: 0.9143 (t0) cc_final: 0.8850 (p0) REVERT: A 276 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9177 (m) REVERT: A 279 ASP cc_start: 0.9479 (m-30) cc_final: 0.9237 (m-30) REVERT: A 299 ASN cc_start: 0.9433 (m-40) cc_final: 0.9188 (m110) REVERT: A 467 MET cc_start: 0.8372 (tmm) cc_final: 0.7982 (tmm) REVERT: A 520 ASP cc_start: 0.8681 (t0) cc_final: 0.8306 (p0) REVERT: A 541 GLU cc_start: 0.7573 (pm20) cc_final: 0.7184 (pm20) REVERT: A 804 MET cc_start: 0.7858 (mmt) cc_final: 0.7560 (mmt) REVERT: A 921 MET cc_start: 0.7567 (mmt) cc_final: 0.7198 (mmm) REVERT: B 91 PHE cc_start: 0.9563 (m-80) cc_final: 0.9313 (m-80) REVERT: B 146 TRP cc_start: 0.9496 (m-90) cc_final: 0.9214 (m-90) REVERT: B 158 PHE cc_start: 0.8758 (t80) cc_final: 0.8215 (t80) REVERT: B 193 LEU cc_start: 0.9006 (tt) cc_final: 0.8756 (mm) REVERT: B 279 ASP cc_start: 0.9367 (m-30) cc_final: 0.9104 (m-30) REVERT: B 310 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 520 ASP cc_start: 0.8381 (t0) cc_final: 0.7956 (p0) REVERT: B 804 MET cc_start: 0.7177 (mmt) cc_final: 0.6925 (mmt) REVERT: B 819 ASP cc_start: 0.9030 (m-30) cc_final: 0.8767 (m-30) REVERT: C 158 PHE cc_start: 0.8688 (t80) cc_final: 0.8265 (t80) REVERT: C 214 GLU cc_start: 0.8447 (tp30) cc_final: 0.8206 (tp30) REVERT: C 217 PHE cc_start: 0.7019 (m-80) cc_final: 0.5476 (t80) REVERT: C 260 ASP cc_start: 0.9424 (t0) cc_final: 0.8998 (t0) REVERT: C 279 ASP cc_start: 0.9380 (m-30) cc_final: 0.9147 (m-30) REVERT: C 299 ASN cc_start: 0.9339 (m-40) cc_final: 0.9082 (m110) REVERT: C 310 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8473 (tm-30) REVERT: C 531 GLU cc_start: 0.9336 (tp30) cc_final: 0.9078 (tp30) REVERT: C 573 HIS cc_start: 0.7471 (t-90) cc_final: 0.6997 (t-90) REVERT: C 804 MET cc_start: 0.7471 (mmt) cc_final: 0.7249 (mmt) REVERT: C 867 ASP cc_start: 0.8551 (t70) cc_final: 0.8319 (t0) REVERT: D 92 TYR cc_start: 0.9291 (p90) cc_final: 0.8972 (p90) REVERT: D 158 PHE cc_start: 0.8943 (t80) cc_final: 0.8653 (t80) REVERT: D 177 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8903 (mp0) REVERT: D 193 LEU cc_start: 0.8770 (tt) cc_final: 0.8443 (mm) REVERT: D 215 ASP cc_start: 0.9146 (m-30) cc_final: 0.8484 (p0) REVERT: D 276 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8735 (p) REVERT: D 279 ASP cc_start: 0.9354 (m-30) cc_final: 0.8895 (p0) REVERT: D 456 ASN cc_start: 0.8317 (p0) cc_final: 0.8085 (p0) REVERT: D 467 MET cc_start: 0.8373 (tmm) cc_final: 0.7981 (tmm) REVERT: D 804 MET cc_start: 0.7807 (mmt) cc_final: 0.7537 (mmt) REVERT: D 921 MET cc_start: 0.8110 (mmm) cc_final: 0.7686 (mmm) REVERT: D 980 MET cc_start: 0.8143 (mmm) cc_final: 0.7901 (mmp) REVERT: E 146 TRP cc_start: 0.8989 (m-90) cc_final: 0.8783 (m100) REVERT: E 180 LEU cc_start: 0.9329 (mm) cc_final: 0.9064 (mm) REVERT: E 215 ASP cc_start: 0.9064 (m-30) cc_final: 0.8697 (p0) REVERT: E 276 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8966 (p) REVERT: E 279 ASP cc_start: 0.9359 (m-30) cc_final: 0.9108 (m-30) REVERT: E 310 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8404 (tm-30) REVERT: E 632 GLN cc_start: 0.8442 (mt0) cc_final: 0.8116 (tm-30) REVERT: E 795 MET cc_start: 0.8944 (mmt) cc_final: 0.8658 (mmt) REVERT: E 819 ASP cc_start: 0.8994 (m-30) cc_final: 0.8728 (m-30) REVERT: E 848 LYS cc_start: 0.9062 (pttp) cc_final: 0.8355 (pttp) REVERT: E 921 MET cc_start: 0.7913 (mmt) cc_final: 0.7710 (mmt) REVERT: F 109 PHE cc_start: 0.8929 (m-10) cc_final: 0.8543 (m-80) REVERT: F 158 PHE cc_start: 0.8704 (t80) cc_final: 0.8282 (t80) REVERT: F 214 GLU cc_start: 0.8535 (tp30) cc_final: 0.8280 (tp30) REVERT: F 217 PHE cc_start: 0.7140 (m-80) cc_final: 0.5781 (t80) REVERT: F 260 ASP cc_start: 0.9418 (t0) cc_final: 0.9062 (t0) REVERT: F 279 ASP cc_start: 0.9358 (m-30) cc_final: 0.9084 (m-30) REVERT: F 299 ASN cc_start: 0.9387 (m-40) cc_final: 0.9138 (m110) REVERT: F 372 ASP cc_start: 0.9193 (m-30) cc_final: 0.8977 (m-30) REVERT: F 458 MET cc_start: 0.8801 (tpp) cc_final: 0.8566 (tpp) REVERT: F 471 MET cc_start: 0.8775 (mmp) cc_final: 0.7928 (mmp) REVERT: F 475 ARG cc_start: 0.8687 (ttp80) cc_final: 0.7671 (tmt170) REVERT: F 520 ASP cc_start: 0.8196 (t0) cc_final: 0.7928 (p0) REVERT: F 531 GLU cc_start: 0.9327 (tp30) cc_final: 0.9062 (tp30) REVERT: F 980 MET cc_start: 0.8137 (mmp) cc_final: 0.7842 (mmm) outliers start: 77 outliers final: 47 residues processed: 588 average time/residue: 0.4624 time to fit residues: 473.0694 Evaluate side-chains 532 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 481 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 359 optimal weight: 0.9980 chunk 536 optimal weight: 5.9990 chunk 568 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 508 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 ASN C 632 GLN D 264 ASN E 138 GLN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 48234 Z= 0.335 Angle : 0.625 10.530 65292 Z= 0.325 Chirality : 0.040 0.224 7866 Planarity : 0.004 0.052 8112 Dihedral : 4.226 24.860 6204 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.73 % Allowed : 14.34 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 5856 helix: 1.48 (0.08), residues: 4248 sheet: None (None), residues: 0 loop : -1.10 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 146 HIS 0.007 0.001 HIS B 942 PHE 0.047 0.002 PHE B 89 TYR 0.034 0.002 TYR E 92 ARG 0.011 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 468 time to evaluate : 4.224 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 148 PHE cc_start: 0.9073 (m-10) cc_final: 0.8810 (m-10) REVERT: A 158 PHE cc_start: 0.8616 (t80) cc_final: 0.8015 (t80) REVERT: A 194 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8427 (mt) REVERT: A 260 ASP cc_start: 0.9302 (t0) cc_final: 0.8988 (p0) REVERT: A 276 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9189 (m) REVERT: A 279 ASP cc_start: 0.9442 (m-30) cc_final: 0.9209 (m-30) REVERT: A 286 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8818 (mp0) REVERT: A 299 ASN cc_start: 0.9461 (m-40) cc_final: 0.9193 (m110) REVERT: A 310 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 467 MET cc_start: 0.8373 (tmm) cc_final: 0.7911 (tmm) REVERT: A 520 ASP cc_start: 0.8724 (t0) cc_final: 0.8484 (t0) REVERT: A 804 MET cc_start: 0.8084 (mmt) cc_final: 0.7808 (mmt) REVERT: B 146 TRP cc_start: 0.9508 (m-90) cc_final: 0.9281 (m-90) REVERT: B 158 PHE cc_start: 0.8803 (t80) cc_final: 0.8242 (t80) REVERT: B 193 LEU cc_start: 0.8998 (tt) cc_final: 0.8765 (mm) REVERT: B 279 ASP cc_start: 0.9369 (m-30) cc_final: 0.9091 (m-30) REVERT: B 471 MET cc_start: 0.8537 (mmm) cc_final: 0.7700 (mmm) REVERT: B 475 ARG cc_start: 0.8909 (ttm110) cc_final: 0.8416 (ttp-110) REVERT: B 520 ASP cc_start: 0.8389 (t0) cc_final: 0.7981 (p0) REVERT: B 652 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8967 (mtpp) REVERT: B 804 MET cc_start: 0.7427 (mmt) cc_final: 0.7145 (mmt) REVERT: B 819 ASP cc_start: 0.9075 (m-30) cc_final: 0.8829 (m-30) REVERT: B 921 MET cc_start: 0.8139 (mmt) cc_final: 0.7930 (mmt) REVERT: C 158 PHE cc_start: 0.8689 (t80) cc_final: 0.8125 (t80) REVERT: C 279 ASP cc_start: 0.9372 (m-30) cc_final: 0.9143 (m-30) REVERT: C 286 GLU cc_start: 0.9417 (mp0) cc_final: 0.8852 (mp0) REVERT: C 299 ASN cc_start: 0.9391 (m-40) cc_final: 0.9144 (m110) REVERT: C 531 GLU cc_start: 0.9330 (tp30) cc_final: 0.9109 (tp30) REVERT: C 632 GLN cc_start: 0.8470 (tm130) cc_final: 0.8185 (tm-30) REVERT: C 804 MET cc_start: 0.7847 (mmt) cc_final: 0.7580 (mmt) REVERT: C 867 ASP cc_start: 0.8717 (t70) cc_final: 0.8410 (t0) REVERT: D 158 PHE cc_start: 0.8949 (t80) cc_final: 0.8654 (t80) REVERT: D 177 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8938 (mp0) REVERT: D 193 LEU cc_start: 0.8794 (tt) cc_final: 0.8503 (mm) REVERT: D 275 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8574 (p) REVERT: D 467 MET cc_start: 0.8392 (tmm) cc_final: 0.7942 (tmm) REVERT: D 804 MET cc_start: 0.8029 (mmt) cc_final: 0.7760 (mmt) REVERT: D 921 MET cc_start: 0.8499 (mmm) cc_final: 0.8276 (tpt) REVERT: D 980 MET cc_start: 0.8212 (mmm) cc_final: 0.7970 (mmp) REVERT: E 92 TYR cc_start: 0.9359 (p90) cc_final: 0.9126 (p90) REVERT: E 146 TRP cc_start: 0.9085 (m-90) cc_final: 0.8771 (m100) REVERT: E 158 PHE cc_start: 0.8846 (t80) cc_final: 0.8589 (t80) REVERT: E 276 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8986 (p) REVERT: E 279 ASP cc_start: 0.9367 (m-30) cc_final: 0.9120 (m-30) REVERT: E 520 ASP cc_start: 0.8394 (t0) cc_final: 0.7947 (p0) REVERT: E 819 ASP cc_start: 0.9071 (m-30) cc_final: 0.8817 (m-30) REVERT: E 848 LYS cc_start: 0.9129 (pttp) cc_final: 0.8868 (pttp) REVERT: F 109 PHE cc_start: 0.9028 (m-10) cc_final: 0.8817 (m-80) REVERT: F 158 PHE cc_start: 0.8726 (t80) cc_final: 0.8296 (t80) REVERT: F 214 GLU cc_start: 0.8693 (tp30) cc_final: 0.8452 (tp30) REVERT: F 217 PHE cc_start: 0.6876 (m-80) cc_final: 0.6219 (t80) REVERT: F 260 ASP cc_start: 0.9481 (t0) cc_final: 0.9049 (t0) REVERT: F 279 ASP cc_start: 0.9347 (m-30) cc_final: 0.9074 (m-30) REVERT: F 299 ASN cc_start: 0.9395 (m-40) cc_final: 0.9153 (m110) REVERT: F 458 MET cc_start: 0.8916 (tpp) cc_final: 0.8532 (tpp) REVERT: F 520 ASP cc_start: 0.8238 (t0) cc_final: 0.7943 (p0) REVERT: F 531 GLU cc_start: 0.9300 (tp30) cc_final: 0.9076 (tp30) REVERT: F 980 MET cc_start: 0.8181 (mmp) cc_final: 0.7892 (mmm) outliers start: 149 outliers final: 97 residues processed: 581 average time/residue: 0.4195 time to fit residues: 423.0708 Evaluate side-chains 516 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 413 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 657 ILE Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 839 MET Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 840 ASP Chi-restraints excluded: chain D residue 937 THR Chi-restraints excluded: chain D residue 983 THR Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 657 ILE Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 840 ASP Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 910 ASP Chi-restraints excluded: chain E residue 937 THR Chi-restraints excluded: chain E residue 983 THR Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain E residue 987 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 834 PHE Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 919 LEU Chi-restraints excluded: chain F residue 937 THR Chi-restraints excluded: chain F residue 985 VAL Chi-restraints excluded: chain F residue 987 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 423 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 485 optimal weight: 0.8980 chunk 392 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 290 optimal weight: 2.9990 chunk 510 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** E 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 994 GLN ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 48234 Z= 0.183 Angle : 0.566 10.204 65292 Z= 0.291 Chirality : 0.038 0.289 7866 Planarity : 0.003 0.053 8112 Dihedral : 4.107 23.017 6204 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 2.62 % Allowed : 15.57 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 5856 helix: 1.55 (0.08), residues: 4266 sheet: None (None), residues: 0 loop : -1.15 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 146 HIS 0.003 0.000 HIS B 749 PHE 0.025 0.001 PHE E 89 TYR 0.036 0.001 TYR B 92 ARG 0.007 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 488 time to evaluate : 4.255 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 146 TRP cc_start: 0.9068 (m100) cc_final: 0.8562 (m100) REVERT: A 158 PHE cc_start: 0.8596 (t80) cc_final: 0.8092 (t80) REVERT: A 190 ARG cc_start: 0.9123 (tpm170) cc_final: 0.8846 (tpm170) REVERT: A 260 ASP cc_start: 0.9192 (t0) cc_final: 0.8988 (p0) REVERT: A 276 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9156 (m) REVERT: A 279 ASP cc_start: 0.9425 (m-30) cc_final: 0.9182 (m-30) REVERT: A 286 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8812 (mt-10) REVERT: A 299 ASN cc_start: 0.9451 (m-40) cc_final: 0.9189 (m110) REVERT: A 310 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 467 MET cc_start: 0.8374 (tmm) cc_final: 0.7966 (tmm) REVERT: A 520 ASP cc_start: 0.8723 (t0) cc_final: 0.8488 (t0) REVERT: A 804 MET cc_start: 0.7921 (mmt) cc_final: 0.7682 (mmt) REVERT: A 837 PHE cc_start: 0.8216 (m-80) cc_final: 0.7899 (m-80) REVERT: B 146 TRP cc_start: 0.9508 (m-90) cc_final: 0.9255 (m-90) REVERT: B 158 PHE cc_start: 0.8769 (t80) cc_final: 0.8217 (t80) REVERT: B 193 LEU cc_start: 0.9005 (tt) cc_final: 0.8770 (mm) REVERT: B 279 ASP cc_start: 0.9354 (m-30) cc_final: 0.9080 (m-30) REVERT: B 471 MET cc_start: 0.8510 (mmm) cc_final: 0.8103 (mmp) REVERT: B 520 ASP cc_start: 0.8358 (t0) cc_final: 0.7988 (p0) REVERT: B 652 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8871 (mtpp) REVERT: B 819 ASP cc_start: 0.9025 (m-30) cc_final: 0.8772 (m-30) REVERT: C 158 PHE cc_start: 0.8646 (t80) cc_final: 0.8096 (t80) REVERT: C 276 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9089 (p) REVERT: C 279 ASP cc_start: 0.9364 (m-30) cc_final: 0.9106 (m-30) REVERT: C 299 ASN cc_start: 0.9385 (m-40) cc_final: 0.9135 (m110) REVERT: C 531 GLU cc_start: 0.9325 (tp30) cc_final: 0.9100 (tp30) REVERT: C 632 GLN cc_start: 0.8451 (tm130) cc_final: 0.8243 (tm-30) REVERT: C 804 MET cc_start: 0.7597 (mmt) cc_final: 0.7333 (mmt) REVERT: C 867 ASP cc_start: 0.8675 (t70) cc_final: 0.8384 (t0) REVERT: D 92 TYR cc_start: 0.9249 (p90) cc_final: 0.9026 (p90) REVERT: D 158 PHE cc_start: 0.8941 (t80) cc_final: 0.8627 (t80) REVERT: D 177 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8876 (mp0) REVERT: D 193 LEU cc_start: 0.8773 (tt) cc_final: 0.8477 (mm) REVERT: D 215 ASP cc_start: 0.9174 (m-30) cc_final: 0.8570 (p0) REVERT: D 279 ASP cc_start: 0.9363 (m-30) cc_final: 0.8764 (p0) REVERT: D 467 MET cc_start: 0.8387 (tmm) cc_final: 0.8004 (tmm) REVERT: D 520 ASP cc_start: 0.8338 (t0) cc_final: 0.8083 (t0) REVERT: D 804 MET cc_start: 0.7928 (mmt) cc_final: 0.7700 (mmt) REVERT: D 837 PHE cc_start: 0.8289 (m-80) cc_final: 0.8041 (m-80) REVERT: D 921 MET cc_start: 0.8440 (mmm) cc_final: 0.8200 (tpt) REVERT: D 980 MET cc_start: 0.8120 (mmm) cc_final: 0.7868 (mmp) REVERT: E 107 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8568 (mm-30) REVERT: E 146 TRP cc_start: 0.9017 (m-90) cc_final: 0.8706 (m100) REVERT: E 158 PHE cc_start: 0.8853 (t80) cc_final: 0.8574 (t80) REVERT: E 260 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8586 (p0) REVERT: E 276 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8917 (p) REVERT: E 279 ASP cc_start: 0.9346 (m-30) cc_final: 0.9093 (m-30) REVERT: E 355 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8421 (tt) REVERT: E 520 ASP cc_start: 0.8394 (t0) cc_final: 0.7987 (p0) REVERT: E 819 ASP cc_start: 0.8982 (m-30) cc_final: 0.8732 (m-30) REVERT: F 109 PHE cc_start: 0.8986 (m-10) cc_final: 0.8513 (m-80) REVERT: F 158 PHE cc_start: 0.8671 (t80) cc_final: 0.8247 (t80) REVERT: F 214 GLU cc_start: 0.8680 (tp30) cc_final: 0.8432 (tp30) REVERT: F 217 PHE cc_start: 0.6713 (m-80) cc_final: 0.5991 (t80) REVERT: F 260 ASP cc_start: 0.9453 (t0) cc_final: 0.8993 (t0) REVERT: F 276 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9037 (p) REVERT: F 279 ASP cc_start: 0.9342 (m-30) cc_final: 0.9052 (m-30) REVERT: F 299 ASN cc_start: 0.9420 (m-40) cc_final: 0.9176 (m110) REVERT: F 458 MET cc_start: 0.8896 (tpp) cc_final: 0.8534 (tpp) REVERT: F 471 MET cc_start: 0.8731 (mmp) cc_final: 0.8430 (mmp) REVERT: F 531 GLU cc_start: 0.9303 (tp30) cc_final: 0.9087 (tp30) outliers start: 143 outliers final: 88 residues processed: 597 average time/residue: 0.4217 time to fit residues: 437.6020 Evaluate side-chains 542 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 445 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 983 THR Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 983 THR Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 834 PHE Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 919 LEU Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 0.8980 chunk 511 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 333 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 568 optimal weight: 0.9990 chunk 472 optimal weight: 10.0000 chunk 263 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48234 Z= 0.167 Angle : 0.573 12.973 65292 Z= 0.289 Chirality : 0.038 0.268 7866 Planarity : 0.003 0.054 8112 Dihedral : 4.046 23.890 6204 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 2.65 % Allowed : 16.37 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.11), residues: 5856 helix: 1.57 (0.08), residues: 4266 sheet: None (None), residues: 0 loop : -1.15 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 146 HIS 0.003 0.000 HIS F 941 PHE 0.044 0.001 PHE A 89 TYR 0.027 0.001 TYR E 92 ARG 0.011 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 498 time to evaluate : 4.287 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: symmetry clash revert: symmetry clash REVERT: A 146 TRP cc_start: 0.9083 (m100) cc_final: 0.8650 (m100) REVERT: A 158 PHE cc_start: 0.8591 (t80) cc_final: 0.8082 (t80) REVERT: A 190 ARG cc_start: 0.9114 (tpm170) cc_final: 0.8860 (tpm170) REVERT: A 260 ASP cc_start: 0.9206 (t0) cc_final: 0.8947 (p0) REVERT: A 276 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9169 (m) REVERT: A 279 ASP cc_start: 0.9419 (m-30) cc_final: 0.9170 (m-30) REVERT: A 299 ASN cc_start: 0.9448 (m-40) cc_final: 0.9188 (m110) REVERT: A 310 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 467 MET cc_start: 0.8377 (tmm) cc_final: 0.7983 (tmm) REVERT: A 520 ASP cc_start: 0.8724 (t0) cc_final: 0.8483 (t0) REVERT: A 541 GLU cc_start: 0.7549 (pm20) cc_final: 0.7146 (mm-30) REVERT: A 804 MET cc_start: 0.7910 (mmt) cc_final: 0.7662 (mmt) REVERT: A 837 PHE cc_start: 0.8190 (m-80) cc_final: 0.7831 (m-80) REVERT: B 146 TRP cc_start: 0.9507 (m-90) cc_final: 0.9262 (m-90) REVERT: B 158 PHE cc_start: 0.8751 (t80) cc_final: 0.8209 (t80) REVERT: B 193 LEU cc_start: 0.8974 (tt) cc_final: 0.8706 (mm) REVERT: B 279 ASP cc_start: 0.9366 (m-30) cc_final: 0.9080 (m-30) REVERT: B 471 MET cc_start: 0.8391 (mmm) cc_final: 0.8168 (mmm) REVERT: B 520 ASP cc_start: 0.8329 (t0) cc_final: 0.7991 (p0) REVERT: B 819 ASP cc_start: 0.9002 (m-30) cc_final: 0.8739 (m-30) REVERT: B 921 MET cc_start: 0.8025 (mmt) cc_final: 0.7770 (mmt) REVERT: C 146 TRP cc_start: 0.8965 (m100) cc_final: 0.8653 (m100) REVERT: C 158 PHE cc_start: 0.8642 (t80) cc_final: 0.8109 (t80) REVERT: C 260 ASP cc_start: 0.9339 (t0) cc_final: 0.8892 (t0) REVERT: C 276 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9082 (p) REVERT: C 279 ASP cc_start: 0.9360 (m-30) cc_final: 0.9099 (m-30) REVERT: C 299 ASN cc_start: 0.9414 (m-40) cc_final: 0.9181 (m110) REVERT: C 520 ASP cc_start: 0.7260 (p0) cc_final: 0.7010 (p0) REVERT: C 531 GLU cc_start: 0.9332 (tp30) cc_final: 0.9102 (tp30) REVERT: C 632 GLN cc_start: 0.8458 (tm130) cc_final: 0.8244 (tm-30) REVERT: C 804 MET cc_start: 0.7539 (mmt) cc_final: 0.7288 (mmt) REVERT: C 867 ASP cc_start: 0.8645 (t70) cc_final: 0.8360 (t0) REVERT: D 158 PHE cc_start: 0.8951 (t80) cc_final: 0.8638 (t80) REVERT: D 193 LEU cc_start: 0.8771 (tt) cc_final: 0.8476 (mm) REVERT: D 458 MET cc_start: 0.8755 (tpp) cc_final: 0.8539 (tpp) REVERT: D 467 MET cc_start: 0.8365 (tmm) cc_final: 0.7978 (tmm) REVERT: D 804 MET cc_start: 0.7888 (mmt) cc_final: 0.7673 (mmt) REVERT: D 921 MET cc_start: 0.8431 (mmm) cc_final: 0.8161 (tpt) REVERT: D 980 MET cc_start: 0.8063 (mmm) cc_final: 0.7827 (mmp) REVERT: E 107 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8608 (mm-30) REVERT: E 146 TRP cc_start: 0.9019 (m-90) cc_final: 0.8696 (m100) REVERT: E 158 PHE cc_start: 0.8838 (t80) cc_final: 0.8566 (t80) REVERT: E 276 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8917 (p) REVERT: E 279 ASP cc_start: 0.9339 (m-30) cc_final: 0.9085 (m-30) REVERT: E 520 ASP cc_start: 0.8371 (t0) cc_final: 0.7982 (p0) REVERT: E 722 ILE cc_start: 0.9124 (mt) cc_final: 0.8909 (mt) REVERT: E 819 ASP cc_start: 0.8963 (m-30) cc_final: 0.8711 (m-30) REVERT: F 109 PHE cc_start: 0.8874 (m-10) cc_final: 0.8506 (m-80) REVERT: F 158 PHE cc_start: 0.8692 (t80) cc_final: 0.8268 (t80) REVERT: F 214 GLU cc_start: 0.8628 (tp30) cc_final: 0.8284 (tp30) REVERT: F 217 PHE cc_start: 0.6618 (m-80) cc_final: 0.5633 (t80) REVERT: F 260 ASP cc_start: 0.9444 (t0) cc_final: 0.8944 (t0) REVERT: F 276 VAL cc_start: 0.9426 (OUTLIER) cc_final: 0.9045 (p) REVERT: F 279 ASP cc_start: 0.9334 (m-30) cc_final: 0.9043 (m-30) REVERT: F 299 ASN cc_start: 0.9425 (m-40) cc_final: 0.9183 (m110) REVERT: F 458 MET cc_start: 0.8918 (tpp) cc_final: 0.8561 (tpp) REVERT: F 531 GLU cc_start: 0.9308 (tp30) cc_final: 0.9076 (tp30) outliers start: 145 outliers final: 93 residues processed: 607 average time/residue: 0.4242 time to fit residues: 448.1071 Evaluate side-chains 562 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 464 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 983 THR Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 983 THR Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 657 ILE Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 949 VAL Chi-restraints excluded: chain E residue 983 THR Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 834 PHE Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 415 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 478 optimal weight: 1.9990 chunk 317 optimal weight: 0.9980 chunk 566 optimal weight: 0.3980 chunk 354 optimal weight: 0.0020 chunk 345 optimal weight: 0.0060 chunk 261 optimal weight: 0.6980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN D 264 ASN ** E 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 48234 Z= 0.149 Angle : 0.580 12.775 65292 Z= 0.290 Chirality : 0.038 0.206 7866 Planarity : 0.003 0.055 8112 Dihedral : 3.998 27.202 6204 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.21 % Allowed : 17.47 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.11), residues: 5856 helix: 1.59 (0.08), residues: 4254 sheet: None (None), residues: 0 loop : -1.12 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 146 HIS 0.003 0.000 HIS E 79 PHE 0.022 0.001 PHE B 363 TYR 0.025 0.001 TYR F 92 ARG 0.008 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 558 time to evaluate : 4.212 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: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.8584 (t80) cc_final: 0.8079 (t80) REVERT: A 190 ARG cc_start: 0.9146 (tpm170) cc_final: 0.8845 (tpm170) REVERT: A 260 ASP cc_start: 0.9179 (t0) cc_final: 0.8952 (p0) REVERT: A 276 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.9150 (m) REVERT: A 279 ASP cc_start: 0.9410 (m-30) cc_final: 0.9156 (m-30) REVERT: A 299 ASN cc_start: 0.9426 (m-40) cc_final: 0.9169 (m110) REVERT: A 310 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 467 MET cc_start: 0.8375 (tmm) cc_final: 0.7989 (tmm) REVERT: A 520 ASP cc_start: 0.8694 (t0) cc_final: 0.8486 (t0) REVERT: A 541 GLU cc_start: 0.7514 (pm20) cc_final: 0.7157 (pm20) REVERT: A 804 MET cc_start: 0.7868 (mmt) cc_final: 0.7611 (mmt) REVERT: A 837 PHE cc_start: 0.8038 (m-80) cc_final: 0.7642 (m-80) REVERT: B 146 TRP cc_start: 0.9517 (m-90) cc_final: 0.9262 (m-90) REVERT: B 158 PHE cc_start: 0.8759 (t80) cc_final: 0.8131 (t80) REVERT: B 193 LEU cc_start: 0.8952 (tt) cc_final: 0.8684 (mm) REVERT: B 279 ASP cc_start: 0.9352 (m-30) cc_final: 0.9062 (m-30) REVERT: B 520 ASP cc_start: 0.8310 (t0) cc_final: 0.8036 (p0) REVERT: B 564 ILE cc_start: 0.6515 (mm) cc_final: 0.6240 (mm) REVERT: B 819 ASP cc_start: 0.8934 (m-30) cc_final: 0.8682 (m-30) REVERT: B 921 MET cc_start: 0.7993 (mmt) cc_final: 0.7756 (mmt) REVERT: C 146 TRP cc_start: 0.8863 (m100) cc_final: 0.8530 (m100) REVERT: C 158 PHE cc_start: 0.8563 (t80) cc_final: 0.8045 (t80) REVERT: C 260 ASP cc_start: 0.9318 (t0) cc_final: 0.8874 (t0) REVERT: C 276 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9072 (p) REVERT: C 279 ASP cc_start: 0.9356 (m-30) cc_final: 0.9091 (m-30) REVERT: C 299 ASN cc_start: 0.9395 (m-40) cc_final: 0.9167 (m110) REVERT: C 310 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8341 (tm-30) REVERT: C 520 ASP cc_start: 0.7439 (p0) cc_final: 0.7193 (p0) REVERT: C 531 GLU cc_start: 0.9326 (tp30) cc_final: 0.9087 (tp30) REVERT: C 804 MET cc_start: 0.7439 (mmt) cc_final: 0.7195 (mmt) REVERT: C 867 ASP cc_start: 0.8598 (t70) cc_final: 0.8340 (t0) REVERT: D 153 LYS cc_start: 0.9625 (mmtt) cc_final: 0.9380 (mmtt) REVERT: D 158 PHE cc_start: 0.8940 (t80) cc_final: 0.8617 (t80) REVERT: D 193 LEU cc_start: 0.8750 (tt) cc_final: 0.8434 (mm) REVERT: D 456 ASN cc_start: 0.8397 (p0) cc_final: 0.8191 (p0) REVERT: D 467 MET cc_start: 0.8389 (tmm) cc_final: 0.8011 (tmm) REVERT: D 804 MET cc_start: 0.7790 (mmt) cc_final: 0.7583 (mmt) REVERT: D 921 MET cc_start: 0.8376 (mmm) cc_final: 0.8113 (tpt) REVERT: E 107 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8618 (mm-30) REVERT: E 146 TRP cc_start: 0.9007 (m-90) cc_final: 0.8710 (m100) REVERT: E 158 PHE cc_start: 0.8785 (t80) cc_final: 0.8508 (t80) REVERT: E 276 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8851 (p) REVERT: E 279 ASP cc_start: 0.9329 (m-30) cc_final: 0.9077 (m-30) REVERT: E 364 GLU cc_start: 0.9493 (tm-30) cc_final: 0.9279 (tp30) REVERT: E 520 ASP cc_start: 0.8352 (t0) cc_final: 0.7996 (p0) REVERT: E 564 ILE cc_start: 0.6632 (mm) cc_final: 0.6426 (mm) REVERT: E 674 SER cc_start: 0.9430 (m) cc_final: 0.9160 (p) REVERT: E 793 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8423 (mm-30) REVERT: E 819 ASP cc_start: 0.8900 (m-30) cc_final: 0.8639 (m-30) REVERT: E 839 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7788 (ttp) REVERT: F 109 PHE cc_start: 0.8921 (m-10) cc_final: 0.8505 (m-80) REVERT: F 158 PHE cc_start: 0.8655 (t80) cc_final: 0.8242 (t80) REVERT: F 214 GLU cc_start: 0.8569 (tp30) cc_final: 0.8296 (tp30) REVERT: F 217 PHE cc_start: 0.6594 (m-80) cc_final: 0.5639 (t80) REVERT: F 260 ASP cc_start: 0.9405 (t0) cc_final: 0.8998 (t0) REVERT: F 276 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9018 (p) REVERT: F 279 ASP cc_start: 0.9331 (m-30) cc_final: 0.9036 (m-30) REVERT: F 299 ASN cc_start: 0.9439 (m-40) cc_final: 0.9182 (m110) REVERT: F 458 MET cc_start: 0.8912 (tpp) cc_final: 0.8583 (tpp) REVERT: F 471 MET cc_start: 0.8714 (mmp) cc_final: 0.8483 (mmm) REVERT: F 531 GLU cc_start: 0.9306 (tp30) cc_final: 0.9061 (tp30) outliers start: 121 outliers final: 79 residues processed: 647 average time/residue: 0.4192 time to fit residues: 470.1552 Evaluate side-chains 586 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 501 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 949 VAL Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 834 PHE Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 949 VAL Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 0.0570 chunk 226 optimal weight: 0.9990 chunk 338 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 360 optimal weight: 0.6980 chunk 386 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 445 optimal weight: 0.0980 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 48234 Z= 0.157 Angle : 0.596 16.624 65292 Z= 0.295 Chirality : 0.039 0.322 7866 Planarity : 0.003 0.054 8112 Dihedral : 3.973 25.740 6204 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.03 % Allowed : 18.53 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.11), residues: 5856 helix: 1.60 (0.08), residues: 4260 sheet: None (None), residues: 0 loop : -1.14 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 146 HIS 0.004 0.000 HIS F 941 PHE 0.035 0.001 PHE F 89 TYR 0.041 0.001 TYR B 92 ARG 0.009 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 524 time to evaluate : 4.277 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: symmetry clash REVERT: A 146 TRP cc_start: 0.9055 (m100) cc_final: 0.8780 (m100) REVERT: A 158 PHE cc_start: 0.8615 (t80) cc_final: 0.8108 (t80) REVERT: A 190 ARG cc_start: 0.9176 (tpm170) cc_final: 0.8871 (tpm170) REVERT: A 276 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9141 (m) REVERT: A 279 ASP cc_start: 0.9392 (m-30) cc_final: 0.9134 (m-30) REVERT: A 286 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8788 (mt-10) REVERT: A 299 ASN cc_start: 0.9435 (m-40) cc_final: 0.9180 (m110) REVERT: A 310 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 467 MET cc_start: 0.8377 (tmm) cc_final: 0.7984 (tmm) REVERT: A 520 ASP cc_start: 0.8686 (t0) cc_final: 0.8481 (t0) REVERT: A 541 GLU cc_start: 0.7522 (pm20) cc_final: 0.7190 (pm20) REVERT: A 564 ILE cc_start: 0.6385 (mm) cc_final: 0.6088 (mm) REVERT: A 804 MET cc_start: 0.7881 (mmt) cc_final: 0.7624 (mmt) REVERT: A 837 PHE cc_start: 0.8034 (m-80) cc_final: 0.7771 (m-80) REVERT: A 987 LEU cc_start: 0.8164 (mm) cc_final: 0.7856 (tt) REVERT: B 158 PHE cc_start: 0.8764 (t80) cc_final: 0.8143 (t80) REVERT: B 193 LEU cc_start: 0.8935 (tt) cc_final: 0.8668 (mm) REVERT: B 279 ASP cc_start: 0.9344 (m-30) cc_final: 0.9054 (m-30) REVERT: B 520 ASP cc_start: 0.8325 (t0) cc_final: 0.8060 (p0) REVERT: B 564 ILE cc_start: 0.6503 (mm) cc_final: 0.6296 (mm) REVERT: B 819 ASP cc_start: 0.8933 (m-30) cc_final: 0.8675 (m-30) REVERT: B 921 MET cc_start: 0.8044 (mmt) cc_final: 0.7805 (mmt) REVERT: C 146 TRP cc_start: 0.8789 (m100) cc_final: 0.8426 (m100) REVERT: C 158 PHE cc_start: 0.8579 (t80) cc_final: 0.8058 (t80) REVERT: C 260 ASP cc_start: 0.9301 (t0) cc_final: 0.8867 (t0) REVERT: C 276 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9068 (p) REVERT: C 279 ASP cc_start: 0.9348 (m-30) cc_final: 0.9091 (m-30) REVERT: C 299 ASN cc_start: 0.9401 (m-40) cc_final: 0.9179 (m110) REVERT: C 310 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8337 (tm-30) REVERT: C 531 GLU cc_start: 0.9327 (tp30) cc_final: 0.9082 (tp30) REVERT: C 804 MET cc_start: 0.7405 (mmt) cc_final: 0.7179 (mmt) REVERT: C 867 ASP cc_start: 0.8559 (t70) cc_final: 0.8300 (t0) REVERT: D 153 LYS cc_start: 0.9625 (mmtt) cc_final: 0.9392 (mmtt) REVERT: D 158 PHE cc_start: 0.8935 (t80) cc_final: 0.8612 (t80) REVERT: D 193 LEU cc_start: 0.8761 (tt) cc_final: 0.8457 (mm) REVERT: D 215 ASP cc_start: 0.9234 (m-30) cc_final: 0.8553 (p0) REVERT: D 279 ASP cc_start: 0.9283 (m-30) cc_final: 0.8764 (p0) REVERT: D 342 ASP cc_start: 0.8122 (p0) cc_final: 0.7878 (p0) REVERT: D 456 ASN cc_start: 0.8391 (p0) cc_final: 0.8179 (p0) REVERT: D 467 MET cc_start: 0.8375 (tmm) cc_final: 0.7948 (tmm) REVERT: D 804 MET cc_start: 0.7851 (mmt) cc_final: 0.7619 (mmt) REVERT: D 921 MET cc_start: 0.8366 (mmm) cc_final: 0.8141 (mmm) REVERT: D 987 LEU cc_start: 0.8189 (mm) cc_final: 0.7885 (tt) REVERT: E 146 TRP cc_start: 0.9004 (m-90) cc_final: 0.8693 (m100) REVERT: E 158 PHE cc_start: 0.8758 (t80) cc_final: 0.8483 (t80) REVERT: E 276 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8880 (p) REVERT: E 279 ASP cc_start: 0.9321 (m-30) cc_final: 0.9066 (m-30) REVERT: E 520 ASP cc_start: 0.8373 (t0) cc_final: 0.8019 (p0) REVERT: E 564 ILE cc_start: 0.6627 (mm) cc_final: 0.6353 (mm) REVERT: E 793 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8470 (mm-30) REVERT: E 819 ASP cc_start: 0.8916 (m-30) cc_final: 0.8656 (m-30) REVERT: E 839 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7768 (ttp) REVERT: F 109 PHE cc_start: 0.8970 (m-10) cc_final: 0.8588 (m-80) REVERT: F 158 PHE cc_start: 0.8649 (t80) cc_final: 0.8248 (t80) REVERT: F 214 GLU cc_start: 0.8578 (tp30) cc_final: 0.8182 (tp30) REVERT: F 217 PHE cc_start: 0.6658 (m-80) cc_final: 0.5745 (t80) REVERT: F 260 ASP cc_start: 0.9391 (t0) cc_final: 0.8985 (t0) REVERT: F 276 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9014 (p) REVERT: F 279 ASP cc_start: 0.9327 (m-30) cc_final: 0.9023 (m-30) REVERT: F 299 ASN cc_start: 0.9455 (m-40) cc_final: 0.9206 (m110) REVERT: F 458 MET cc_start: 0.8925 (tpp) cc_final: 0.8626 (tpp) REVERT: F 471 MET cc_start: 0.8699 (mmp) cc_final: 0.8405 (mmm) REVERT: F 531 GLU cc_start: 0.9307 (tp30) cc_final: 0.9053 (tp30) REVERT: F 845 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7835 (mmtm) outliers start: 111 outliers final: 81 residues processed: 606 average time/residue: 0.4308 time to fit residues: 455.2411 Evaluate side-chains 580 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 493 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 839 MET Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 949 VAL Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain F residue 834 PHE Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 840 ASP Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 1.9990 chunk 542 optimal weight: 1.9990 chunk 495 optimal weight: 5.9990 chunk 528 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 477 optimal weight: 0.0270 chunk 499 optimal weight: 7.9990 chunk 526 optimal weight: 2.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 264 ASN F 181 HIS ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48234 Z= 0.196 Angle : 0.613 15.486 65292 Z= 0.304 Chirality : 0.039 0.226 7866 Planarity : 0.003 0.055 8112 Dihedral : 4.023 25.290 6204 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.10 % Allowed : 18.73 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 5856 helix: 1.62 (0.08), residues: 4266 sheet: None (None), residues: 0 loop : -1.16 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 146 HIS 0.003 0.001 HIS F 941 PHE 0.052 0.001 PHE C 89 TYR 0.024 0.001 TYR B 92 ARG 0.009 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 489 time to evaluate : 4.240 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TRP cc_start: 0.9082 (m100) cc_final: 0.8786 (m100) REVERT: A 158 PHE cc_start: 0.8617 (t80) cc_final: 0.8110 (t80) REVERT: A 190 ARG cc_start: 0.9173 (tpm170) cc_final: 0.8849 (tpm170) REVERT: A 276 VAL cc_start: 0.9431 (OUTLIER) cc_final: 0.9148 (m) REVERT: A 279 ASP cc_start: 0.9403 (m-30) cc_final: 0.9149 (m-30) REVERT: A 286 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8803 (mt-10) REVERT: A 299 ASN cc_start: 0.9439 (m-40) cc_final: 0.9183 (m110) REVERT: A 310 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 467 MET cc_start: 0.8384 (tmm) cc_final: 0.7946 (tmm) REVERT: A 520 ASP cc_start: 0.8653 (t0) cc_final: 0.8429 (t0) REVERT: A 804 MET cc_start: 0.7935 (mmt) cc_final: 0.7687 (mmt) REVERT: A 837 PHE cc_start: 0.8173 (m-80) cc_final: 0.7786 (m-80) REVERT: A 987 LEU cc_start: 0.8187 (mm) cc_final: 0.7871 (tt) REVERT: B 146 TRP cc_start: 0.9489 (m-90) cc_final: 0.9271 (m-90) REVERT: B 158 PHE cc_start: 0.8784 (t80) cc_final: 0.8169 (t80) REVERT: B 193 LEU cc_start: 0.8881 (tt) cc_final: 0.8613 (mm) REVERT: B 279 ASP cc_start: 0.9337 (m-30) cc_final: 0.9022 (m-30) REVERT: B 520 ASP cc_start: 0.8261 (t0) cc_final: 0.8038 (p0) REVERT: B 564 ILE cc_start: 0.6601 (mm) cc_final: 0.6302 (mm) REVERT: B 819 ASP cc_start: 0.8977 (m-30) cc_final: 0.8716 (m-30) REVERT: B 921 MET cc_start: 0.8239 (mmt) cc_final: 0.7979 (mmt) REVERT: C 146 TRP cc_start: 0.8768 (m100) cc_final: 0.8392 (m100) REVERT: C 158 PHE cc_start: 0.8625 (t80) cc_final: 0.8075 (t80) REVERT: C 260 ASP cc_start: 0.9267 (t0) cc_final: 0.8757 (t0) REVERT: C 276 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9070 (p) REVERT: C 279 ASP cc_start: 0.9342 (m-30) cc_final: 0.9086 (m-30) REVERT: C 299 ASN cc_start: 0.9418 (m-40) cc_final: 0.9171 (m110) REVERT: C 310 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 531 GLU cc_start: 0.9319 (tp30) cc_final: 0.9077 (tp30) REVERT: C 575 GLU cc_start: 0.9281 (pm20) cc_final: 0.9020 (pm20) REVERT: C 804 MET cc_start: 0.7508 (mmt) cc_final: 0.7266 (mmt) REVERT: C 867 ASP cc_start: 0.8598 (t70) cc_final: 0.8314 (t0) REVERT: D 158 PHE cc_start: 0.8891 (t80) cc_final: 0.8543 (t80) REVERT: D 193 LEU cc_start: 0.8765 (tt) cc_final: 0.8465 (mm) REVERT: D 215 ASP cc_start: 0.9263 (m-30) cc_final: 0.8577 (p0) REVERT: D 279 ASP cc_start: 0.9284 (m-30) cc_final: 0.8755 (p0) REVERT: D 467 MET cc_start: 0.8380 (tmm) cc_final: 0.7950 (tmm) REVERT: D 804 MET cc_start: 0.7851 (mmt) cc_final: 0.7640 (mmt) REVERT: D 921 MET cc_start: 0.8433 (mmm) cc_final: 0.8147 (tpt) REVERT: D 987 LEU cc_start: 0.8158 (mm) cc_final: 0.7835 (tt) REVERT: E 146 TRP cc_start: 0.9037 (m-90) cc_final: 0.8746 (m100) REVERT: E 158 PHE cc_start: 0.8793 (t80) cc_final: 0.8528 (t80) REVERT: E 276 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8892 (p) REVERT: E 279 ASP cc_start: 0.9320 (m-30) cc_final: 0.9051 (m-30) REVERT: E 520 ASP cc_start: 0.8361 (t0) cc_final: 0.8015 (p0) REVERT: E 564 ILE cc_start: 0.6615 (mm) cc_final: 0.6320 (mm) REVERT: E 793 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8441 (mm-30) REVERT: E 819 ASP cc_start: 0.8939 (m-30) cc_final: 0.8682 (m-30) REVERT: E 839 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7740 (ttp) REVERT: F 109 PHE cc_start: 0.9014 (m-10) cc_final: 0.8692 (m-80) REVERT: F 158 PHE cc_start: 0.8660 (t80) cc_final: 0.8265 (t80) REVERT: F 214 GLU cc_start: 0.8638 (tp30) cc_final: 0.8369 (tp30) REVERT: F 217 PHE cc_start: 0.6852 (m-80) cc_final: 0.5845 (t80) REVERT: F 260 ASP cc_start: 0.9384 (t0) cc_final: 0.8960 (t0) REVERT: F 276 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9021 (p) REVERT: F 279 ASP cc_start: 0.9327 (m-30) cc_final: 0.9026 (m-30) REVERT: F 299 ASN cc_start: 0.9471 (m-40) cc_final: 0.9223 (m110) REVERT: F 458 MET cc_start: 0.8944 (tpp) cc_final: 0.8637 (tpp) REVERT: F 471 MET cc_start: 0.8703 (mmp) cc_final: 0.8387 (mmm) REVERT: F 531 GLU cc_start: 0.9298 (tp30) cc_final: 0.9045 (tp30) REVERT: F 845 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7787 (mmtm) outliers start: 115 outliers final: 88 residues processed: 570 average time/residue: 0.4211 time to fit residues: 418.0548 Evaluate side-chains 575 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 481 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 839 MET Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 983 THR Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 840 ASP Chi-restraints excluded: chain E residue 949 VAL Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain F residue 834 PHE Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 5.9990 chunk 558 optimal weight: 0.9990 chunk 340 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 388 optimal weight: 0.6980 chunk 585 optimal weight: 3.9990 chunk 539 optimal weight: 0.9980 chunk 466 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 360 optimal weight: 7.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 264 ASN ** E 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48234 Z= 0.169 Angle : 0.612 15.000 65292 Z= 0.303 Chirality : 0.039 0.202 7866 Planarity : 0.003 0.056 8112 Dihedral : 4.015 24.981 6204 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.76 % Allowed : 19.19 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 5856 helix: 1.63 (0.08), residues: 4254 sheet: None (None), residues: 0 loop : -1.14 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 146 HIS 0.003 0.000 HIS F 941 PHE 0.028 0.001 PHE C 89 TYR 0.022 0.001 TYR F 92 ARG 0.010 0.000 ARG A 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11712 Ramachandran restraints generated. 5856 Oldfield, 0 Emsley, 5856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 509 time to evaluate : 4.304 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TRP cc_start: 0.9100 (m100) cc_final: 0.8794 (m100) REVERT: A 158 PHE cc_start: 0.8618 (t80) cc_final: 0.8108 (t80) REVERT: A 190 ARG cc_start: 0.9182 (tpm170) cc_final: 0.8860 (tpm170) REVERT: A 276 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9136 (m) REVERT: A 279 ASP cc_start: 0.9387 (m-30) cc_final: 0.9121 (m-30) REVERT: A 286 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8795 (mt-10) REVERT: A 299 ASN cc_start: 0.9436 (m-40) cc_final: 0.9182 (m110) REVERT: A 310 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8470 (tm-30) REVERT: A 467 MET cc_start: 0.8381 (tmm) cc_final: 0.7943 (tmm) REVERT: A 520 ASP cc_start: 0.8654 (t0) cc_final: 0.8443 (t0) REVERT: A 541 GLU cc_start: 0.7603 (pm20) cc_final: 0.7183 (mm-30) REVERT: A 804 MET cc_start: 0.7914 (mmt) cc_final: 0.7683 (mmt) REVERT: A 837 PHE cc_start: 0.8180 (m-80) cc_final: 0.7770 (m-80) REVERT: A 980 MET cc_start: 0.7635 (mmp) cc_final: 0.7069 (mpp) REVERT: A 987 LEU cc_start: 0.8162 (mm) cc_final: 0.7854 (tt) REVERT: B 146 TRP cc_start: 0.9490 (m-90) cc_final: 0.9217 (m-90) REVERT: B 158 PHE cc_start: 0.8750 (t80) cc_final: 0.8141 (t80) REVERT: B 193 LEU cc_start: 0.8819 (tt) cc_final: 0.8552 (mt) REVERT: B 279 ASP cc_start: 0.9328 (m-30) cc_final: 0.9010 (m-30) REVERT: B 372 ASP cc_start: 0.9158 (m-30) cc_final: 0.8945 (m-30) REVERT: B 520 ASP cc_start: 0.8247 (t0) cc_final: 0.8031 (p0) REVERT: B 564 ILE cc_start: 0.6615 (mm) cc_final: 0.6318 (mm) REVERT: B 819 ASP cc_start: 0.8956 (m-30) cc_final: 0.8699 (m-30) REVERT: B 921 MET cc_start: 0.8231 (mmt) cc_final: 0.8008 (mmt) REVERT: C 146 TRP cc_start: 0.8751 (m100) cc_final: 0.8382 (m100) REVERT: C 158 PHE cc_start: 0.8629 (t80) cc_final: 0.8074 (t80) REVERT: C 260 ASP cc_start: 0.9212 (t0) cc_final: 0.8571 (t0) REVERT: C 276 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9045 (p) REVERT: C 279 ASP cc_start: 0.9339 (m-30) cc_final: 0.9078 (m-30) REVERT: C 299 ASN cc_start: 0.9421 (m-40) cc_final: 0.9197 (m110) REVERT: C 310 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 531 GLU cc_start: 0.9327 (tp30) cc_final: 0.9089 (tp30) REVERT: C 575 GLU cc_start: 0.9271 (pm20) cc_final: 0.8928 (pm20) REVERT: C 804 MET cc_start: 0.7430 (mmt) cc_final: 0.7199 (mmt) REVERT: C 867 ASP cc_start: 0.8580 (t70) cc_final: 0.8293 (t0) REVERT: D 158 PHE cc_start: 0.8892 (t80) cc_final: 0.8574 (t80) REVERT: D 193 LEU cc_start: 0.8766 (tt) cc_final: 0.8467 (mm) REVERT: D 215 ASP cc_start: 0.9267 (m-30) cc_final: 0.8592 (p0) REVERT: D 467 MET cc_start: 0.8385 (tmm) cc_final: 0.7953 (tmm) REVERT: D 804 MET cc_start: 0.7813 (mmt) cc_final: 0.7608 (mmt) REVERT: D 921 MET cc_start: 0.8437 (mmm) cc_final: 0.8168 (tpt) REVERT: D 987 LEU cc_start: 0.8140 (mm) cc_final: 0.7824 (tt) REVERT: E 146 TRP cc_start: 0.9018 (m-90) cc_final: 0.8723 (m100) REVERT: E 158 PHE cc_start: 0.8792 (t80) cc_final: 0.8532 (t80) REVERT: E 276 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8876 (p) REVERT: E 279 ASP cc_start: 0.9316 (m-30) cc_final: 0.9044 (m-30) REVERT: E 520 ASP cc_start: 0.8330 (t0) cc_final: 0.8022 (p0) REVERT: E 564 ILE cc_start: 0.6630 (mm) cc_final: 0.6335 (mm) REVERT: E 793 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8468 (mm-30) REVERT: E 819 ASP cc_start: 0.8927 (m-30) cc_final: 0.8666 (m-30) REVERT: E 839 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7751 (ttp) REVERT: F 109 PHE cc_start: 0.9020 (m-10) cc_final: 0.8684 (m-80) REVERT: F 158 PHE cc_start: 0.8660 (t80) cc_final: 0.8254 (t80) REVERT: F 214 GLU cc_start: 0.8634 (tp30) cc_final: 0.8237 (tp30) REVERT: F 217 PHE cc_start: 0.6843 (m-80) cc_final: 0.5953 (t80) REVERT: F 260 ASP cc_start: 0.9371 (t0) cc_final: 0.8956 (t0) REVERT: F 276 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9010 (p) REVERT: F 279 ASP cc_start: 0.9320 (m-30) cc_final: 0.9005 (m-30) REVERT: F 299 ASN cc_start: 0.9466 (m-40) cc_final: 0.9218 (m110) REVERT: F 458 MET cc_start: 0.8918 (tpp) cc_final: 0.8581 (tpp) REVERT: F 471 MET cc_start: 0.8698 (mmp) cc_final: 0.8388 (mmm) REVERT: F 531 GLU cc_start: 0.9315 (tp30) cc_final: 0.9068 (tp30) REVERT: F 845 LYS cc_start: 0.8431 (mmmt) cc_final: 0.7830 (mmtm) outliers start: 96 outliers final: 85 residues processed: 574 average time/residue: 0.4293 time to fit residues: 428.2795 Evaluate side-chains 584 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 493 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 839 MET Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 840 ASP Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 949 VAL Chi-restraints excluded: chain E residue 985 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain F residue 834 PHE Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 4.9990 chunk 496 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 430 optimal weight: 1.9990 chunk 68 optimal weight: 0.0270 chunk 129 optimal weight: 0.9980 chunk 467 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 479 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 264 ASN ** E 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.093377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061836 restraints weight = 128018.552| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.37 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48234 Z= 0.173 Angle : 0.615 14.765 65292 Z= 0.305 Chirality : 0.039 0.311 7866 Planarity : 0.003 0.056 8112 Dihedral : 4.018 24.495 6204 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.85 % Allowed : 19.19 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.11), residues: 5856 helix: 1.65 (0.08), residues: 4254 sheet: None (None), residues: 0 loop : -1.13 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 146 HIS 0.003 0.000 HIS F 941 PHE 0.044 0.001 PHE E 89 TYR 0.034 0.001 TYR E 92 ARG 0.010 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8586.51 seconds wall clock time: 153 minutes 0.74 seconds (9180.74 seconds total)