Starting phenix.real_space_refine on Mon May 26 15:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8taz_41143/05_2025/8taz_41143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8taz_41143/05_2025/8taz_41143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8taz_41143/05_2025/8taz_41143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8taz_41143/05_2025/8taz_41143.map" model { file = "/net/cci-nas-00/data/ceres_data/8taz_41143/05_2025/8taz_41143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8taz_41143/05_2025/8taz_41143.cif" } resolution = 3.75 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 18042 2.51 5 N 4722 2.21 5 O 5370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28269 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8291 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 58, 'TRANS': 1003} Chain breaks: 7 Chain: "B" Number of atoms: 8312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8312 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 58, 'TRANS': 1006} Chain breaks: 7 Chain: "C" Number of atoms: 6755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6755 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 47, 'TRANS': 820} Chain breaks: 8 Chain: "D" Number of atoms: 4911 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Conformer: "B" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} bond proxies already assigned to first conformer: 5038 Time building chain proxies: 17.37, per 1000 atoms: 0.61 Number of scatterers: 28269 At special positions: 0 Unit cell: (142.08, 155.4, 246.42, 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 135 16.00 O 5370 8.00 N 4722 7.00 C 18042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.07 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.04 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: 6.16 Conformation dependent library (CDL) restraints added in 3.8 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6752 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 43 sheets defined 30.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.284A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.274A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.539A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.725A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.331A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.631A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.505A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.223A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.671A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.504A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.613A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.664A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.538A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.874A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.201A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.083A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 4.067A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.094A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.042A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.817A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.353A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.881A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.105A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.134A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.736A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.289A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.820A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 4.492A pdb=" N LEU D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 68 through 83 removed outlier: 4.422A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.613A pdb=" N GLN D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 171 Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.879A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.682A pdb=" N ASP D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.740A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 249 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.415A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.742A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 406 through 414 removed outlier: 3.696A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.772A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.798A pdb=" N GLU D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.222A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 549 No H-bonds generated for 'chain 'D' and resid 547 through 549' Processing helix chain 'D' and resid 550 through 555 Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.544A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.520A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.115A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.004A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 3.929A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 67 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.769A pdb=" N LEU A 82 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 238 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.769A pdb=" N LEU A 82 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 238 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.246A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 326 removed outlier: 3.519A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.724A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.991A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.587A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.372A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.126A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.551A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.926A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.926A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.228A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.561A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.751A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.268A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 192 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 194 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 88 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.232A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.525A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.405A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.609A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.314A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.002A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.002A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.577A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.995A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 194 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 88 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.943A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.098A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.375A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.882A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.882A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.664A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 348 removed outlier: 3.545A pdb=" N LYS D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.64 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.31: 4678 1.31 - 1.84: 24258 1.84 - 2.36: 10 2.36 - 2.88: 0 2.88 - 3.40: 1 Bond restraints: 28947 Sorted by residual: bond pdb=" CB ARG D 245 " pdb=" CG ARG D 245 " ideal model delta sigma weight residual 1.520 3.403 -1.883 3.00e-02 1.11e+03 3.94e+03 bond pdb=" CB LEU D 444 " pdb=" CG LEU D 444 " ideal model delta sigma weight residual 1.530 2.294 -0.764 2.00e-02 2.50e+03 1.46e+03 bond pdb=" CD1 TYR D 279 " pdb=" CE1 TYR D 279 " ideal model delta sigma weight residual 1.382 2.342 -0.960 3.00e-02 1.11e+03 1.02e+03 bond pdb=" CD2 TYR D 279 " pdb=" CE2 TYR D 279 " ideal model delta sigma weight residual 1.382 2.326 -0.944 3.00e-02 1.11e+03 9.90e+02 bond pdb=" CE1 TYR D 279 " pdb=" CZ TYR D 279 " ideal model delta sigma weight residual 1.378 1.953 -0.575 2.40e-02 1.74e+03 5.73e+02 ... (remaining 28942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.05: 39367 9.05 - 18.10: 22 18.10 - 27.15: 7 27.15 - 36.20: 0 36.20 - 45.25: 1 Bond angle restraints: 39397 Sorted by residual: angle pdb=" CA PRO D 590 " pdb=" N PRO D 590 " pdb=" CD PRO D 590 " ideal model delta sigma weight residual 112.00 91.99 20.01 1.40e+00 5.10e-01 2.04e+02 angle pdb=" N PRO D 590 " pdb=" CD PRO D 590 " pdb=" CG PRO D 590 " ideal model delta sigma weight residual 103.20 81.98 21.22 1.50e+00 4.44e-01 2.00e+02 angle pdb=" CA LEU D 444 " pdb=" CB LEU D 444 " pdb=" CG LEU D 444 " ideal model delta sigma weight residual 116.30 161.55 -45.25 3.50e+00 8.16e-02 1.67e+02 angle pdb=" CA PRO D 469 " pdb=" N PRO D 469 " pdb=" CD PRO D 469 " ideal model delta sigma weight residual 112.00 97.73 14.27 1.40e+00 5.10e-01 1.04e+02 angle pdb=" N PRO D 590 " pdb=" CA PRO D 590 " pdb=" CB PRO D 590 " ideal model delta sigma weight residual 103.25 92.85 10.40 1.05e+00 9.07e-01 9.81e+01 ... (remaining 39392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 15139 17.61 - 35.23: 1719 35.23 - 52.84: 325 52.84 - 70.45: 66 70.45 - 88.07: 36 Dihedral angle restraints: 17285 sinusoidal: 6818 harmonic: 10467 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual -86.00 1.42 -87.42 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CA TYR D 497 " pdb=" C TYR D 497 " pdb=" N CYS D 498 " pdb=" CA CYS D 498 " ideal model delta harmonic sigma weight residual -180.00 -133.48 -46.52 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.39 -76.61 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 17282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 4419 0.202 - 0.405: 2 0.405 - 0.607: 1 0.607 - 0.809: 0 0.809 - 1.011: 1 Chirality restraints: 4423 Sorted by residual: chirality pdb=" CG LEU D 444 " pdb=" CB LEU D 444 " pdb=" CD1 LEU D 444 " pdb=" CD2 LEU D 444 " both_signs ideal model delta sigma weight residual False -2.59 -1.58 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA PRO D 590 " pdb=" N PRO D 590 " pdb=" C PRO D 590 " pdb=" CB PRO D 590 " both_signs ideal model delta sigma weight residual False 2.72 2.22 0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" CB ILE D 119 " pdb=" CA ILE D 119 " pdb=" CG1 ILE D 119 " pdb=" CG2 ILE D 119 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 4420 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.102 5.00e-02 4.00e+02 1.56e-01 3.87e+01 pdb=" N PRO D 500 " 0.269 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 589 " 0.103 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO D 590 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO D 590 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 590 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 468 " -0.084 5.00e-02 4.00e+02 1.16e-01 2.17e+01 pdb=" N PRO D 469 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " -0.063 5.00e-02 4.00e+02 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 679 2.67 - 3.23: 27616 3.23 - 3.79: 42580 3.79 - 4.34: 54492 4.34 - 4.90: 88436 Nonbonded interactions: 213803 Sorted by model distance: nonbonded pdb=" O PHE D 588 " pdb=" N PHE D 592 " model vdw 2.119 3.120 nonbonded pdb=" O ILE A 197 " pdb=" NZ LYS A 202 " model vdw 2.132 3.120 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.154 3.040 nonbonded pdb=" CE2 TYR D 279 " pdb=" CB LEU D 444 " model vdw 2.170 3.740 nonbonded pdb=" CD2 TYR D 279 " pdb=" CB LEU D 444 " model vdw 2.171 3.740 ... (remaining 213798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 827 or resid 848 through 1147)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 60.550 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 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 : 0.017 1.883 28988 Z= 0.650 Angle : 0.941 45.254 39479 Z= 0.511 Chirality : 0.050 1.011 4423 Planarity : 0.007 0.156 5115 Dihedral : 15.305 88.066 10410 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.32 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 16.47 % Favored : 83.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.61 (0.14), residues: 3540 helix: 0.83 (0.18), residues: 925 sheet: -0.64 (0.22), residues: 529 loop : -2.20 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP D 165 HIS 0.010 0.001 HIS D 493 PHE 0.055 0.002 PHE D 464 TYR 0.032 0.002 TYR D 279 ARG 0.012 0.001 ARG D 169 Details of bonding type rmsd hydrogen bonds : bond 0.20196 ( 1042) hydrogen bonds : angle 7.59857 ( 3035) SS BOND : bond 0.00730 ( 41) SS BOND : angle 1.93292 ( 82) covalent geometry : bond 0.01735 (28947) covalent geometry : angle 0.93797 (39397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 422 time to evaluate : 2.907 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 77 PHE cc_start: 0.7010 (t80) cc_final: 0.6687 (t80) REVERT: A 190 ARG cc_start: 0.7307 (mpt-90) cc_final: 0.6812 (mtm180) REVERT: A 204 TYR cc_start: 0.7518 (m-10) cc_final: 0.7155 (m-10) REVERT: A 298 GLU cc_start: 0.8927 (tt0) cc_final: 0.8727 (tm-30) REVERT: A 394 ASN cc_start: 0.7342 (m-40) cc_final: 0.6933 (m-40) REVERT: A 641 ASN cc_start: 0.7737 (m110) cc_final: 0.7053 (t0) REVERT: A 740 MET cc_start: 0.8189 (tmm) cc_final: 0.7604 (tmm) REVERT: B 99 ASN cc_start: 0.8313 (m-40) cc_final: 0.7652 (t0) REVERT: B 159 VAL cc_start: 0.7193 (t) cc_final: 0.6683 (t) REVERT: B 202 LYS cc_start: 0.8010 (mttp) cc_final: 0.7691 (mppt) REVERT: B 226 LEU cc_start: 0.8039 (tt) cc_final: 0.7532 (tp) REVERT: B 229 LEU cc_start: 0.7914 (tp) cc_final: 0.6947 (mp) REVERT: B 321 GLN cc_start: 0.8672 (mm110) cc_final: 0.8225 (mp10) REVERT: B 787 GLN cc_start: 0.9054 (mp10) cc_final: 0.8773 (mm110) REVERT: B 902 MET cc_start: 0.8461 (tpp) cc_final: 0.8214 (tpt) REVERT: C 14 GLN cc_start: 0.6541 (mt0) cc_final: 0.5576 (tp40) REVERT: C 133 PHE cc_start: 0.8292 (m-80) cc_final: 0.8084 (m-10) REVERT: C 190 ARG cc_start: 0.6580 (mtt180) cc_final: 0.6044 (mpt-90) REVERT: C 984 LEU cc_start: 0.7164 (mm) cc_final: 0.6907 (mm) REVERT: D 85 LEU cc_start: 0.3459 (mm) cc_final: 0.3038 (tp) REVERT: D 306 ARG cc_start: 0.4085 (tpt90) cc_final: 0.3252 (tpt170) REVERT: D 360 MET cc_start: -0.1694 (pmm) cc_final: -0.3079 (ttm) REVERT: D 455 MET cc_start: -0.4098 (tmm) cc_final: -0.4568 (tmm) REVERT: D 483 ASP cc_start: 0.5453 (m-30) cc_final: 0.5140 (t0) REVERT: D 608 THR cc_start: 0.7478 (m) cc_final: 0.6944 (p) outliers start: 1 outliers final: 0 residues processed: 423 average time/residue: 0.4019 time to fit residues: 267.5083 Evaluate side-chains 214 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 170 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 164 ASN A 675 GLN A 762 GLN B 66 HIS B 196 ASN B 613 GLN B 644 GLN C 17 ASN C 121 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 53 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 607 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095295 restraints weight = 142279.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096942 restraints weight = 73478.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096568 restraints weight = 44226.757| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.895 28988 Z= 0.627 Angle : 0.814 45.309 39479 Z= 0.405 Chirality : 0.049 0.949 4423 Planarity : 0.006 0.122 5115 Dihedral : 5.658 42.610 3842 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.18 % Favored : 92.65 % Rotamer: Outliers : 2.73 % Allowed : 15.77 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.58 (0.14), residues: 3540 helix: 0.79 (0.17), residues: 947 sheet: -0.49 (0.21), residues: 575 loop : -2.25 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 165 HIS 0.009 0.001 HIS D 374 PHE 0.036 0.002 PHE D 464 TYR 0.030 0.002 TYR D 279 ARG 0.009 0.001 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.07206 ( 1042) hydrogen bonds : angle 5.97067 ( 3035) SS BOND : bond 0.00404 ( 41) SS BOND : angle 1.83637 ( 82) covalent geometry : bond 0.01672 (28947) covalent geometry : angle 0.81053 (39397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 240 time to evaluate : 3.021 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 77 PHE cc_start: 0.7258 (t80) cc_final: 0.6720 (t80) REVERT: A 131 CYS cc_start: -0.2788 (OUTLIER) cc_final: -0.3321 (p) REVERT: A 190 ARG cc_start: 0.7311 (mpt-90) cc_final: 0.6989 (mtm180) REVERT: A 200 TYR cc_start: 0.8579 (m-80) cc_final: 0.8332 (t80) REVERT: A 223 LEU cc_start: 0.8083 (mp) cc_final: 0.7386 (tt) REVERT: A 393 THR cc_start: 0.2798 (p) cc_final: 0.2546 (p) REVERT: A 505 TYR cc_start: 0.3463 (OUTLIER) cc_final: 0.3161 (t80) REVERT: A 641 ASN cc_start: 0.7567 (m110) cc_final: 0.6980 (t0) REVERT: A 740 MET cc_start: 0.8141 (tmm) cc_final: 0.7070 (tmm) REVERT: B 65 PHE cc_start: 0.7184 (t80) cc_final: 0.6831 (t80) REVERT: B 153 MET cc_start: 0.5299 (pmm) cc_final: 0.5043 (pmm) REVERT: B 229 LEU cc_start: 0.8130 (tp) cc_final: 0.7329 (mp) REVERT: B 1012 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8969 (mm) REVERT: C 14 GLN cc_start: 0.5962 (mp10) cc_final: 0.5212 (tp40) REVERT: C 15 CYS cc_start: -0.2015 (OUTLIER) cc_final: -0.2255 (t) REVERT: C 118 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8745 (mp) REVERT: C 133 PHE cc_start: 0.8132 (m-80) cc_final: 0.7744 (m-10) REVERT: C 190 ARG cc_start: 0.6927 (mtt180) cc_final: 0.6263 (mmt180) REVERT: D 56 ASP cc_start: 0.6297 (p0) cc_final: 0.6056 (m-30) REVERT: D 176 LEU cc_start: 0.4759 (OUTLIER) cc_final: 0.4446 (pt) REVERT: D 306 ARG cc_start: 0.4797 (tpt90) cc_final: 0.4580 (tpt170) REVERT: D 335 GLU cc_start: 0.0731 (mt-10) cc_final: 0.0103 (pp20) REVERT: D 345 HIS cc_start: 0.4081 (t-170) cc_final: 0.3781 (m170) REVERT: D 360 MET cc_start: -0.0193 (pmm) cc_final: -0.2057 (ttm) REVERT: D 462 MET cc_start: 0.3238 (mmt) cc_final: 0.2946 (mmt) REVERT: D 606 TRP cc_start: -0.0470 (OUTLIER) cc_final: -0.1191 (t60) outliers start: 86 outliers final: 37 residues processed: 309 average time/residue: 0.3836 time to fit residues: 192.7413 Evaluate side-chains 230 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 36 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 chunk 328 optimal weight: 20.0000 chunk 319 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 307 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 130 optimal weight: 0.0770 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 66 HIS B 196 ASN B 506 GLN B 613 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.130089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091576 restraints weight = 135395.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094520 restraints weight = 68386.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093713 restraints weight = 36281.369| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.881 28988 Z= 0.640 Angle : 0.808 45.275 39479 Z= 0.407 Chirality : 0.049 0.911 4423 Planarity : 0.006 0.111 5115 Dihedral : 5.566 29.942 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.00 % Favored : 91.86 % Rotamer: Outliers : 3.81 % Allowed : 17.10 % Favored : 79.08 % 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: -1.64 (0.14), residues: 3540 helix: 0.68 (0.17), residues: 954 sheet: -0.54 (0.22), residues: 568 loop : -2.26 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 165 HIS 0.029 0.002 HIS B 66 PHE 0.033 0.002 PHE D 464 TYR 0.028 0.002 TYR D 279 ARG 0.022 0.001 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.07965 ( 1042) hydrogen bonds : angle 5.73334 ( 3035) SS BOND : bond 0.00876 ( 41) SS BOND : angle 1.83547 ( 82) covalent geometry : bond 0.01697 (28947) covalent geometry : angle 0.80459 (39397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 192 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7291 (t80) cc_final: 0.7082 (t80) REVERT: A 131 CYS cc_start: -0.2709 (OUTLIER) cc_final: -0.3202 (p) REVERT: A 200 TYR cc_start: 0.8572 (m-80) cc_final: 0.8261 (t80) REVERT: A 505 TYR cc_start: 0.3971 (OUTLIER) cc_final: 0.3409 (t80) REVERT: A 740 MET cc_start: 0.8425 (tmm) cc_final: 0.7157 (tmm) REVERT: B 33 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7367 (p) REVERT: B 115 GLN cc_start: 0.6064 (OUTLIER) cc_final: 0.5388 (mm-40) REVERT: B 780 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 14 GLN cc_start: 0.5873 (mp10) cc_final: 0.5008 (tp40) REVERT: C 15 CYS cc_start: -0.1190 (OUTLIER) cc_final: -0.2022 (t) REVERT: C 126 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8673 (t) REVERT: C 190 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6424 (mmt180) REVERT: D 56 ASP cc_start: 0.6706 (p0) cc_final: 0.6333 (m-30) REVERT: D 230 PHE cc_start: 0.4829 (t80) cc_final: 0.4553 (t80) REVERT: D 335 GLU cc_start: 0.1571 (mt-10) cc_final: 0.0685 (pp20) REVERT: D 345 HIS cc_start: 0.5453 (t-170) cc_final: 0.5014 (m90) REVERT: D 360 MET cc_start: -0.0539 (pmm) cc_final: -0.2906 (ttm) REVERT: D 455 MET cc_start: -0.2670 (tmm) cc_final: -0.3402 (tmm) outliers start: 120 outliers final: 73 residues processed: 293 average time/residue: 0.3539 time to fit residues: 175.0711 Evaluate side-chains 251 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 242 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1088 HIS A1135 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 493 GLN B 901 GLN C 52 GLN C 134 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 101 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS D 437 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.129008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088427 restraints weight = 124695.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090418 restraints weight = 70758.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088208 restraints weight = 47888.526| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.874 28988 Z= 0.683 Angle : 0.918 45.584 39479 Z= 0.470 Chirality : 0.053 0.901 4423 Planarity : 0.006 0.097 5115 Dihedral : 6.083 29.968 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.86 % Favored : 90.03 % Rotamer: Outliers : 4.96 % Allowed : 18.53 % Favored : 76.51 % 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: -2.07 (0.13), residues: 3540 helix: 0.16 (0.16), residues: 967 sheet: -0.72 (0.21), residues: 557 loop : -2.48 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 271 HIS 0.015 0.002 HIS D 493 PHE 0.032 0.003 PHE B1089 TYR 0.028 0.003 TYR C1067 ARG 0.015 0.001 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.10028 ( 1042) hydrogen bonds : angle 6.11120 ( 3035) SS BOND : bond 0.00697 ( 41) SS BOND : angle 2.10637 ( 82) covalent geometry : bond 0.01786 (28947) covalent geometry : angle 0.91407 (39397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 187 time to evaluate : 2.957 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 104 TRP cc_start: 0.6832 (OUTLIER) cc_final: 0.6005 (m-10) REVERT: A 131 CYS cc_start: -0.2929 (OUTLIER) cc_final: -0.3308 (p) REVERT: A 153 MET cc_start: 0.5199 (ptm) cc_final: 0.4983 (ptm) REVERT: A 158 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7582 (mmp-170) REVERT: A 190 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7589 (mtm-85) REVERT: A 200 TYR cc_start: 0.8544 (m-80) cc_final: 0.8214 (t80) REVERT: A 425 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7557 (mp) REVERT: A 505 TYR cc_start: 0.3027 (OUTLIER) cc_final: 0.2524 (t80) REVERT: A 759 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7238 (p90) REVERT: B 115 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.5433 (mm-40) REVERT: B 229 LEU cc_start: 0.7798 (tt) cc_final: 0.7067 (mp) REVERT: B 374 PHE cc_start: 0.7449 (p90) cc_final: 0.7088 (p90) REVERT: B 409 GLN cc_start: 0.7525 (mt0) cc_final: 0.7293 (tp40) REVERT: B 759 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8174 (t80) REVERT: C 14 GLN cc_start: 0.5604 (mp10) cc_final: 0.4877 (tp40) REVERT: C 126 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8699 (m) REVERT: C 190 ARG cc_start: 0.7265 (mtt180) cc_final: 0.6546 (mmt180) REVERT: C 869 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7963 (pmm) REVERT: D 92 ILE cc_start: 0.3292 (OUTLIER) cc_final: 0.3073 (tt) REVERT: D 345 HIS cc_start: 0.4701 (t-170) cc_final: 0.4389 (m90) REVERT: D 449 THR cc_start: 0.4485 (OUTLIER) cc_final: 0.4199 (m) REVERT: D 455 MET cc_start: -0.1763 (tmm) cc_final: -0.2404 (tmm) REVERT: D 510 TYR cc_start: 0.2598 (t80) cc_final: 0.2367 (t80) REVERT: D 562 ARG cc_start: 0.3895 (mtt180) cc_final: 0.2522 (tpt170) outliers start: 156 outliers final: 100 residues processed: 318 average time/residue: 0.3599 time to fit residues: 186.8703 Evaluate side-chains 272 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 159 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 72 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 331 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 308 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 344 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 17 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 655 HIS ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.132482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.091004 restraints weight = 123288.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092284 restraints weight = 67314.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.090957 restraints weight = 50531.240| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.880 28988 Z= 0.622 Angle : 0.747 45.227 39479 Z= 0.371 Chirality : 0.048 0.913 4423 Planarity : 0.005 0.074 5115 Dihedral : 5.416 28.770 3842 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.27 % Favored : 93.59 % Rotamer: Outliers : 3.66 % Allowed : 20.06 % Favored : 76.29 % 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: -1.66 (0.14), residues: 3540 helix: 0.73 (0.17), residues: 962 sheet: -0.50 (0.21), residues: 558 loop : -2.33 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 165 HIS 0.008 0.001 HIS D 374 PHE 0.028 0.001 PHE D 464 TYR 0.037 0.002 TYR D 521 ARG 0.006 0.000 ARG D 460 Details of bonding type rmsd hydrogen bonds : bond 0.07364 ( 1042) hydrogen bonds : angle 5.35711 ( 3035) SS BOND : bond 0.00382 ( 41) SS BOND : angle 1.56469 ( 82) covalent geometry : bond 0.01658 (28947) covalent geometry : angle 0.74477 (39397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 187 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6772 (OUTLIER) cc_final: 0.5987 (m-10) REVERT: A 131 CYS cc_start: -0.3193 (OUTLIER) cc_final: -0.3449 (p) REVERT: A 425 LEU cc_start: 0.8062 (mt) cc_final: 0.7846 (mp) REVERT: A 505 TYR cc_start: 0.2842 (OUTLIER) cc_final: 0.2458 (t80) REVERT: A 508 TYR cc_start: 0.5662 (OUTLIER) cc_final: 0.5127 (m-10) REVERT: A 755 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: A 853 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: B 115 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.5434 (mm-40) REVERT: B 226 LEU cc_start: 0.8241 (tp) cc_final: 0.7869 (tp) REVERT: B 229 LEU cc_start: 0.7808 (tt) cc_final: 0.7028 (mp) REVERT: B 417 LYS cc_start: 0.9047 (mmtm) cc_final: 0.8820 (tppt) REVERT: B 759 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7832 (t80) REVERT: B 900 MET cc_start: 0.8278 (mtp) cc_final: 0.7950 (mtp) REVERT: B 988 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7593 (tp30) REVERT: C 14 GLN cc_start: 0.5504 (mp10) cc_final: 0.4632 (tp40) REVERT: C 126 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8657 (m) REVERT: C 190 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7037 (mmt180) REVERT: C 1029 MET cc_start: 0.9239 (tpp) cc_final: 0.8825 (tmm) REVERT: D 335 GLU cc_start: 0.0916 (mt-10) cc_final: 0.0690 (pp20) REVERT: D 347 THR cc_start: 0.2095 (OUTLIER) cc_final: 0.1711 (p) REVERT: D 455 MET cc_start: -0.1524 (tmm) cc_final: -0.1916 (tmm) REVERT: D 562 ARG cc_start: 0.4423 (mtt180) cc_final: 0.2773 (tpt170) outliers start: 115 outliers final: 73 residues processed: 286 average time/residue: 0.3623 time to fit residues: 170.1185 Evaluate side-chains 248 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 165 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 311 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 343 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 223 optimal weight: 0.7980 chunk 336 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.129993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089817 restraints weight = 111200.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091961 restraints weight = 56419.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093234 restraints weight = 36726.197| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.878 28988 Z= 0.627 Angle : 0.745 45.482 39479 Z= 0.369 Chirality : 0.047 0.898 4423 Planarity : 0.005 0.078 5115 Dihedral : 5.259 29.052 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.03 % Rotamer: Outliers : 3.72 % Allowed : 20.44 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.54 (0.14), residues: 3540 helix: 0.96 (0.17), residues: 955 sheet: -0.49 (0.21), residues: 577 loop : -2.32 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 165 HIS 0.013 0.001 HIS D 373 PHE 0.023 0.001 PHE D 464 TYR 0.029 0.002 TYR D 521 ARG 0.006 0.000 ARG C 634 Details of bonding type rmsd hydrogen bonds : bond 0.07358 ( 1042) hydrogen bonds : angle 5.26928 ( 3035) SS BOND : bond 0.00389 ( 41) SS BOND : angle 1.59718 ( 82) covalent geometry : bond 0.01672 (28947) covalent geometry : angle 0.74270 (39397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 172 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7509 (OUTLIER) cc_final: 0.6591 (m100) REVERT: A 131 CYS cc_start: -0.3598 (OUTLIER) cc_final: -0.4106 (p) REVERT: A 200 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7771 (t80) REVERT: A 505 TYR cc_start: 0.3468 (OUTLIER) cc_final: 0.2724 (t80) REVERT: A 508 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.5507 (t80) REVERT: A 697 MET cc_start: 0.7661 (ptt) cc_final: 0.7440 (ptm) REVERT: A 755 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: A 853 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: B 226 LEU cc_start: 0.8181 (tp) cc_final: 0.7861 (tp) REVERT: B 759 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7803 (t80) REVERT: B 988 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 1111 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: C 14 GLN cc_start: 0.5139 (mp10) cc_final: 0.4552 (tp40) REVERT: C 126 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8813 (m) REVERT: C 190 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7061 (mmt180) REVERT: C 869 MET cc_start: 0.8287 (pmm) cc_final: 0.7912 (pmm) REVERT: C 1019 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8406 (tpt-90) REVERT: C 1029 MET cc_start: 0.9192 (tpp) cc_final: 0.8805 (tmm) REVERT: D 335 GLU cc_start: 0.1471 (mt-10) cc_final: 0.0999 (pp20) REVERT: D 347 THR cc_start: 0.2616 (OUTLIER) cc_final: 0.2395 (p) REVERT: D 455 MET cc_start: -0.2030 (tmm) cc_final: -0.2422 (tmm) REVERT: D 462 MET cc_start: 0.3858 (mmp) cc_final: 0.3301 (mmt) REVERT: D 562 ARG cc_start: 0.4091 (mtt180) cc_final: 0.1658 (tpt170) outliers start: 117 outliers final: 85 residues processed: 273 average time/residue: 0.3562 time to fit residues: 161.0011 Evaluate side-chains 258 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 161 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 69 optimal weight: 3.9990 chunk 306 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.127609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090334 restraints weight = 132231.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092078 restraints weight = 77504.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091859 restraints weight = 46452.115| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.877 28988 Z= 0.631 Angle : 0.752 45.685 39479 Z= 0.372 Chirality : 0.047 0.893 4423 Planarity : 0.005 0.074 5115 Dihedral : 5.212 27.784 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.17 % Rotamer: Outliers : 4.26 % Allowed : 20.63 % Favored : 75.11 % 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: -1.50 (0.14), residues: 3540 helix: 0.98 (0.17), residues: 961 sheet: -0.51 (0.21), residues: 566 loop : -2.27 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 459 HIS 0.009 0.001 HIS D 493 PHE 0.021 0.001 PHE D 464 TYR 0.036 0.002 TYR D 381 ARG 0.006 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.07520 ( 1042) hydrogen bonds : angle 5.22622 ( 3035) SS BOND : bond 0.00399 ( 41) SS BOND : angle 1.59136 ( 82) covalent geometry : bond 0.01680 (28947) covalent geometry : angle 0.74948 (39397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 172 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7418 (OUTLIER) cc_final: 0.6492 (m100) REVERT: A 131 CYS cc_start: -0.3455 (OUTLIER) cc_final: -0.3905 (p) REVERT: A 153 MET cc_start: 0.5133 (ptt) cc_final: 0.4520 (ptm) REVERT: A 190 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7466 (mtm-85) REVERT: A 200 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 258 TRP cc_start: 0.2391 (OUTLIER) cc_final: 0.1230 (p90) REVERT: A 421 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.4148 (m-80) REVERT: A 505 TYR cc_start: 0.3623 (OUTLIER) cc_final: 0.2752 (t80) REVERT: A 508 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.5354 (t80) REVERT: A 755 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: A 853 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: A 869 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7496 (mtm) REVERT: A 1029 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: B 115 GLN cc_start: 0.6059 (OUTLIER) cc_final: 0.5210 (mm-40) REVERT: B 226 LEU cc_start: 0.8202 (tp) cc_final: 0.7898 (tp) REVERT: B 236 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8951 (p) REVERT: B 386 LYS cc_start: 0.9302 (tptt) cc_final: 0.8954 (tptp) REVERT: B 417 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8958 (tppt) REVERT: B 759 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7893 (t80) REVERT: B 988 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 1111 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: C 14 GLN cc_start: 0.5077 (mp10) cc_final: 0.4355 (tp40) REVERT: C 15 CYS cc_start: -0.1390 (OUTLIER) cc_final: -0.2434 (t) REVERT: C 126 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8647 (m) REVERT: C 190 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7229 (mmt180) REVERT: C 869 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7977 (pmm) REVERT: C 1029 MET cc_start: 0.9198 (tpp) cc_final: 0.8833 (tmm) REVERT: D 51 ASN cc_start: 0.5283 (m-40) cc_final: 0.4941 (m110) REVERT: D 265 HIS cc_start: -0.0904 (OUTLIER) cc_final: -0.1710 (p90) REVERT: D 335 GLU cc_start: 0.1707 (mt-10) cc_final: 0.1195 (pp20) REVERT: D 347 THR cc_start: 0.2651 (OUTLIER) cc_final: 0.2414 (p) REVERT: D 455 MET cc_start: -0.2197 (tmm) cc_final: -0.2521 (tmm) REVERT: D 462 MET cc_start: 0.3868 (mmp) cc_final: 0.3332 (mmp) REVERT: D 504 PHE cc_start: 0.2674 (OUTLIER) cc_final: 0.2420 (m-80) outliers start: 134 outliers final: 86 residues processed: 284 average time/residue: 0.3632 time to fit residues: 170.5398 Evaluate side-chains 272 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 164 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 156 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 351 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.129536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089211 restraints weight = 107802.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.090078 restraints weight = 65807.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089269 restraints weight = 48898.641| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.876 28988 Z= 0.641 Angle : 0.789 45.754 39479 Z= 0.390 Chirality : 0.048 0.889 4423 Planarity : 0.005 0.078 5115 Dihedral : 5.335 27.057 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.96 % Favored : 90.96 % Rotamer: Outliers : 4.55 % Allowed : 20.76 % Favored : 74.70 % 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: -1.62 (0.13), residues: 3540 helix: 0.93 (0.17), residues: 953 sheet: -0.62 (0.21), residues: 555 loop : -2.33 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 478 HIS 0.008 0.001 HIS D 493 PHE 0.021 0.002 PHE D 464 TYR 0.037 0.002 TYR D 381 ARG 0.008 0.001 ARG D 460 Details of bonding type rmsd hydrogen bonds : bond 0.08112 ( 1042) hydrogen bonds : angle 5.35594 ( 3035) SS BOND : bond 0.00407 ( 41) SS BOND : angle 1.74587 ( 82) covalent geometry : bond 0.01702 (28947) covalent geometry : angle 0.78568 (39397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 169 time to evaluate : 2.879 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 104 TRP cc_start: 0.7039 (OUTLIER) cc_final: 0.6291 (m100) REVERT: A 131 CYS cc_start: -0.3748 (OUTLIER) cc_final: -0.4065 (p) REVERT: A 134 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 139 PRO cc_start: 0.6017 (Cg_exo) cc_final: 0.5606 (Cg_endo) REVERT: A 200 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7438 (t80) REVERT: A 258 TRP cc_start: 0.1996 (OUTLIER) cc_final: 0.0861 (p90) REVERT: A 353 TRP cc_start: 0.6064 (p-90) cc_final: 0.5822 (p-90) REVERT: A 421 TYR cc_start: 0.4878 (OUTLIER) cc_final: 0.4327 (m-80) REVERT: A 505 TYR cc_start: 0.2881 (OUTLIER) cc_final: 0.2324 (t80) REVERT: A 508 TYR cc_start: 0.5639 (OUTLIER) cc_final: 0.5333 (t80) REVERT: A 755 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: A 853 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: A 1029 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8320 (tpp) REVERT: A 1142 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8287 (mm110) REVERT: B 115 GLN cc_start: 0.6174 (OUTLIER) cc_final: 0.5214 (mm-40) REVERT: B 236 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9041 (p) REVERT: B 386 LYS cc_start: 0.9295 (tptt) cc_final: 0.9002 (tptp) REVERT: B 464 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: B 759 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8041 (t80) REVERT: B 1111 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: C 14 GLN cc_start: 0.4904 (mp10) cc_final: 0.4170 (tp40) REVERT: C 15 CYS cc_start: -0.0897 (OUTLIER) cc_final: -0.1779 (t) REVERT: C 126 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8609 (m) REVERT: C 190 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7343 (mtt-85) REVERT: C 869 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7910 (pmm) REVERT: C 1029 MET cc_start: 0.9260 (tpp) cc_final: 0.8893 (tmm) REVERT: D 28 PHE cc_start: 0.0188 (OUTLIER) cc_final: -0.0270 (t80) REVERT: D 51 ASN cc_start: 0.5081 (m-40) cc_final: 0.4832 (m110) REVERT: D 83 TYR cc_start: -0.0532 (OUTLIER) cc_final: -0.0861 (t80) REVERT: D 96 GLN cc_start: 0.2259 (OUTLIER) cc_final: 0.0995 (mt0) REVERT: D 265 HIS cc_start: -0.0972 (OUTLIER) cc_final: -0.1454 (p90) REVERT: D 335 GLU cc_start: 0.0992 (mt-10) cc_final: 0.0722 (pp20) REVERT: D 455 MET cc_start: -0.1274 (tmm) cc_final: -0.1648 (tmm) REVERT: D 462 MET cc_start: 0.3682 (mmp) cc_final: 0.3434 (mmp) REVERT: D 478 TRP cc_start: 0.2238 (m100) cc_final: 0.0679 (t60) outliers start: 143 outliers final: 97 residues processed: 292 average time/residue: 0.3495 time to fit residues: 168.9860 Evaluate side-chains 282 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 161 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 354 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 351 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.127815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086039 restraints weight = 138878.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086928 restraints weight = 73663.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086884 restraints weight = 54095.857| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.874 28988 Z= 0.666 Angle : 0.861 46.142 39479 Z= 0.432 Chirality : 0.051 0.879 4423 Planarity : 0.006 0.084 5115 Dihedral : 5.727 27.195 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.97 % Favored : 90.00 % Rotamer: Outliers : 4.55 % Allowed : 21.04 % Favored : 74.41 % 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: -1.89 (0.13), residues: 3540 helix: 0.60 (0.17), residues: 968 sheet: -0.67 (0.21), residues: 555 loop : -2.51 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 478 HIS 0.009 0.002 HIS D 265 PHE 0.046 0.002 PHE B 453 TYR 0.037 0.002 TYR D 381 ARG 0.006 0.001 ARG D 460 Details of bonding type rmsd hydrogen bonds : bond 0.09185 ( 1042) hydrogen bonds : angle 5.69100 ( 3035) SS BOND : bond 0.00499 ( 41) SS BOND : angle 1.93985 ( 82) covalent geometry : bond 0.01755 (28947) covalent geometry : angle 0.85737 (39397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 154 time to evaluate : 3.029 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 102 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6747 (mmt180) REVERT: A 104 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.6210 (m100) REVERT: A 131 CYS cc_start: -0.3951 (OUTLIER) cc_final: -0.4232 (p) REVERT: A 258 TRP cc_start: 0.1629 (OUTLIER) cc_final: 0.0408 (p90) REVERT: A 421 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.4404 (m-80) REVERT: A 505 TYR cc_start: 0.2872 (OUTLIER) cc_final: 0.2340 (t80) REVERT: A 508 TYR cc_start: 0.5583 (OUTLIER) cc_final: 0.5335 (t80) REVERT: A 755 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 853 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: A 1029 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8468 (tpp) REVERT: A 1142 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8434 (mm110) REVERT: B 115 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5194 (mm-40) REVERT: B 236 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9050 (p) REVERT: B 386 LYS cc_start: 0.9282 (tptt) cc_final: 0.8751 (tptp) REVERT: B 417 LYS cc_start: 0.9148 (mmtm) cc_final: 0.8920 (tppt) REVERT: B 464 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: B 759 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8176 (t80) REVERT: B 1111 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: C 14 GLN cc_start: 0.4888 (mp10) cc_final: 0.4161 (tp40) REVERT: C 15 CYS cc_start: -0.0844 (OUTLIER) cc_final: -0.1679 (t) REVERT: C 126 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8651 (m) REVERT: C 543 PHE cc_start: 0.2736 (OUTLIER) cc_final: 0.2406 (t80) REVERT: C 869 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7919 (pmm) REVERT: C 1019 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8327 (tpt-90) REVERT: D 83 TYR cc_start: -0.0196 (OUTLIER) cc_final: -0.0765 (m-80) REVERT: D 96 GLN cc_start: 0.2472 (OUTLIER) cc_final: 0.1142 (mt0) REVERT: D 265 HIS cc_start: -0.1121 (OUTLIER) cc_final: -0.1475 (p90) REVERT: D 335 GLU cc_start: 0.0962 (mt-10) cc_final: 0.0702 (pp20) REVERT: D 455 MET cc_start: -0.1354 (tmm) cc_final: -0.1835 (tmm) REVERT: D 462 MET cc_start: 0.3439 (mmp) cc_final: 0.3230 (mmp) outliers start: 143 outliers final: 100 residues processed: 279 average time/residue: 0.3638 time to fit residues: 168.5424 Evaluate side-chains 268 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 144 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 351 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.124590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087790 restraints weight = 140597.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.089980 restraints weight = 72827.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089355 restraints weight = 43936.725| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.876 28988 Z= 0.644 Angle : 0.810 46.370 39479 Z= 0.402 Chirality : 0.049 0.909 4423 Planarity : 0.005 0.066 5115 Dihedral : 5.617 27.193 3842 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.96 % Favored : 90.99 % Rotamer: Outliers : 4.10 % Allowed : 21.84 % Favored : 74.06 % 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: -1.84 (0.13), residues: 3540 helix: 0.81 (0.17), residues: 948 sheet: -0.75 (0.21), residues: 563 loop : -2.51 (0.12), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 478 HIS 0.008 0.001 HIS D 265 PHE 0.061 0.002 PHE B 453 TYR 0.025 0.002 TYR D 521 ARG 0.009 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.08570 ( 1042) hydrogen bonds : angle 5.53968 ( 3035) SS BOND : bond 0.00460 ( 41) SS BOND : angle 1.83171 ( 82) covalent geometry : bond 0.01708 (28947) covalent geometry : angle 0.80625 (39397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 155 time to evaluate : 3.043 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 102 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6872 (mmt180) REVERT: A 104 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.6548 (m100) REVERT: A 131 CYS cc_start: -0.4176 (OUTLIER) cc_final: -0.4590 (p) REVERT: A 200 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 258 TRP cc_start: 0.2014 (OUTLIER) cc_final: 0.0709 (p90) REVERT: A 421 TYR cc_start: 0.5002 (OUTLIER) cc_final: 0.3958 (m-80) REVERT: A 505 TYR cc_start: 0.3701 (OUTLIER) cc_final: 0.2705 (t80) REVERT: A 508 TYR cc_start: 0.5884 (OUTLIER) cc_final: 0.5377 (t80) REVERT: A 633 TRP cc_start: 0.5781 (m-10) cc_final: 0.5524 (m-10) REVERT: A 755 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: A 853 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: A 855 PHE cc_start: 0.8289 (m-80) cc_final: 0.8059 (t80) REVERT: A 988 GLU cc_start: 0.8257 (tp30) cc_final: 0.7937 (mp0) REVERT: A 1029 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8369 (tpp) REVERT: A 1142 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8347 (mm110) REVERT: B 115 GLN cc_start: 0.6047 (OUTLIER) cc_final: 0.5080 (mm-40) REVERT: B 236 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9100 (p) REVERT: B 386 LYS cc_start: 0.9324 (tptt) cc_final: 0.8780 (tptp) REVERT: B 759 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8070 (t80) REVERT: B 1111 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: C 14 GLN cc_start: 0.4781 (mp10) cc_final: 0.4009 (tp40) REVERT: C 15 CYS cc_start: -0.0988 (OUTLIER) cc_final: -0.1947 (t) REVERT: C 126 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8637 (m) REVERT: C 543 PHE cc_start: 0.2948 (OUTLIER) cc_final: 0.2623 (t80) REVERT: C 869 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7956 (pmm) REVERT: C 1019 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8269 (tpt-90) REVERT: D 96 GLN cc_start: 0.2328 (OUTLIER) cc_final: 0.0904 (mt0) REVERT: D 152 MET cc_start: 0.2712 (tpt) cc_final: 0.2309 (mmm) REVERT: D 265 HIS cc_start: -0.0589 (OUTLIER) cc_final: -0.1329 (p90) REVERT: D 335 GLU cc_start: 0.1587 (mt-10) cc_final: 0.1072 (pp20) REVERT: D 455 MET cc_start: -0.2183 (tmm) cc_final: -0.2624 (tmm) REVERT: D 462 MET cc_start: 0.4225 (mmp) cc_final: 0.3697 (mmp) REVERT: D 478 TRP cc_start: 0.1365 (m100) cc_final: 0.0274 (t60) REVERT: D 513 ILE cc_start: 0.1307 (mp) cc_final: 0.1051 (mt) outliers start: 129 outliers final: 94 residues processed: 266 average time/residue: 0.3626 time to fit residues: 160.4461 Evaluate side-chains 265 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 148 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 273 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 338 optimal weight: 0.0670 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.124596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087766 restraints weight = 135340.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090110 restraints weight = 70155.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.089324 restraints weight = 42653.455| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.876 28988 Z= 0.653 Angle : 0.901 59.198 39479 Z= 0.474 Chirality : 0.049 0.853 4423 Planarity : 0.005 0.111 5115 Dihedral : 5.632 30.600 3842 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.04 % Favored : 90.90 % Rotamer: Outliers : 3.81 % Allowed : 21.93 % Favored : 74.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.85 (0.13), residues: 3540 helix: 0.81 (0.17), residues: 948 sheet: -0.76 (0.21), residues: 558 loop : -2.51 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 478 HIS 0.009 0.001 HIS D 373 PHE 0.048 0.002 PHE B 453 TYR 0.025 0.002 TYR D 521 ARG 0.013 0.001 ARG D 204 Details of bonding type rmsd hydrogen bonds : bond 0.08478 ( 1042) hydrogen bonds : angle 5.53123 ( 3035) SS BOND : bond 0.00434 ( 41) SS BOND : angle 1.80729 ( 82) covalent geometry : bond 0.01715 (28947) covalent geometry : angle 0.89831 (39397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11899.53 seconds wall clock time: 208 minutes 9.45 seconds (12489.45 seconds total)