Starting phenix.real_space_refine on Wed Jan 15 03:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usp_42510/01_2025/8usp_42510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usp_42510/01_2025/8usp_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_42510/01_2025/8usp_42510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usp_42510/01_2025/8usp_42510.map" model { file = "/net/cci-nas-00/data/ceres_data/8usp_42510/01_2025/8usp_42510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usp_42510/01_2025/8usp_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-5571/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: 20.11, 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: 9.54 Conformation dependent library (CDL) restraints added in 4.7 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: 3.49 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: 15.75 Time building geometry restraints manager: 11.25 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: 0.06 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.030 Extract box with map and model: 1.480 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 79.580 Find NCS groups from input model: 1.380 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: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.200 ------------------------------------------------------------------------------- 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 : 4.333 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: 0.4202 time to fit residues: 500.0133 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 : 4.252 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.100210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067821 restraints weight = 130289.089| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.93 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 4.786 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: 0.8572 (t80) cc_final: 0.8089 (t80) REVERT: A 279 ASP cc_start: 0.9538 (m-30) cc_final: 0.9320 (m-30) REVERT: A 299 ASN cc_start: 0.9460 (m-40) cc_final: 0.9206 (m110) REVERT: A 467 MET cc_start: 0.8386 (tmm) cc_final: 0.7981 (tmm) REVERT: A 520 ASP cc_start: 0.8781 (t0) cc_final: 0.8341 (p0) REVERT: A 804 MET cc_start: 0.7869 (mmt) cc_final: 0.7570 (mmt) REVERT: B 91 PHE cc_start: 0.9557 (m-80) cc_final: 0.9336 (m-80) REVERT: B 158 PHE cc_start: 0.8761 (t80) cc_final: 0.8192 (t80) REVERT: B 193 LEU cc_start: 0.9081 (tt) cc_final: 0.8789 (mm) REVERT: B 279 ASP cc_start: 0.9450 (m-30) cc_final: 0.9199 (m-30) REVERT: B 520 ASP cc_start: 0.8483 (t0) cc_final: 0.8017 (p0) REVERT: B 804 MET cc_start: 0.7166 (mmt) cc_final: 0.6851 (mmt) REVERT: B 819 ASP cc_start: 0.9220 (m-30) cc_final: 0.8955 (m-30) REVERT: C 109 PHE cc_start: 0.9230 (m-10) cc_final: 0.8854 (m-80) REVERT: C 158 PHE cc_start: 0.8706 (t80) cc_final: 0.8259 (t80) REVERT: C 276 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9263 (m) REVERT: C 279 ASP cc_start: 0.9449 (m-30) cc_final: 0.9215 (m-30) REVERT: C 299 ASN cc_start: 0.9338 (m-40) cc_final: 0.9041 (m110) REVERT: C 310 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8450 (tm-30) REVERT: C 475 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8523 (ttm110) REVERT: C 531 GLU cc_start: 0.9443 (tp30) cc_final: 0.9220 (tp30) REVERT: C 867 ASP cc_start: 0.8619 (t70) cc_final: 0.8400 (t0) REVERT: D 92 TYR cc_start: 0.9317 (p90) cc_final: 0.9029 (p90) REVERT: D 158 PHE cc_start: 0.8876 (t80) cc_final: 0.8674 (t80) REVERT: D 177 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8887 (pm20) REVERT: D 193 LEU cc_start: 0.8847 (tt) cc_final: 0.8503 (mm) REVERT: D 456 ASN cc_start: 0.8347 (p0) cc_final: 0.8137 (p0) REVERT: D 467 MET cc_start: 0.8383 (tmm) cc_final: 0.7981 (tmm) REVERT: D 520 ASP cc_start: 0.8768 (t0) cc_final: 0.8347 (p0) REVERT: D 804 MET cc_start: 0.7804 (mmt) cc_final: 0.7558 (mmt) REVERT: D 921 MET cc_start: 0.7996 (mmm) cc_final: 0.7558 (mmm) REVERT: D 980 MET cc_start: 0.8123 (mmm) cc_final: 0.7895 (mmp) REVERT: E 158 PHE cc_start: 0.8828 (t80) cc_final: 0.8557 (t80) REVERT: E 177 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8941 (pm20) REVERT: E 180 LEU cc_start: 0.9395 (mm) cc_final: 0.9160 (mm) REVERT: E 215 ASP cc_start: 0.9240 (m-30) cc_final: 0.8922 (p0) REVERT: E 279 ASP cc_start: 0.9444 (m-30) cc_final: 0.9191 (m-30) REVERT: E 520 ASP cc_start: 0.8510 (t0) cc_final: 0.8054 (p0) REVERT: E 632 GLN cc_start: 0.8616 (mt0) cc_final: 0.8188 (tm-30) REVERT: E 795 MET cc_start: 0.8895 (mmt) cc_final: 0.8650 (mmt) REVERT: E 819 ASP cc_start: 0.9159 (m-30) cc_final: 0.8926 (m-30) REVERT: E 921 MET cc_start: 0.7713 (mmt) cc_final: 0.7458 (mmt) REVERT: F 109 PHE cc_start: 0.9036 (m-10) cc_final: 0.8648 (m-80) REVERT: F 158 PHE cc_start: 0.8748 (t80) cc_final: 0.8305 (t80) REVERT: F 276 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9226 (m) REVERT: F 279 ASP cc_start: 0.9421 (m-30) cc_final: 0.9144 (m-30) REVERT: F 299 ASN cc_start: 0.9323 (m-40) cc_final: 0.9016 (m110) REVERT: F 471 MET cc_start: 0.8645 (mmm) cc_final: 0.8444 (mmp) REVERT: F 475 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8511 (ttm110) REVERT: F 531 GLU cc_start: 0.9425 (tp30) cc_final: 0.9201 (tp30) outliers start: 53 outliers final: 37 residues processed: 550 average time/residue: 0.4257 time to fit residues: 407.7469 Evaluate side-chains 504 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 463 time to evaluate : 4.319 ------------------------------------------------------------------------------- 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 177 GLU 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 556 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 469 optimal weight: 6.9990 chunk 267 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 98 optimal weight: 50.0000 chunk 92 optimal weight: 0.7980 chunk 338 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.094283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062858 restraints weight = 128218.497| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.37 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1681 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= 0.177 Angle : 0.545 7.848 65292 Z= 0.283 Chirality : 0.038 0.225 7866 Planarity : 0.003 0.051 8112 Dihedral : 3.948 22.491 6204 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 1.34 % Allowed : 13.15 % Favored : 85.51 % 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 0.046 0.001 TYR E 92 ARG 0.013 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 606 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 533 time to evaluate : 4.332 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: 0.9176 (m100) cc_final: 0.8716 (m100) REVERT: A 158 PHE cc_start: 0.8426 (t80) cc_final: 0.7909 (t80) REVERT: A 170 ARG cc_start: 0.9431 (mpp-170) cc_final: 0.9212 (mpp-170) REVERT: A 260 ASP cc_start: 0.9102 (t0) cc_final: 0.8873 (p0) REVERT: A 276 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9135 (m) REVERT: A 279 ASP cc_start: 0.9411 (m-30) cc_final: 0.9161 (m-30) REVERT: A 467 MET cc_start: 0.8563 (tmm) cc_final: 0.8171 (tmm) REVERT: A 541 GLU cc_start: 0.7549 (pm20) cc_final: 0.7182 (pm20) REVERT: A 804 MET cc_start: 0.8183 (mmt) cc_final: 0.7854 (mmt) REVERT: A 921 MET cc_start: 0.8037 (mmt) cc_final: 0.7615 (mmm) REVERT: B 91 PHE cc_start: 0.9520 (m-80) cc_final: 0.9242 (m-80) REVERT: B 146 TRP cc_start: 0.9383 (m-90) cc_final: 0.9138 (m-90) REVERT: B 158 PHE cc_start: 0.8607 (t80) cc_final: 0.8062 (t80) REVERT: B 193 LEU cc_start: 0.9148 (tt) cc_final: 0.8863 (mm) REVERT: B 279 ASP cc_start: 0.9355 (m-30) cc_final: 0.9084 (m-30) REVERT: B 310 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 471 MET cc_start: 0.8622 (mmp) cc_final: 0.8407 (mmm) REVERT: B 520 ASP cc_start: 0.8432 (t0) cc_final: 0.8127 (p0) REVERT: B 804 MET cc_start: 0.7446 (mmt) cc_final: 0.7205 (mmt) REVERT: B 819 ASP cc_start: 0.9030 (m-30) cc_final: 0.8779 (m-30) REVERT: C 158 PHE cc_start: 0.8560 (t80) cc_final: 0.8122 (t80) REVERT: C 214 GLU cc_start: 0.8382 (tp30) cc_final: 0.8163 (tp30) REVERT: C 217 PHE cc_start: 0.7303 (m-80) cc_final: 0.5775 (t80) REVERT: C 260 ASP cc_start: 0.9346 (t0) cc_final: 0.8914 (t0) REVERT: C 279 ASP cc_start: 0.9359 (m-30) cc_final: 0.9105 (m-30) REVERT: C 531 GLU cc_start: 0.9222 (tp30) cc_final: 0.8975 (tp30) REVERT: C 573 HIS cc_start: 0.7541 (t-90) cc_final: 0.7079 (t-90) REVERT: D 92 TYR cc_start: 0.9225 (p90) cc_final: 0.8943 (p90) REVERT: D 158 PHE cc_start: 0.8754 (t80) cc_final: 0.8461 (t80) REVERT: D 177 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: D 193 LEU cc_start: 0.8949 (tt) cc_final: 0.8576 (mm) REVERT: D 215 ASP cc_start: 0.9230 (m-30) cc_final: 0.8493 (p0) REVERT: D 276 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8740 (p) REVERT: D 279 ASP cc_start: 0.9293 (m-30) cc_final: 0.8856 (p0) REVERT: D 467 MET cc_start: 0.8584 (tmm) cc_final: 0.8185 (tmm) REVERT: D 804 MET cc_start: 0.8132 (mmt) cc_final: 0.7837 (mmt) REVERT: D 921 MET cc_start: 0.8440 (mmm) cc_final: 0.7975 (mmm) REVERT: D 980 MET cc_start: 0.8314 (mmm) cc_final: 0.8054 (mmp) REVERT: E 177 GLU cc_start: 0.9181 (pm20) cc_final: 0.8886 (pm20) REVERT: E 180 LEU cc_start: 0.9321 (mm) cc_final: 0.9102 (mm) REVERT: E 215 ASP cc_start: 0.9241 (m-30) cc_final: 0.8782 (p0) REVERT: E 279 ASP cc_start: 0.9358 (m-30) cc_final: 0.9085 (m-30) REVERT: E 632 GLN cc_start: 0.8693 (mt0) cc_final: 0.8211 (tm-30) REVERT: E 795 MET cc_start: 0.9030 (mmt) cc_final: 0.8723 (mmt) REVERT: E 819 ASP cc_start: 0.8977 (m-30) cc_final: 0.8721 (m-30) REVERT: E 845 LYS cc_start: 0.9130 (mppt) cc_final: 0.8925 (mmmm) REVERT: E 848 LYS cc_start: 0.8952 (pttp) cc_final: 0.8300 (pttp) REVERT: E 921 MET cc_start: 0.8207 (mmt) cc_final: 0.7978 (mmt) REVERT: F 109 PHE cc_start: 0.8959 (m-10) cc_final: 0.8603 (m-80) REVERT: F 158 PHE cc_start: 0.8595 (t80) cc_final: 0.8160 (t80) REVERT: F 214 GLU cc_start: 0.8386 (tp30) cc_final: 0.8180 (tp30) REVERT: F 217 PHE cc_start: 0.7315 (m-80) cc_final: 0.5994 (t80) REVERT: F 260 ASP cc_start: 0.9334 (t0) cc_final: 0.8994 (t0) REVERT: F 279 ASP cc_start: 0.9323 (m-30) cc_final: 0.9025 (m-30) REVERT: F 458 MET cc_start: 0.8989 (tpp) cc_final: 0.8707 (tpp) REVERT: F 475 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8423 (ttm110) REVERT: F 531 GLU cc_start: 0.9238 (tp30) cc_final: 0.8989 (tp30) REVERT: F 632 GLN cc_start: 0.8489 (tm130) cc_final: 0.8272 (tm-30) REVERT: F 980 MET cc_start: 0.8221 (mmp) cc_final: 0.7929 (mmm) outliers start: 73 outliers final: 49 residues processed: 582 average time/residue: 0.4311 time to fit residues: 433.6585 Evaluate side-chains 522 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 470 time to evaluate : 4.273 ------------------------------------------------------------------------------- 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 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 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 983 THR Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 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 301 THR 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 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 188 optimal weight: 0.1980 chunk 1 optimal weight: 9.9990 chunk 551 optimal weight: 0.5980 chunk 531 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 328 optimal weight: 0.7980 chunk 451 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 123 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 994 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.095369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.064143 restraints weight = 126936.442| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.39 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 48234 Z= 0.145 Angle : 0.530 8.917 65292 Z= 0.275 Chirality : 0.037 0.179 7866 Planarity : 0.003 0.053 8112 Dihedral : 3.897 21.034 6204 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 2.18 % Allowed : 14.31 % Favored : 83.52 % 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: 1.63 (0.08), residues: 4230 sheet: None (None), residues: 0 loop : -1.02 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 146 HIS 0.002 0.000 HIS B 749 PHE 0.051 0.001 PHE B 89 TYR 0.033 0.001 TYR F 92 ARG 0.008 0.000 ARG C 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 680 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 561 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.8403 (t80) cc_final: 0.7891 (t80) REVERT: A 170 ARG cc_start: 0.9439 (mpp-170) cc_final: 0.9216 (mpp-170) REVERT: A 190 ARG cc_start: 0.8929 (tpm170) cc_final: 0.8685 (tpm170) REVERT: A 260 ASP cc_start: 0.9071 (t0) cc_final: 0.8830 (p0) REVERT: A 276 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9097 (m) REVERT: A 279 ASP cc_start: 0.9375 (m-30) cc_final: 0.9131 (m-30) REVERT: A 286 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8783 (mt-10) REVERT: A 467 MET cc_start: 0.8583 (tmm) cc_final: 0.8206 (tmm) REVERT: A 531 GLU cc_start: 0.9190 (tp30) cc_final: 0.8984 (tp30) REVERT: A 541 GLU cc_start: 0.7528 (pm20) cc_final: 0.7262 (mm-30) REVERT: A 804 MET cc_start: 0.8150 (mmt) cc_final: 0.7827 (mmt) REVERT: B 91 PHE cc_start: 0.9505 (m-80) cc_final: 0.9215 (m-80) REVERT: B 146 TRP cc_start: 0.9404 (m-90) cc_final: 0.9152 (m-90) REVERT: B 158 PHE cc_start: 0.8595 (t80) cc_final: 0.8057 (t80) REVERT: B 193 LEU cc_start: 0.9116 (tt) cc_final: 0.8787 (mm) REVERT: B 279 ASP cc_start: 0.9337 (m-30) cc_final: 0.9060 (m-30) REVERT: B 467 MET cc_start: 0.8718 (tmm) cc_final: 0.8448 (tmm) REVERT: B 471 MET cc_start: 0.8718 (mmp) cc_final: 0.8330 (mmp) REVERT: B 520 ASP cc_start: 0.8402 (t0) cc_final: 0.8140 (p0) REVERT: B 547 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8569 (mp) REVERT: B 652 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8740 (ttpp) REVERT: B 804 MET cc_start: 0.7461 (mmt) cc_final: 0.7245 (mmt) REVERT: B 819 ASP cc_start: 0.8957 (m-30) cc_final: 0.8714 (m-30) REVERT: B 834 PHE cc_start: 0.9168 (t80) cc_final: 0.8681 (t80) REVERT: C 158 PHE cc_start: 0.8502 (t80) cc_final: 0.8082 (t80) REVERT: C 214 GLU cc_start: 0.8288 (tp30) cc_final: 0.8026 (tp30) REVERT: C 217 PHE cc_start: 0.7215 (m-80) cc_final: 0.5770 (t80) REVERT: C 260 ASP cc_start: 0.9380 (t0) cc_final: 0.8930 (t0) REVERT: C 276 VAL cc_start: 0.9475 (OUTLIER) cc_final: 0.9083 (p) REVERT: C 279 ASP cc_start: 0.9326 (m-30) cc_final: 0.9051 (m-30) REVERT: C 286 GLU cc_start: 0.9407 (mp0) cc_final: 0.8836 (mp0) REVERT: C 531 GLU cc_start: 0.9216 (tp30) cc_final: 0.8968 (tp30) REVERT: D 92 TYR cc_start: 0.9184 (p90) cc_final: 0.8963 (p90) REVERT: D 158 PHE cc_start: 0.8705 (t80) cc_final: 0.8386 (t80) REVERT: D 177 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8876 (mp0) REVERT: D 193 LEU cc_start: 0.8951 (tt) cc_final: 0.8581 (mm) REVERT: D 215 ASP cc_start: 0.9202 (m-30) cc_final: 0.8538 (p0) REVERT: D 275 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8522 (p) REVERT: D 467 MET cc_start: 0.8583 (tmm) cc_final: 0.8197 (tmm) REVERT: D 804 MET cc_start: 0.8115 (mmt) cc_final: 0.7810 (mmt) REVERT: D 921 MET cc_start: 0.8483 (mmm) cc_final: 0.8021 (mmm) REVERT: E 92 TYR cc_start: 0.9332 (p90) cc_final: 0.9122 (p90) REVERT: E 158 PHE cc_start: 0.8572 (t80) cc_final: 0.8313 (t80) REVERT: E 177 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: E 215 ASP cc_start: 0.9244 (m-30) cc_final: 0.8688 (p0) REVERT: E 276 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8936 (p) REVERT: E 279 ASP cc_start: 0.9349 (m-30) cc_final: 0.9085 (m-30) REVERT: E 615 TYR cc_start: 0.8376 (t80) cc_final: 0.8160 (t80) REVERT: E 632 GLN cc_start: 0.8674 (mt0) cc_final: 0.8208 (tm-30) REVERT: E 795 MET cc_start: 0.8983 (mmt) cc_final: 0.8778 (mmt) REVERT: E 819 ASP cc_start: 0.8913 (m-30) cc_final: 0.8661 (m-30) REVERT: E 848 LYS cc_start: 0.8921 (pttp) cc_final: 0.8281 (pttp) REVERT: F 109 PHE cc_start: 0.8824 (m-10) cc_final: 0.8537 (m-80) REVERT: F 158 PHE cc_start: 0.8560 (t80) cc_final: 0.8143 (t80) REVERT: F 214 GLU cc_start: 0.8302 (tp30) cc_final: 0.8045 (tp30) REVERT: F 217 PHE cc_start: 0.7314 (m-80) cc_final: 0.6208 (t80) REVERT: F 260 ASP cc_start: 0.9366 (t0) cc_final: 0.8943 (t0) REVERT: F 276 VAL cc_start: 0.9437 (OUTLIER) cc_final: 0.9097 (m) REVERT: F 279 ASP cc_start: 0.9298 (m-30) cc_final: 0.8976 (m-30) REVERT: F 458 MET cc_start: 0.9050 (tpp) cc_final: 0.8785 (tpp) REVERT: F 531 GLU cc_start: 0.9193 (tp30) cc_final: 0.8934 (tp30) outliers start: 119 outliers final: 63 residues processed: 645 average time/residue: 0.4222 time to fit residues: 473.6260 Evaluate side-chains 571 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 499 time to evaluate : 4.322 ------------------------------------------------------------------------------- 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 538 GLU Chi-restraints excluded: chain A residue 555 LEU 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 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 481 VAL Chi-restraints excluded: chain B residue 547 ILE 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 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 276 VAL 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 834 PHE Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 910 ASP 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 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 555 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 177 GLU 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 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 839 MET 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 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 350 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 985 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 102 optimal weight: 0.9990 chunk 389 optimal weight: 0.8980 chunk 542 optimal weight: 4.9990 chunk 550 optimal weight: 0.8980 chunk 447 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 397 optimal weight: 7.9990 chunk 564 optimal weight: 6.9990 chunk 520 optimal weight: 6.9990 chunk 449 optimal weight: 0.7980 chunk 285 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 573 HIS D 93 GLN D 264 ASN E 93 GLN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.095120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063841 restraints weight = 126543.689| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.40 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 48234 Z= 0.155 Angle : 0.552 11.254 65292 Z= 0.281 Chirality : 0.038 0.302 7866 Planarity : 0.003 0.053 8112 Dihedral : 3.889 21.387 6204 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 2.32 % Allowed : 15.33 % Favored : 82.35 % 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: 1.63 (0.08), residues: 4242 sheet: None (None), residues: 0 loop : -1.03 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 146 HIS 0.003 0.000 HIS D 79 PHE 0.029 0.001 PHE E 89 TYR 0.037 0.001 TYR B 92 ARG 0.006 0.000 ARG C 475 *********************** 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 652 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 525 time to evaluate : 4.347 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 146 TRP cc_start: 0.9117 (m100) cc_final: 0.8730 (m100) REVERT: A 158 PHE cc_start: 0.8422 (t80) cc_final: 0.7863 (t80) REVERT: A 260 ASP cc_start: 0.9103 (t0) cc_final: 0.8819 (p0) REVERT: A 276 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.9084 (m) REVERT: A 279 ASP cc_start: 0.9373 (m-30) cc_final: 0.9122 (m-30) REVERT: A 286 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8781 (mt-10) REVERT: A 467 MET cc_start: 0.8582 (tmm) cc_final: 0.8192 (tmm) REVERT: A 531 GLU cc_start: 0.9194 (tp30) cc_final: 0.8989 (tp30) REVERT: A 541 GLU cc_start: 0.7494 (pm20) cc_final: 0.7233 (mm-30) REVERT: A 804 MET cc_start: 0.8152 (mmt) cc_final: 0.7846 (mmt) REVERT: A 921 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7242 (mmm) REVERT: B 146 TRP cc_start: 0.9398 (m-90) cc_final: 0.9158 (m-90) REVERT: B 158 PHE cc_start: 0.8584 (t80) cc_final: 0.8046 (t80) REVERT: B 193 LEU cc_start: 0.9115 (tt) cc_final: 0.8786 (mm) REVERT: B 279 ASP cc_start: 0.9327 (m-30) cc_final: 0.9046 (m-30) REVERT: B 310 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8011 (pp20) REVERT: B 467 MET cc_start: 0.8708 (tmm) cc_final: 0.8433 (tmm) REVERT: B 520 ASP cc_start: 0.8389 (t0) cc_final: 0.8139 (p0) REVERT: B 547 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 804 MET cc_start: 0.7467 (mmt) cc_final: 0.7248 (mmt) REVERT: B 819 ASP cc_start: 0.8946 (m-30) cc_final: 0.8704 (m-30) REVERT: B 834 PHE cc_start: 0.9170 (t80) cc_final: 0.8625 (t80) REVERT: C 158 PHE cc_start: 0.8443 (t80) cc_final: 0.8029 (t80) REVERT: C 214 GLU cc_start: 0.8303 (tp30) cc_final: 0.8049 (tp30) REVERT: C 217 PHE cc_start: 0.7239 (m-80) cc_final: 0.5920 (t80) REVERT: C 260 ASP cc_start: 0.9391 (t0) cc_final: 0.8982 (t0) REVERT: C 276 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9078 (p) REVERT: C 279 ASP cc_start: 0.9327 (m-30) cc_final: 0.9049 (m-30) REVERT: C 286 GLU cc_start: 0.9414 (mp0) cc_final: 0.8838 (mp0) REVERT: C 531 GLU cc_start: 0.9222 (tp30) cc_final: 0.8972 (tp30) REVERT: C 980 MET cc_start: 0.8067 (mmp) cc_final: 0.7835 (mmm) REVERT: D 158 PHE cc_start: 0.8710 (t80) cc_final: 0.8418 (t80) REVERT: D 177 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8878 (mp0) REVERT: D 193 LEU cc_start: 0.8942 (tt) cc_final: 0.8566 (mm) REVERT: D 215 ASP cc_start: 0.9232 (m-30) cc_final: 0.8591 (p0) REVERT: D 279 ASP cc_start: 0.9258 (m-30) cc_final: 0.8716 (p0) REVERT: D 467 MET cc_start: 0.8582 (tmm) cc_final: 0.8195 (tmm) REVERT: D 804 MET cc_start: 0.8103 (mmt) cc_final: 0.7815 (mmt) REVERT: D 921 MET cc_start: 0.8523 (mmm) cc_final: 0.8084 (mmm) REVERT: E 158 PHE cc_start: 0.8586 (t80) cc_final: 0.8296 (t80) REVERT: E 215 ASP cc_start: 0.9210 (m-30) cc_final: 0.8667 (p0) REVERT: E 276 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8901 (p) REVERT: E 279 ASP cc_start: 0.9322 (m-30) cc_final: 0.9048 (m-30) REVERT: E 520 ASP cc_start: 0.8482 (t0) cc_final: 0.8156 (p0) REVERT: E 632 GLN cc_start: 0.8716 (mt0) cc_final: 0.8238 (tm-30) REVERT: E 819 ASP cc_start: 0.8908 (m-30) cc_final: 0.8656 (m-30) REVERT: E 834 PHE cc_start: 0.9167 (t80) cc_final: 0.8673 (t80) REVERT: E 848 LYS cc_start: 0.8917 (pttp) cc_final: 0.8287 (pttp) REVERT: E 921 MET cc_start: 0.8052 (mmt) cc_final: 0.7783 (mmt) REVERT: E 934 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8336 (tt) REVERT: F 109 PHE cc_start: 0.8875 (m-10) cc_final: 0.8547 (m-80) REVERT: F 158 PHE cc_start: 0.8567 (t80) cc_final: 0.8146 (t80) REVERT: F 214 GLU cc_start: 0.8315 (tp30) cc_final: 0.8024 (tp30) REVERT: F 217 PHE cc_start: 0.7390 (m-80) cc_final: 0.6314 (t80) REVERT: F 260 ASP cc_start: 0.9381 (t0) cc_final: 0.8950 (t0) REVERT: F 276 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9120 (m) REVERT: F 279 ASP cc_start: 0.9296 (m-30) cc_final: 0.8970 (m-30) REVERT: F 458 MET cc_start: 0.9069 (tpp) cc_final: 0.8773 (tpp) REVERT: F 471 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8413 (mmm) REVERT: F 531 GLU cc_start: 0.9194 (tp30) cc_final: 0.8930 (tp30) outliers start: 127 outliers final: 75 residues processed: 619 average time/residue: 0.4130 time to fit residues: 447.3188 Evaluate side-chains 581 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 496 time to evaluate : 4.314 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 921 MET 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 269 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 547 ILE 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 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 471 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 573 HIS Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 910 ASP 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 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 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 840 ASP Chi-restraints excluded: chain D residue 919 LEU Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 115 MET 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 276 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 839 MET Chi-restraints excluded: chain E residue 934 LEU 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 182 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 471 MET 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 840 ASP Chi-restraints excluded: chain F residue 859 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 449 optimal weight: 4.9990 chunk 529 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 565 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 332 optimal weight: 0.0670 chunk 232 optimal weight: 0.9990 chunk 566 optimal weight: 0.9990 chunk 541 optimal weight: 4.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 573 HIS ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062373 restraints weight = 128372.401| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.38 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 48234 Z= 0.191 Angle : 0.571 14.345 65292 Z= 0.288 Chirality : 0.038 0.226 7866 Planarity : 0.003 0.053 8112 Dihedral : 3.912 23.897 6204 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 2.27 % Allowed : 16.23 % Favored : 81.50 % 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: 1.64 (0.08), residues: 4260 sheet: None (None), residues: 0 loop : -1.12 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 146 HIS 0.017 0.001 HIS C 573 PHE 0.044 0.001 PHE F 89 TYR 0.049 0.001 TYR D 92 ARG 0.010 0.000 ARG A 190 *********************** 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 630 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 506 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TRP cc_start: 0.9068 (m100) cc_final: 0.8664 (m100) REVERT: A 148 PHE cc_start: 0.9103 (m-10) cc_final: 0.8896 (m-10) REVERT: A 158 PHE cc_start: 0.8477 (t80) cc_final: 0.7949 (t80) REVERT: A 190 ARG cc_start: 0.8718 (tpm170) cc_final: 0.8512 (tpm170) REVERT: A 260 ASP cc_start: 0.9149 (t0) cc_final: 0.8862 (p0) REVERT: A 276 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9104 (m) REVERT: A 279 ASP cc_start: 0.9384 (m-30) cc_final: 0.9125 (m-30) REVERT: A 286 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8796 (mt-10) REVERT: A 467 MET cc_start: 0.8594 (tmm) cc_final: 0.8192 (tmm) REVERT: A 804 MET cc_start: 0.8138 (mmt) cc_final: 0.7826 (mmt) REVERT: B 158 PHE cc_start: 0.8640 (t80) cc_final: 0.8096 (t80) REVERT: B 193 LEU cc_start: 0.9084 (tt) cc_final: 0.8776 (mm) REVERT: B 279 ASP cc_start: 0.9365 (m-30) cc_final: 0.9057 (m-30) REVERT: B 310 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8164 (pp20) REVERT: B 471 MET cc_start: 0.8792 (mmp) cc_final: 0.8329 (mmm) REVERT: B 520 ASP cc_start: 0.8425 (t0) cc_final: 0.8122 (p0) REVERT: B 819 ASP cc_start: 0.8978 (m-30) cc_final: 0.8735 (m-30) REVERT: C 158 PHE cc_start: 0.8492 (t80) cc_final: 0.7951 (t80) REVERT: C 214 GLU cc_start: 0.8387 (tp30) cc_final: 0.8146 (tp30) REVERT: C 217 PHE cc_start: 0.7106 (m-80) cc_final: 0.5925 (t80) REVERT: C 260 ASP cc_start: 0.9419 (t0) cc_final: 0.8914 (t0) REVERT: C 276 VAL cc_start: 0.9480 (OUTLIER) cc_final: 0.9095 (p) REVERT: C 279 ASP cc_start: 0.9346 (m-30) cc_final: 0.9069 (m-30) REVERT: C 286 GLU cc_start: 0.9440 (mp0) cc_final: 0.8805 (mp0) REVERT: C 531 GLU cc_start: 0.9250 (tp30) cc_final: 0.8998 (tp30) REVERT: C 575 GLU cc_start: 0.9470 (pm20) cc_final: 0.9256 (pm20) REVERT: C 980 MET cc_start: 0.8063 (mmp) cc_final: 0.7809 (mmm) REVERT: D 153 LYS cc_start: 0.9685 (mmtt) cc_final: 0.9403 (mmtt) REVERT: D 158 PHE cc_start: 0.8754 (t80) cc_final: 0.8448 (t80) REVERT: D 177 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8873 (mp0) REVERT: D 193 LEU cc_start: 0.8915 (tt) cc_final: 0.8543 (mm) REVERT: D 467 MET cc_start: 0.8585 (tmm) cc_final: 0.8183 (tmm) REVERT: D 804 MET cc_start: 0.8076 (mmt) cc_final: 0.7837 (mmt) REVERT: D 921 MET cc_start: 0.8572 (mmm) cc_final: 0.8334 (tpt) REVERT: E 158 PHE cc_start: 0.8643 (t80) cc_final: 0.8341 (t80) REVERT: E 276 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8934 (p) REVERT: E 279 ASP cc_start: 0.9345 (m-30) cc_final: 0.9073 (m-30) REVERT: E 520 ASP cc_start: 0.8429 (t0) cc_final: 0.8114 (p0) REVERT: E 819 ASP cc_start: 0.8954 (m-30) cc_final: 0.8705 (m-30) REVERT: E 921 MET cc_start: 0.8209 (mmt) cc_final: 0.7876 (mmt) REVERT: E 934 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8285 (tt) REVERT: F 109 PHE cc_start: 0.8831 (m-10) cc_final: 0.8539 (m-80) REVERT: F 158 PHE cc_start: 0.8558 (t80) cc_final: 0.8152 (t80) REVERT: F 214 GLU cc_start: 0.8365 (tp30) cc_final: 0.8077 (tp30) REVERT: F 217 PHE cc_start: 0.7452 (m-80) cc_final: 0.6520 (t80) REVERT: F 260 ASP cc_start: 0.9414 (t0) cc_final: 0.9008 (t0) REVERT: F 276 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9043 (p) REVERT: F 279 ASP cc_start: 0.9322 (m-30) cc_final: 0.8998 (m-30) REVERT: F 458 MET cc_start: 0.9097 (tpp) cc_final: 0.8768 (tpp) REVERT: F 471 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8369 (mmm) REVERT: F 531 GLU cc_start: 0.9237 (tp30) cc_final: 0.8983 (tp30) REVERT: F 980 MET cc_start: 0.8226 (mmp) cc_final: 0.7833 (mpp) outliers start: 124 outliers final: 89 residues processed: 596 average time/residue: 0.4227 time to fit residues: 436.8358 Evaluate side-chains 570 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 473 time to evaluate : 4.298 ------------------------------------------------------------------------------- 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 243 LEU 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 538 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 840 ASP 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 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 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 276 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 573 HIS 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 910 ASP 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 105 VAL Chi-restraints excluded: chain D residue 177 GLU 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 840 ASP Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 115 MET 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 267 ASP 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 934 LEU 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 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 471 MET 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 840 ASP 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 235 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 587 optimal weight: 2.9990 chunk 545 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 505 optimal weight: 0.7980 chunk 508 optimal weight: 3.9990 chunk 551 optimal weight: 0.0170 chunk 147 optimal weight: 8.9990 chunk 575 optimal weight: 10.0000 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS D 264 ASN E 79 HIS E 138 GLN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.093225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061629 restraints weight = 128511.930| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.37 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 48234 Z= 0.202 Angle : 0.580 11.245 65292 Z= 0.292 Chirality : 0.039 0.223 7866 Planarity : 0.003 0.052 8112 Dihedral : 3.962 27.451 6204 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 16.72 % Favored : 80.79 % 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: 1.32 (0.11), residues: 5856 helix: 1.62 (0.08), residues: 4278 sheet: None (None), residues: 0 loop : -1.18 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 146 HIS 0.031 0.001 HIS C 573 PHE 0.022 0.001 PHE C 363 TYR 0.038 0.001 TYR F 92 ARG 0.007 0.000 ARG A 170 *********************** 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 636 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 500 time to evaluate : 4.415 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 128 ARG cc_start: 0.9277 (mmm160) cc_final: 0.9050 (mmm160) REVERT: A 148 PHE cc_start: 0.9078 (m-10) cc_final: 0.8846 (m-10) REVERT: A 158 PHE cc_start: 0.8433 (t80) cc_final: 0.7915 (t80) REVERT: A 190 ARG cc_start: 0.8763 (tpm170) cc_final: 0.8429 (tpm170) REVERT: A 260 ASP cc_start: 0.9174 (t0) cc_final: 0.8861 (p0) REVERT: A 276 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9097 (m) REVERT: A 279 ASP cc_start: 0.9395 (m-30) cc_final: 0.9125 (m-30) REVERT: A 286 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8807 (mt-10) REVERT: A 310 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8100 (pp20) REVERT: A 467 MET cc_start: 0.8579 (tmm) cc_final: 0.8166 (tmm) REVERT: A 541 GLU cc_start: 0.7564 (pm20) cc_final: 0.7274 (mm-30) REVERT: A 804 MET cc_start: 0.8185 (mmt) cc_final: 0.7866 (mmt) REVERT: B 91 PHE cc_start: 0.9495 (m-80) cc_final: 0.9207 (m-80) REVERT: B 158 PHE cc_start: 0.8649 (t80) cc_final: 0.8107 (t80) REVERT: B 193 LEU cc_start: 0.9028 (tt) cc_final: 0.8724 (mm) REVERT: B 279 ASP cc_start: 0.9364 (m-30) cc_final: 0.9055 (m-30) REVERT: B 310 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8161 (pp20) REVERT: B 520 ASP cc_start: 0.8420 (t0) cc_final: 0.8191 (p0) REVERT: B 819 ASP cc_start: 0.8972 (m-30) cc_final: 0.8727 (m-30) REVERT: C 158 PHE cc_start: 0.8474 (t80) cc_final: 0.7942 (t80) REVERT: C 214 GLU cc_start: 0.8450 (tp30) cc_final: 0.8245 (tp30) REVERT: C 217 PHE cc_start: 0.7012 (m-80) cc_final: 0.5908 (t80) REVERT: C 260 ASP cc_start: 0.9422 (t0) cc_final: 0.8895 (t0) REVERT: C 276 VAL cc_start: 0.9477 (OUTLIER) cc_final: 0.9093 (p) REVERT: C 279 ASP cc_start: 0.9343 (m-30) cc_final: 0.9074 (m-30) REVERT: C 286 GLU cc_start: 0.9450 (mp0) cc_final: 0.8808 (mp0) REVERT: C 531 GLU cc_start: 0.9256 (tp30) cc_final: 0.9022 (tp30) REVERT: C 575 GLU cc_start: 0.9453 (pm20) cc_final: 0.9199 (pm20) REVERT: C 980 MET cc_start: 0.8083 (mmp) cc_final: 0.7817 (mmm) REVERT: D 153 LYS cc_start: 0.9691 (mmtt) cc_final: 0.9427 (mmtt) REVERT: D 158 PHE cc_start: 0.8768 (t80) cc_final: 0.8447 (t80) REVERT: D 193 LEU cc_start: 0.8927 (tt) cc_final: 0.8559 (mm) REVERT: D 279 ASP cc_start: 0.9222 (m-30) cc_final: 0.8679 (p0) REVERT: D 467 MET cc_start: 0.8589 (tmm) cc_final: 0.8178 (tmm) REVERT: D 804 MET cc_start: 0.8086 (mmt) cc_final: 0.7859 (mmt) REVERT: D 921 MET cc_start: 0.8653 (mmm) cc_final: 0.8423 (tpt) REVERT: E 158 PHE cc_start: 0.8660 (t80) cc_final: 0.8359 (t80) REVERT: E 276 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8922 (p) REVERT: E 279 ASP cc_start: 0.9349 (m-30) cc_final: 0.9077 (m-30) REVERT: E 520 ASP cc_start: 0.8485 (t0) cc_final: 0.8144 (p0) REVERT: E 819 ASP cc_start: 0.8955 (m-30) cc_final: 0.8710 (m-30) REVERT: E 921 MET cc_start: 0.8363 (mmt) cc_final: 0.8053 (mmt) REVERT: E 934 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8308 (tt) REVERT: E 987 LEU cc_start: 0.8340 (mm) cc_final: 0.8126 (tt) REVERT: F 109 PHE cc_start: 0.8944 (m-10) cc_final: 0.8563 (m-80) REVERT: F 158 PHE cc_start: 0.8575 (t80) cc_final: 0.8167 (t80) REVERT: F 214 GLU cc_start: 0.8407 (tp30) cc_final: 0.8128 (tp30) REVERT: F 217 PHE cc_start: 0.7287 (m-80) cc_final: 0.6467 (t80) REVERT: F 260 ASP cc_start: 0.9414 (t0) cc_final: 0.8999 (t0) REVERT: F 276 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9047 (p) REVERT: F 279 ASP cc_start: 0.9323 (m-30) cc_final: 0.8997 (m-30) REVERT: F 458 MET cc_start: 0.9120 (tpp) cc_final: 0.8751 (tpp) REVERT: F 531 GLU cc_start: 0.9204 (tp30) cc_final: 0.8956 (tp30) outliers start: 136 outliers final: 91 residues processed: 594 average time/residue: 0.4253 time to fit residues: 439.3545 Evaluate side-chains 559 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 462 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 243 LEU 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 538 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 840 ASP 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 245 THR 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 840 ASP Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 977 LEU 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 276 VAL Chi-restraints excluded: chain C residue 301 THR 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 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 938 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 656 ILE Chi-restraints excluded: chain D residue 840 ASP 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 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 267 ASP 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 839 MET Chi-restraints excluded: chain E residue 840 ASP Chi-restraints excluded: chain E residue 934 LEU 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 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 555 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 834 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 213 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 414 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 186 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS D 172 ASN ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062276 restraints weight = 127462.027| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.39 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48234 Z= 0.169 Angle : 0.583 11.425 65292 Z= 0.292 Chirality : 0.039 0.321 7866 Planarity : 0.003 0.055 8112 Dihedral : 3.950 26.391 6204 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.20 % Allowed : 17.54 % Favored : 80.26 % 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: 1.34 (0.11), residues: 5856 helix: 1.62 (0.08), residues: 4266 sheet: None (None), residues: 0 loop : -1.13 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 146 HIS 0.003 0.000 HIS A 79 PHE 0.033 0.001 PHE C 89 TYR 0.041 0.001 TYR B 92 ARG 0.004 0.000 ARG F 475 *********************** 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 615 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 495 time to evaluate : 4.383 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 128 ARG cc_start: 0.9295 (mmm160) cc_final: 0.9060 (mmm160) REVERT: A 146 TRP cc_start: 0.8985 (m100) cc_final: 0.8623 (m100) REVERT: A 148 PHE cc_start: 0.9067 (m-10) cc_final: 0.8820 (m-10) REVERT: A 158 PHE cc_start: 0.8455 (t80) cc_final: 0.7934 (t80) REVERT: A 190 ARG cc_start: 0.8835 (tpm170) cc_final: 0.8553 (tpm170) REVERT: A 260 ASP cc_start: 0.9144 (t0) cc_final: 0.8845 (p0) REVERT: A 276 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9105 (m) REVERT: A 279 ASP cc_start: 0.9383 (m-30) cc_final: 0.9103 (m-30) REVERT: A 310 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8061 (pp20) REVERT: A 467 MET cc_start: 0.8571 (tmm) cc_final: 0.8156 (tmm) REVERT: A 541 GLU cc_start: 0.7518 (pm20) cc_final: 0.7235 (mm-30) REVERT: A 804 MET cc_start: 0.8158 (mmt) cc_final: 0.7870 (mmt) REVERT: B 158 PHE cc_start: 0.8657 (t80) cc_final: 0.8020 (t80) REVERT: B 193 LEU cc_start: 0.9022 (tt) cc_final: 0.8710 (mt) REVERT: B 279 ASP cc_start: 0.9356 (m-30) cc_final: 0.9043 (m-30) REVERT: B 310 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8108 (pp20) REVERT: B 471 MET cc_start: 0.8799 (mmp) cc_final: 0.8483 (mmm) REVERT: B 531 GLU cc_start: 0.9161 (tp30) cc_final: 0.8957 (tp30) REVERT: B 819 ASP cc_start: 0.8963 (m-30) cc_final: 0.8716 (m-30) REVERT: C 158 PHE cc_start: 0.8449 (t80) cc_final: 0.7925 (t80) REVERT: C 214 GLU cc_start: 0.8410 (tp30) cc_final: 0.8204 (tp30) REVERT: C 217 PHE cc_start: 0.6932 (m-80) cc_final: 0.5847 (t80) REVERT: C 260 ASP cc_start: 0.9382 (t0) cc_final: 0.8860 (t0) REVERT: C 276 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9060 (p) REVERT: C 279 ASP cc_start: 0.9340 (m-30) cc_final: 0.9064 (m-30) REVERT: C 531 GLU cc_start: 0.9250 (tp30) cc_final: 0.9013 (tp30) REVERT: C 575 GLU cc_start: 0.9437 (pm20) cc_final: 0.9196 (pm20) REVERT: C 980 MET cc_start: 0.8034 (mmp) cc_final: 0.7748 (mmm) REVERT: D 158 PHE cc_start: 0.8761 (t80) cc_final: 0.8433 (t80) REVERT: D 193 LEU cc_start: 0.8924 (tt) cc_final: 0.8573 (mm) REVERT: D 467 MET cc_start: 0.8583 (tmm) cc_final: 0.8206 (tmm) REVERT: D 804 MET cc_start: 0.8052 (mmt) cc_final: 0.7838 (mmt) REVERT: D 921 MET cc_start: 0.8665 (mmm) cc_final: 0.8402 (tpt) REVERT: E 158 PHE cc_start: 0.8688 (t80) cc_final: 0.8390 (t80) REVERT: E 276 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8894 (p) REVERT: E 279 ASP cc_start: 0.9337 (m-30) cc_final: 0.9062 (m-30) REVERT: E 520 ASP cc_start: 0.8443 (t0) cc_final: 0.8152 (p0) REVERT: E 674 SER cc_start: 0.9385 (m) cc_final: 0.9174 (p) REVERT: E 819 ASP cc_start: 0.8946 (m-30) cc_final: 0.8696 (m-30) REVERT: E 921 MET cc_start: 0.8389 (mmt) cc_final: 0.8094 (mmt) REVERT: E 987 LEU cc_start: 0.8316 (mm) cc_final: 0.8106 (tt) REVERT: F 109 PHE cc_start: 0.8981 (m-10) cc_final: 0.8551 (m-80) REVERT: F 158 PHE cc_start: 0.8617 (t80) cc_final: 0.8210 (t80) REVERT: F 214 GLU cc_start: 0.8373 (tp30) cc_final: 0.8160 (tp30) REVERT: F 217 PHE cc_start: 0.7188 (m-80) cc_final: 0.6394 (t80) REVERT: F 260 ASP cc_start: 0.9347 (t0) cc_final: 0.8971 (t0) REVERT: F 276 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9021 (p) REVERT: F 279 ASP cc_start: 0.9313 (m-30) cc_final: 0.8983 (m-30) REVERT: F 458 MET cc_start: 0.9129 (tpp) cc_final: 0.8754 (tpp) REVERT: F 471 MET cc_start: 0.8573 (mmm) cc_final: 0.8126 (mmm) REVERT: F 505 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: F 531 GLU cc_start: 0.9207 (tp30) cc_final: 0.8956 (tp30) REVERT: F 980 MET cc_start: 0.8169 (mmp) cc_final: 0.7552 (mpp) outliers start: 120 outliers final: 88 residues processed: 581 average time/residue: 0.4248 time to fit residues: 431.6825 Evaluate side-chains 566 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 473 time to evaluate : 4.342 ------------------------------------------------------------------------------- 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 243 LEU 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 538 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 840 ASP 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 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 657 ILE 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 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 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 910 ASP Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 938 THR 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 267 ASP 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 582 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 919 LEU 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 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 267 ASP 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 839 MET Chi-restraints excluded: chain E residue 840 ASP 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 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 505 GLU 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 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 11 optimal weight: 0.9980 chunk 416 optimal weight: 9.9990 chunk 485 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 524 optimal weight: 0.3980 chunk 167 optimal weight: 0.0970 chunk 450 optimal weight: 0.8980 chunk 311 optimal weight: 10.0000 chunk 498 optimal weight: 6.9990 chunk 245 optimal weight: 0.7980 chunk 191 optimal weight: 0.1980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 16 ASN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.095520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063945 restraints weight = 127400.610| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.44 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 48234 Z= 0.148 Angle : 0.584 10.829 65292 Z= 0.291 Chirality : 0.039 0.270 7866 Planarity : 0.003 0.057 8112 Dihedral : 3.903 23.693 6204 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.79 % Allowed : 18.13 % Favored : 80.08 % 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: 1.35 (0.11), residues: 5856 helix: 1.64 (0.08), residues: 4248 sheet: None (None), residues: 0 loop : -1.11 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 146 HIS 0.003 0.000 HIS F 941 PHE 0.029 0.001 PHE B 363 TYR 0.032 0.001 TYR C 92 ARG 0.003 0.000 ARG C 475 *********************** 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 656 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 558 time to evaluate : 4.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TRP cc_start: 0.8970 (m100) cc_final: 0.8596 (m100) REVERT: A 158 PHE cc_start: 0.8392 (t80) cc_final: 0.7879 (t80) REVERT: A 190 ARG cc_start: 0.8880 (tpm170) cc_final: 0.8645 (tpm170) REVERT: A 260 ASP cc_start: 0.9135 (t0) cc_final: 0.8877 (p0) REVERT: A 276 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9068 (m) REVERT: A 279 ASP cc_start: 0.9345 (m-30) cc_final: 0.9054 (m-30) REVERT: A 286 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8764 (mt-10) REVERT: A 310 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8044 (pp20) REVERT: A 467 MET cc_start: 0.8561 (tmm) cc_final: 0.8164 (tmm) REVERT: A 723 LEU cc_start: 0.9343 (mt) cc_final: 0.9140 (mt) REVERT: A 804 MET cc_start: 0.8103 (mmt) cc_final: 0.7835 (mmt) REVERT: B 158 PHE cc_start: 0.8578 (t80) cc_final: 0.7978 (t80) REVERT: B 193 LEU cc_start: 0.8955 (tt) cc_final: 0.8656 (mm) REVERT: B 279 ASP cc_start: 0.9335 (m-30) cc_final: 0.9016 (m-30) REVERT: B 310 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8102 (pp20) REVERT: B 564 ILE cc_start: 0.6712 (mm) cc_final: 0.6468 (mm) REVERT: B 819 ASP cc_start: 0.8897 (m-30) cc_final: 0.8650 (m-30) REVERT: B 1024 TYR cc_start: 0.8706 (t80) cc_final: 0.8467 (t80) REVERT: C 158 PHE cc_start: 0.8394 (t80) cc_final: 0.7880 (t80) REVERT: C 217 PHE cc_start: 0.6885 (m-80) cc_final: 0.6105 (t80) REVERT: C 260 ASP cc_start: 0.9354 (t0) cc_final: 0.8925 (t0) REVERT: C 276 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9047 (p) REVERT: C 279 ASP cc_start: 0.9317 (m-30) cc_final: 0.9018 (m-30) REVERT: C 531 GLU cc_start: 0.9228 (tp30) cc_final: 0.8992 (tp30) REVERT: C 575 GLU cc_start: 0.9405 (pm20) cc_final: 0.9169 (pm20) REVERT: D 153 LYS cc_start: 0.9672 (mmtt) cc_final: 0.9433 (mmtt) REVERT: D 158 PHE cc_start: 0.8729 (t80) cc_final: 0.8417 (t80) REVERT: D 193 LEU cc_start: 0.8905 (tt) cc_final: 0.8543 (mm) REVERT: D 467 MET cc_start: 0.8577 (tmm) cc_final: 0.8193 (tmm) REVERT: D 804 MET cc_start: 0.8071 (mmt) cc_final: 0.7830 (mmt) REVERT: E 158 PHE cc_start: 0.8603 (t80) cc_final: 0.8308 (t80) REVERT: E 276 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8827 (p) REVERT: E 279 ASP cc_start: 0.9324 (m-30) cc_final: 0.9044 (m-30) REVERT: E 520 ASP cc_start: 0.8438 (t0) cc_final: 0.8119 (p0) REVERT: E 632 GLN cc_start: 0.8763 (mt0) cc_final: 0.8297 (tm-30) REVERT: E 674 SER cc_start: 0.9367 (m) cc_final: 0.9149 (p) REVERT: E 793 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8633 (mm-30) REVERT: E 819 ASP cc_start: 0.8896 (m-30) cc_final: 0.8638 (m-30) REVERT: E 839 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7751 (ttp) REVERT: E 921 MET cc_start: 0.8350 (mmt) cc_final: 0.8084 (mmt) REVERT: F 109 PHE cc_start: 0.9003 (m-10) cc_final: 0.8685 (m-80) REVERT: F 158 PHE cc_start: 0.8661 (t80) cc_final: 0.8256 (t80) REVERT: F 214 GLU cc_start: 0.8319 (tp30) cc_final: 0.8071 (tp30) REVERT: F 217 PHE cc_start: 0.7278 (m-80) cc_final: 0.6395 (t80) REVERT: F 260 ASP cc_start: 0.9304 (t0) cc_final: 0.8946 (t0) REVERT: F 276 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9002 (p) REVERT: F 279 ASP cc_start: 0.9299 (m-30) cc_final: 0.8964 (m-30) REVERT: F 458 MET cc_start: 0.9132 (tpp) cc_final: 0.8816 (tpp) REVERT: F 471 MET cc_start: 0.8585 (mmm) cc_final: 0.8121 (mmm) REVERT: F 505 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: F 531 GLU cc_start: 0.9176 (tp30) cc_final: 0.8919 (tp30) outliers start: 98 outliers final: 78 residues processed: 626 average time/residue: 0.4180 time to fit residues: 455.5591 Evaluate side-chains 590 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 505 time to evaluate : 4.262 ------------------------------------------------------------------------------- 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 243 LEU 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 538 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 840 ASP 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 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 481 VAL 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 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 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 378 PHE Chi-restraints excluded: chain D residue 555 LEU 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 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 267 ASP 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 839 MET Chi-restraints excluded: chain E residue 840 ASP 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 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 505 GLU 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 840 ASP Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 354 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 188 optimal weight: 0.0470 chunk 127 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 536 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 569 optimal weight: 6.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 264 ASN E 79 HIS F 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.093785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062186 restraints weight = 128138.801| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.37 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2598 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= 0.197 Angle : 0.609 10.456 65292 Z= 0.305 Chirality : 0.039 0.243 7866 Planarity : 0.003 0.054 8112 Dihedral : 3.963 25.795 6204 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 1.68 % Allowed : 18.68 % Favored : 79.64 % 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: 1.37 (0.11), residues: 5856 helix: 1.65 (0.08), residues: 4266 sheet: None (None), residues: 0 loop : -1.13 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 146 HIS 0.003 0.001 HIS A 79 PHE 0.044 0.001 PHE E 89 TYR 0.042 0.001 TYR B 92 ARG 0.007 0.000 ARG B 475 ********************** 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 577 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 485 time to evaluate : 4.359 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: 0.8954 (m100) cc_final: 0.8574 (m100) REVERT: A 158 PHE cc_start: 0.8438 (t80) cc_final: 0.7929 (t80) REVERT: A 260 ASP cc_start: 0.9188 (t0) cc_final: 0.8921 (p0) REVERT: A 276 VAL cc_start: 0.9426 (OUTLIER) cc_final: 0.9092 (m) REVERT: A 279 ASP cc_start: 0.9371 (m-30) cc_final: 0.9086 (m-30) REVERT: A 467 MET cc_start: 0.8577 (tmm) cc_final: 0.8157 (tmm) REVERT: A 804 MET cc_start: 0.8169 (mmt) cc_final: 0.7909 (mmt) REVERT: B 158 PHE cc_start: 0.8633 (t80) cc_final: 0.8029 (t80) REVERT: B 193 LEU cc_start: 0.9010 (tt) cc_final: 0.8698 (mt) REVERT: B 279 ASP cc_start: 0.9346 (m-30) cc_final: 0.9034 (m-30) REVERT: B 531 GLU cc_start: 0.9153 (tp30) cc_final: 0.8951 (tp30) REVERT: B 819 ASP cc_start: 0.8943 (m-30) cc_final: 0.8705 (m-30) REVERT: B 1024 TYR cc_start: 0.8733 (t80) cc_final: 0.8497 (t80) REVERT: C 158 PHE cc_start: 0.8459 (t80) cc_final: 0.7937 (t80) REVERT: C 217 PHE cc_start: 0.7068 (m-80) cc_final: 0.6308 (t80) REVERT: C 260 ASP cc_start: 0.9358 (t0) cc_final: 0.8893 (t0) REVERT: C 276 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9059 (p) REVERT: C 279 ASP cc_start: 0.9319 (m-30) cc_final: 0.9033 (m-30) REVERT: C 531 GLU cc_start: 0.9233 (tp30) cc_final: 0.8997 (tp30) REVERT: C 575 GLU cc_start: 0.9419 (pm20) cc_final: 0.9184 (pm20) REVERT: D 158 PHE cc_start: 0.8728 (t80) cc_final: 0.8419 (t80) REVERT: D 193 LEU cc_start: 0.8904 (tt) cc_final: 0.8547 (mm) REVERT: D 467 MET cc_start: 0.8575 (tmm) cc_final: 0.8158 (tmm) REVERT: D 804 MET cc_start: 0.8096 (mmt) cc_final: 0.7894 (mmt) REVERT: D 987 LEU cc_start: 0.8436 (mm) cc_final: 0.8123 (tt) REVERT: E 158 PHE cc_start: 0.8638 (t80) cc_final: 0.8356 (t80) REVERT: E 276 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8882 (p) REVERT: E 279 ASP cc_start: 0.9334 (m-30) cc_final: 0.9057 (m-30) REVERT: E 520 ASP cc_start: 0.8413 (t0) cc_final: 0.8150 (p0) REVERT: E 632 GLN cc_start: 0.8797 (mt0) cc_final: 0.8307 (tm-30) REVERT: E 674 SER cc_start: 0.9379 (m) cc_final: 0.9169 (p) REVERT: E 819 ASP cc_start: 0.8942 (m-30) cc_final: 0.8692 (m-30) REVERT: E 921 MET cc_start: 0.8423 (mmt) cc_final: 0.8154 (mmt) REVERT: F 158 PHE cc_start: 0.8681 (t80) cc_final: 0.8278 (t80) REVERT: F 214 GLU cc_start: 0.8426 (tp30) cc_final: 0.8136 (tp30) REVERT: F 217 PHE cc_start: 0.7031 (m-80) cc_final: 0.6410 (t80) REVERT: F 260 ASP cc_start: 0.9375 (t0) cc_final: 0.9010 (t0) REVERT: F 276 VAL cc_start: 0.9437 (OUTLIER) cc_final: 0.9025 (p) REVERT: F 279 ASP cc_start: 0.9311 (m-30) cc_final: 0.8979 (m-30) REVERT: F 286 GLU cc_start: 0.9526 (mm-30) cc_final: 0.8945 (mp0) REVERT: F 458 MET cc_start: 0.9151 (tpp) cc_final: 0.8822 (tpp) REVERT: F 471 MET cc_start: 0.8579 (mmm) cc_final: 0.8143 (mmm) REVERT: F 505 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: F 531 GLU cc_start: 0.9205 (tp30) cc_final: 0.8957 (tp30) outliers start: 92 outliers final: 79 residues processed: 555 average time/residue: 0.4202 time to fit residues: 406.9315 Evaluate side-chains 556 residues out of total 5466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 472 time to evaluate : 4.284 ------------------------------------------------------------------------------- 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 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 538 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 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 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 657 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 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 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 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 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 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 267 ASP 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 839 MET Chi-restraints excluded: chain E residue 840 ASP 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 505 GLU 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 840 ASP Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 307 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 330 optimal weight: 1.9990 chunk 456 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 415 optimal weight: 0.9990 chunk 78 optimal weight: 0.0050 chunk 61 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 770 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.094229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062624 restraints weight = 127108.647| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 4.37 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 48234 Z= 0.171 Angle : 0.605 11.892 65292 Z= 0.303 Chirality : 0.039 0.211 7866 Planarity : 0.003 0.054 8112 Dihedral : 3.972 24.912 6204 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 1.66 % Allowed : 18.59 % Favored : 79.75 % 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: 1.66 (0.08), residues: 4248 sheet: None (None), residues: 0 loop : -1.14 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 146 HIS 0.003 0.000 HIS F 941 PHE 0.031 0.001 PHE B 500 TYR 0.048 0.001 TYR B 92 ARG 0.011 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17619.93 seconds wall clock time: 305 minutes 3.11 seconds (18303.11 seconds total)