Starting phenix.real_space_refine on Tue Jun 24 12:18:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8taz_41143/06_2025/8taz_41143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8taz_41143/06_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_41143/06_2025/8taz_41143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8taz_41143/06_2025/8taz_41143.map" model { file = "/net/cci-nas-00/data/ceres_data/8taz_41143/06_2025/8taz_41143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8taz_41143/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.40, per 1000 atoms: 0.69 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: 6.58 Conformation dependent library (CDL) restraints added in 4.0 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: 4.01 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: 11.96 Time building geometry restraints manager: 7.90 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: 42.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 68.150 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.280 ------------------------------------------------------------------------------- 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 : 4.343 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: 0.5604 time to fit residues: 374.7691 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 : 4.235 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095295 restraints weight = 142279.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096915 restraints weight = 73514.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096769 restraints weight = 48224.160| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 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 = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 3.060 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: 0.7249 (t80) cc_final: 0.6720 (t80) REVERT: A 131 CYS cc_start: -0.2744 (OUTLIER) cc_final: -0.3248 (p) REVERT: A 190 ARG cc_start: 0.7360 (mpt-90) cc_final: 0.6953 (mtm180) REVERT: A 200 TYR cc_start: 0.8604 (m-80) cc_final: 0.8328 (t80) REVERT: A 223 LEU cc_start: 0.8133 (mp) cc_final: 0.7406 (tt) REVERT: A 393 THR cc_start: 0.2765 (p) cc_final: 0.2530 (p) REVERT: A 505 TYR cc_start: 0.3514 (OUTLIER) cc_final: 0.3196 (t80) REVERT: A 641 ASN cc_start: 0.7485 (m110) cc_final: 0.6938 (t0) REVERT: A 740 MET cc_start: 0.8038 (tmm) cc_final: 0.7009 (tmm) REVERT: B 65 PHE cc_start: 0.7201 (t80) cc_final: 0.6810 (t80) REVERT: B 153 MET cc_start: 0.5212 (pmm) cc_final: 0.4972 (pmm) REVERT: B 229 LEU cc_start: 0.8117 (tp) cc_final: 0.7312 (mp) REVERT: B 265 TYR cc_start: 0.6228 (p90) cc_final: 0.6023 (p90) REVERT: C 14 GLN cc_start: 0.6185 (mp10) cc_final: 0.5301 (tp40) REVERT: C 15 CYS cc_start: -0.1943 (OUTLIER) cc_final: -0.2413 (t) REVERT: C 79 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7395 (m-40) REVERT: C 118 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8779 (mp) REVERT: C 133 PHE cc_start: 0.8177 (m-80) cc_final: 0.7837 (m-10) REVERT: C 190 ARG cc_start: 0.6960 (mtt180) cc_final: 0.6287 (mmt180) REVERT: D 56 ASP cc_start: 0.6309 (p0) cc_final: 0.6064 (m-30) REVERT: D 176 LEU cc_start: 0.4812 (OUTLIER) cc_final: 0.4519 (pt) REVERT: D 306 ARG cc_start: 0.4801 (tpt90) cc_final: 0.4578 (tpt170) REVERT: D 335 GLU cc_start: 0.0774 (mt-10) cc_final: 0.0127 (pp20) REVERT: D 345 HIS cc_start: 0.4117 (t-170) cc_final: 0.3801 (m170) REVERT: D 360 MET cc_start: -0.0171 (pmm) cc_final: -0.2062 (ttm) REVERT: D 462 MET cc_start: 0.3264 (mmt) cc_final: 0.2967 (mmt) REVERT: D 606 TRP cc_start: -0.0582 (OUTLIER) cc_final: -0.1362 (t60) outliers start: 86 outliers final: 37 residues processed: 309 average time/residue: 0.4346 time to fit residues: 219.1683 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 : 3.502 ------------------------------------------------------------------------------- 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 C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 79 ASN 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: 6.9990 chunk 292 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 319 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 302 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 D 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.129999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091363 restraints weight = 135850.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094401 restraints weight = 68844.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093455 restraints weight = 39997.027| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3043 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= 0.635 Angle : 0.801 45.284 39479 Z= 0.403 Chirality : 0.049 0.920 4423 Planarity : 0.006 0.119 5115 Dihedral : 5.520 30.544 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.71 % Favored : 92.14 % Rotamer: Outliers : 3.72 % Allowed : 17.13 % Favored : 79.15 % 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: -1.60 (0.14), residues: 3540 helix: 0.71 (0.17), residues: 959 sheet: -0.50 (0.22), residues: 567 loop : -2.25 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 165 HIS 0.039 0.002 HIS B 66 PHE 0.035 0.002 PHE D 464 TYR 0.028 0.002 TYR D 279 ARG 0.024 0.001 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.07800 ( 1042) hydrogen bonds : angle 5.64842 ( 3035) SS BOND : bond 0.00484 ( 41) SS BOND : angle 1.83602 ( 82) covalent geometry : bond 0.01689 (28947) covalent geometry : angle 0.79770 (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 322 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 205 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7283 (t80) cc_final: 0.7070 (t80) REVERT: A 131 CYS cc_start: -0.2706 (OUTLIER) cc_final: -0.3169 (p) REVERT: A 200 TYR cc_start: 0.8561 (m-80) cc_final: 0.8249 (t80) REVERT: A 505 TYR cc_start: 0.3927 (OUTLIER) cc_final: 0.3390 (t80) REVERT: A 641 ASN cc_start: 0.7832 (m110) cc_final: 0.7474 (t0) REVERT: B 33 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7344 (p) REVERT: B 65 PHE cc_start: 0.7567 (t80) cc_final: 0.7072 (t80) REVERT: B 115 GLN cc_start: 0.6049 (OUTLIER) cc_final: 0.5393 (mm-40) REVERT: B 265 TYR cc_start: 0.6242 (p90) cc_final: 0.6008 (p90) REVERT: B 780 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 14 GLN cc_start: 0.5976 (mp10) cc_final: 0.5107 (tp40) REVERT: C 15 CYS cc_start: -0.1182 (OUTLIER) cc_final: -0.2049 (t) REVERT: C 79 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7435 (m-40) REVERT: C 190 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6467 (mmt180) REVERT: D 56 ASP cc_start: 0.6638 (p0) cc_final: 0.6293 (m-30) REVERT: D 230 PHE cc_start: 0.4829 (t80) cc_final: 0.4558 (t80) REVERT: D 335 GLU cc_start: 0.1514 (mt-10) cc_final: 0.0662 (pp20) REVERT: D 345 HIS cc_start: 0.5421 (t-170) cc_final: 0.4999 (m90) REVERT: D 360 MET cc_start: -0.0466 (pmm) cc_final: -0.2850 (ttm) REVERT: D 449 THR cc_start: 0.4262 (t) cc_final: 0.3922 (m) REVERT: D 455 MET cc_start: -0.2283 (tmm) cc_final: -0.3030 (tmm) outliers start: 117 outliers final: 68 residues processed: 302 average time/residue: 0.4685 time to fit residues: 238.7819 Evaluate side-chains 247 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 4.534 ------------------------------------------------------------------------------- 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 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 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 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 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 79 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 119 ILE 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 606 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 242 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 321 optimal weight: 0.1980 chunk 114 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 334 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 907 ASN B 196 ASN B 901 GLN C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093012 restraints weight = 119385.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095094 restraints weight = 64710.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094594 restraints weight = 41379.172| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3605 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= 0.627 Angle : 0.750 45.252 39479 Z= 0.372 Chirality : 0.048 0.902 4423 Planarity : 0.005 0.086 5115 Dihedral : 5.269 30.827 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.06 % Favored : 92.82 % Rotamer: Outliers : 3.56 % Allowed : 18.12 % Favored : 78.32 % 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: -1.50 (0.14), residues: 3540 helix: 0.89 (0.17), residues: 949 sheet: -0.43 (0.21), residues: 582 loop : -2.23 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 165 HIS 0.007 0.001 HIS C 207 PHE 0.028 0.001 PHE D 464 TYR 0.027 0.002 TYR D 279 ARG 0.010 0.001 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.07081 ( 1042) hydrogen bonds : angle 5.34733 ( 3035) SS BOND : bond 0.00440 ( 41) SS BOND : angle 1.60767 ( 82) covalent geometry : bond 0.01673 (28947) covalent geometry : angle 0.74686 (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 314 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 202 time to evaluate : 3.507 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 104 TRP cc_start: 0.7023 (OUTLIER) cc_final: 0.6284 (m-10) REVERT: A 131 CYS cc_start: -0.2783 (OUTLIER) cc_final: -0.3218 (p) REVERT: A 158 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7610 (mmp-170) REVERT: A 190 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7727 (mtm-85) REVERT: A 200 TYR cc_start: 0.8603 (m-80) cc_final: 0.8190 (t80) REVERT: A 505 TYR cc_start: 0.3832 (OUTLIER) cc_final: 0.3188 (t80) REVERT: A 853 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: B 33 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7275 (p) REVERT: B 65 PHE cc_start: 0.7572 (t80) cc_final: 0.7114 (t80) REVERT: B 229 LEU cc_start: 0.7813 (tt) cc_final: 0.6997 (mp) REVERT: B 265 TYR cc_start: 0.6314 (p90) cc_final: 0.5932 (p90) REVERT: B 759 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7413 (t80) REVERT: C 14 GLN cc_start: 0.5649 (mp10) cc_final: 0.4880 (tp40) REVERT: C 133 PHE cc_start: 0.8692 (m-80) cc_final: 0.8454 (m-10) REVERT: C 190 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6766 (mmt180) REVERT: C 869 MET cc_start: 0.8356 (pmm) cc_final: 0.7992 (pmm) REVERT: C 1029 MET cc_start: 0.9200 (tpp) cc_final: 0.8814 (tmm) REVERT: D 51 ASN cc_start: 0.5291 (m-40) cc_final: 0.4851 (m-40) REVERT: D 56 ASP cc_start: 0.6777 (p0) cc_final: 0.6374 (m-30) REVERT: D 158 TYR cc_start: -0.0034 (OUTLIER) cc_final: -0.0287 (t80) REVERT: D 305 ARG cc_start: 0.3261 (OUTLIER) cc_final: 0.2989 (tpt170) REVERT: D 335 GLU cc_start: 0.0973 (mt-10) cc_final: 0.0331 (pp20) REVERT: D 345 HIS cc_start: 0.5798 (t-170) cc_final: 0.5400 (m90) REVERT: D 347 THR cc_start: 0.3476 (OUTLIER) cc_final: 0.2967 (p) REVERT: D 360 MET cc_start: -0.0293 (pmm) cc_final: -0.3189 (ttm) REVERT: D 449 THR cc_start: 0.5264 (t) cc_final: 0.5002 (m) REVERT: D 459 TRP cc_start: -0.0818 (t60) cc_final: -0.1100 (t60) outliers start: 112 outliers final: 64 residues processed: 296 average time/residue: 0.5340 time to fit residues: 257.1832 Evaluate side-chains 251 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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 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 638 THR Chi-restraints excluded: chain A residue 750 SER 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 1077 THR Chi-restraints excluded: chain B residue 33 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 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 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 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 649 CYS 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 984 LEU Chi-restraints excluded: chain B residue 994 ASP 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 131 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN 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 546 LEU Chi-restraints excluded: chain C residue 576 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 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 85 LEU Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG 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 560 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: 2.9990 chunk 189 optimal weight: 0.0980 chunk 331 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 311 optimal weight: 6.9990 chunk 344 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.132561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.092010 restraints weight = 117012.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094263 restraints weight = 57651.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095463 restraints weight = 37093.616| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3918 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= 0.620 Angle : 0.721 45.276 39479 Z= 0.355 Chirality : 0.047 0.902 4423 Planarity : 0.005 0.071 5115 Dihedral : 5.009 29.292 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.95 % Favored : 92.91 % Rotamer: Outliers : 3.43 % Allowed : 19.26 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3540 helix: 1.06 (0.17), residues: 950 sheet: -0.19 (0.21), residues: 566 loop : -2.17 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 165 HIS 0.007 0.001 HIS D 493 PHE 0.027 0.001 PHE D 230 TYR 0.030 0.001 TYR D 381 ARG 0.009 0.000 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.06454 ( 1042) hydrogen bonds : angle 5.12250 ( 3035) SS BOND : bond 0.00368 ( 41) SS BOND : angle 1.52322 ( 82) covalent geometry : bond 0.01658 (28947) covalent geometry : angle 0.71815 (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 304 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 196 time to evaluate : 3.311 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 104 TRP cc_start: 0.7283 (OUTLIER) cc_final: 0.6253 (m-10) REVERT: A 131 CYS cc_start: -0.3025 (OUTLIER) cc_final: -0.3510 (p) REVERT: A 158 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7411 (mmp80) REVERT: A 228 ASP cc_start: 0.8473 (m-30) cc_final: 0.7701 (m-30) REVERT: A 505 TYR cc_start: 0.3744 (OUTLIER) cc_final: 0.3107 (t80) REVERT: A 508 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5048 (m-10) REVERT: A 853 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: B 33 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7269 (p) REVERT: B 65 PHE cc_start: 0.7481 (t80) cc_final: 0.7179 (t80) REVERT: B 115 GLN cc_start: 0.5987 (OUTLIER) cc_final: 0.5306 (mm-40) REVERT: B 226 LEU cc_start: 0.8091 (tp) cc_final: 0.7706 (tp) REVERT: B 265 TYR cc_start: 0.6239 (p90) cc_final: 0.5993 (p90) REVERT: B 759 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7285 (t80) REVERT: C 14 GLN cc_start: 0.5286 (mp10) cc_final: 0.4781 (tp40) REVERT: C 190 ARG cc_start: 0.6963 (mtt180) cc_final: 0.6691 (mmt180) REVERT: C 869 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7897 (pmm) REVERT: C 1029 MET cc_start: 0.9116 (tpp) cc_final: 0.8573 (tmm) REVERT: D 75 GLU cc_start: 0.3552 (pp20) cc_final: 0.3254 (pt0) REVERT: D 305 ARG cc_start: 0.3300 (OUTLIER) cc_final: 0.3069 (tpt170) REVERT: D 335 GLU cc_start: 0.1319 (mt-10) cc_final: 0.0950 (pp20) REVERT: D 345 HIS cc_start: 0.5688 (t-170) cc_final: 0.5126 (m90) REVERT: D 347 THR cc_start: 0.3196 (OUTLIER) cc_final: 0.2735 (p) REVERT: D 449 THR cc_start: 0.5335 (t) cc_final: 0.5026 (m) REVERT: D 459 TRP cc_start: -0.0530 (t60) cc_final: -0.1216 (t60) REVERT: D 462 MET cc_start: 0.3932 (mmt) cc_final: 0.3425 (mmp) REVERT: D 512 PHE cc_start: 0.1805 (OUTLIER) cc_final: 0.1449 (m-80) REVERT: D 572 ARG cc_start: 0.2445 (tpp-160) cc_final: 0.0990 (mmt180) outliers start: 108 outliers final: 70 residues processed: 290 average time/residue: 0.3651 time to fit residues: 176.4361 Evaluate side-chains 260 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 177 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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 159 VAL Chi-restraints excluded: chain A residue 176 LEU 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 638 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET 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 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 141 LEU Chi-restraints excluded: chain B residue 203 ILE 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 525 CYS 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 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 994 ASP 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 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 203 ILE 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 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 963 VAL Chi-restraints excluded: chain C residue 991 VAL 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 D residue 28 PHE 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 85 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG 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 512 PHE Chi-restraints excluded: chain D residue 560 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: 0.0170 chunk 93 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 343 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 336 optimal weight: 0.1980 chunk 137 optimal weight: 5.9990 chunk 162 optimal weight: 0.4980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 755 GLN ** 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 374 HIS D 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.133711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.093430 restraints weight = 110025.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095699 restraints weight = 55062.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097253 restraints weight = 35680.258| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.879 28988 Z= 0.618 Angle : 0.705 45.390 39479 Z= 0.342 Chirality : 0.046 0.892 4423 Planarity : 0.005 0.071 5115 Dihedral : 4.802 27.584 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.44 % Rotamer: Outliers : 3.18 % Allowed : 20.03 % Favored : 76.80 % 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: -1.14 (0.14), residues: 3540 helix: 1.27 (0.17), residues: 949 sheet: -0.18 (0.22), residues: 549 loop : -2.04 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 165 HIS 0.008 0.001 HIS D 374 PHE 0.021 0.001 PHE D 464 TYR 0.025 0.001 TYR D 279 ARG 0.010 0.000 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.05784 ( 1042) hydrogen bonds : angle 4.85073 ( 3035) SS BOND : bond 0.00327 ( 41) SS BOND : angle 1.32444 ( 82) covalent geometry : bond 0.01653 (28947) covalent geometry : angle 0.70321 (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 295 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 195 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7496 (OUTLIER) cc_final: 0.6696 (m100) REVERT: A 131 CYS cc_start: -0.3324 (OUTLIER) cc_final: -0.3837 (p) REVERT: A 158 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7232 (mmp80) REVERT: A 200 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7576 (t80) REVERT: A 228 ASP cc_start: 0.8417 (m-30) cc_final: 0.7837 (m-30) REVERT: A 505 TYR cc_start: 0.3773 (OUTLIER) cc_final: 0.3068 (t80) REVERT: A 508 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5089 (m-10) REVERT: A 755 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 853 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: A 855 PHE cc_start: 0.7687 (m-80) cc_final: 0.7406 (m-80) REVERT: A 1031 GLU cc_start: 0.8395 (tp30) cc_final: 0.7923 (tm-30) REVERT: B 33 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.6980 (p) REVERT: B 115 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5327 (mm-40) REVERT: B 226 LEU cc_start: 0.7994 (tp) cc_final: 0.7608 (tp) REVERT: B 265 TYR cc_start: 0.6247 (p90) cc_final: 0.6021 (p90) REVERT: B 755 GLN cc_start: 0.7875 (mp10) cc_final: 0.7327 (pm20) REVERT: C 14 GLN cc_start: 0.4651 (mp10) cc_final: 0.4281 (tp40) REVERT: C 869 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7814 (pmm) REVERT: C 1029 MET cc_start: 0.8960 (tpp) cc_final: 0.8406 (tmm) REVERT: D 75 GLU cc_start: 0.3941 (pp20) cc_final: 0.3673 (pt0) REVERT: D 335 GLU cc_start: 0.1501 (mt-10) cc_final: 0.1041 (pp20) REVERT: D 345 HIS cc_start: 0.5690 (t-170) cc_final: 0.5126 (m90) REVERT: D 347 THR cc_start: 0.3336 (OUTLIER) cc_final: 0.2887 (p) REVERT: D 459 TRP cc_start: -0.0894 (t60) cc_final: -0.2542 (t60) REVERT: D 462 MET cc_start: 0.4113 (mmt) cc_final: 0.3632 (mmp) REVERT: D 480 MET cc_start: -0.0388 (OUTLIER) cc_final: -0.0698 (ptm) REVERT: D 510 TYR cc_start: 0.4366 (t80) cc_final: 0.3917 (t80) REVERT: D 512 PHE cc_start: 0.1888 (OUTLIER) cc_final: 0.1548 (m-80) REVERT: D 572 ARG cc_start: 0.2047 (tpp-160) cc_final: 0.0664 (mmt180) outliers start: 100 outliers final: 64 residues processed: 276 average time/residue: 0.4981 time to fit residues: 230.6677 Evaluate side-chains 258 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 180 time to evaluate : 4.220 ------------------------------------------------------------------------------- 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 158 ARG 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 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 740 MET 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 961 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE 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 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 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS 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 770 ILE Chi-restraints excluded: chain B residue 858 LEU 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 1018 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE 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 267 VAL 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 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1018 ILE 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 69 TRP Chi-restraints excluded: chain D residue 176 LEU 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 480 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 568 PHE 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: 2.9990 chunk 306 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 chunk 230 optimal weight: 0.0270 chunk 13 optimal weight: 4.9990 chunk 184 optimal weight: 0.0970 chunk 148 optimal weight: 1.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 655 HIS ** C 755 GLN ** 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 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.134439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091148 restraints weight = 136501.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092092 restraints weight = 72913.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.093113 restraints weight = 44509.994| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4448 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= 0.619 Angle : 0.704 45.391 39479 Z= 0.341 Chirality : 0.046 0.889 4423 Planarity : 0.005 0.064 5115 Dihedral : 4.703 26.787 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 3.53 % Allowed : 20.09 % Favored : 76.38 % 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: -1.07 (0.14), residues: 3540 helix: 1.32 (0.17), residues: 953 sheet: -0.19 (0.21), residues: 569 loop : -2.00 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 478 HIS 0.005 0.001 HIS D 493 PHE 0.021 0.001 PHE C 135 TYR 0.024 0.001 TYR D 279 ARG 0.004 0.000 ARG D 460 Details of bonding type rmsd hydrogen bonds : bond 0.05857 ( 1042) hydrogen bonds : angle 4.80752 ( 3035) SS BOND : bond 0.00310 ( 41) SS BOND : angle 1.34239 ( 82) covalent geometry : bond 0.01656 (28947) covalent geometry : angle 0.70219 (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 303 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 192 time to evaluate : 3.238 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 32 PHE cc_start: 0.3386 (m-80) cc_final: 0.2834 (m-80) REVERT: A 131 CYS cc_start: -0.2575 (OUTLIER) cc_final: -0.2835 (p) REVERT: A 200 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7395 (t80) REVERT: A 505 TYR cc_start: 0.2807 (OUTLIER) cc_final: 0.2576 (t80) REVERT: A 508 TYR cc_start: 0.5268 (OUTLIER) cc_final: 0.4846 (m-10) REVERT: A 755 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: A 853 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: A 855 PHE cc_start: 0.7752 (m-80) cc_final: 0.7471 (m-80) REVERT: B 33 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7196 (p) REVERT: B 115 GLN cc_start: 0.6080 (OUTLIER) cc_final: 0.5329 (mm-40) REVERT: B 207 HIS cc_start: 0.7831 (t70) cc_final: 0.7605 (t70) REVERT: B 226 LEU cc_start: 0.8000 (tp) cc_final: 0.7672 (tp) REVERT: B 386 LYS cc_start: 0.9225 (tptt) cc_final: 0.8786 (tptp) REVERT: B 755 GLN cc_start: 0.7779 (mp10) cc_final: 0.7383 (pm20) REVERT: B 759 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7234 (t80) REVERT: C 14 GLN cc_start: 0.4897 (mp10) cc_final: 0.4285 (tp40) REVERT: C 190 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6951 (mmt180) REVERT: C 869 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7777 (pmm) REVERT: C 916 LEU cc_start: 0.8755 (tt) cc_final: 0.8531 (tp) REVERT: C 1029 MET cc_start: 0.8948 (tpp) cc_final: 0.8430 (tmm) REVERT: D 28 PHE cc_start: -0.0549 (OUTLIER) cc_final: -0.0813 (t80) REVERT: D 73 TYR cc_start: 0.4611 (t80) cc_final: 0.4274 (m-10) REVERT: D 347 THR cc_start: 0.2142 (OUTLIER) cc_final: 0.1832 (p) REVERT: D 459 TRP cc_start: -0.1594 (t60) cc_final: -0.2295 (t60) REVERT: D 494 ASP cc_start: 0.3984 (p0) cc_final: 0.3620 (m-30) outliers start: 111 outliers final: 81 residues processed: 286 average time/residue: 0.4123 time to fit residues: 195.0028 Evaluate side-chains 270 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 177 time to evaluate : 3.143 ------------------------------------------------------------------------------- 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 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 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 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 740 MET 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 961 THR 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 58 PHE 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 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS 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 759 PHE 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 1018 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE 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 203 ILE 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 576 VAL Chi-restraints excluded: chain C residue 655 HIS 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 963 VAL Chi-restraints excluded: chain C residue 991 VAL 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 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 69 TRP 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 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 392 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 568 PHE 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: 9.9990 chunk 84 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 143 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 351 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 134 GLN C 207 HIS C 641 ASN ** C 755 GLN ** 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 601 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.132886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085758 restraints weight = 108557.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.086735 restraints weight = 59947.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086944 restraints weight = 42316.509| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4723 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= 0.627 Angle : 0.733 45.678 39479 Z= 0.357 Chirality : 0.047 0.883 4423 Planarity : 0.005 0.069 5115 Dihedral : 4.798 28.107 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.66 % Favored : 92.29 % Rotamer: Outliers : 3.66 % Allowed : 20.53 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3540 helix: 1.32 (0.17), residues: 952 sheet: -0.13 (0.21), residues: 558 loop : -2.06 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP D 478 HIS 0.015 0.001 HIS C 655 PHE 0.042 0.001 PHE B 453 TYR 0.023 0.002 TYR D 279 ARG 0.010 0.000 ARG D 460 Details of bonding type rmsd hydrogen bonds : bond 0.06558 ( 1042) hydrogen bonds : angle 4.91416 ( 3035) SS BOND : bond 0.00330 ( 41) SS BOND : angle 1.45162 ( 82) covalent geometry : bond 0.01673 (28947) covalent geometry : angle 0.73123 (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 293 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 178 time to evaluate : 2.893 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 32 PHE cc_start: 0.3806 (m-80) cc_final: 0.3378 (m-80) REVERT: A 200 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.7076 (t80) REVERT: A 508 TYR cc_start: 0.4784 (OUTLIER) cc_final: 0.4554 (m-10) REVERT: A 853 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: A 855 PHE cc_start: 0.7635 (m-80) cc_final: 0.7361 (m-80) REVERT: A 1029 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8363 (tpp) REVERT: B 33 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7340 (p) REVERT: B 115 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.5404 (mm-40) REVERT: B 226 LEU cc_start: 0.8131 (tp) cc_final: 0.7813 (tp) REVERT: B 386 LYS cc_start: 0.9267 (tptt) cc_final: 0.8873 (tptp) REVERT: B 409 GLN cc_start: 0.7439 (mt0) cc_final: 0.6933 (tp40) REVERT: B 755 GLN cc_start: 0.7915 (mp10) cc_final: 0.7673 (mp10) REVERT: B 759 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 14 GLN cc_start: 0.4591 (mp10) cc_final: 0.4157 (tp40) REVERT: C 190 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7114 (mmt180) REVERT: C 916 LEU cc_start: 0.8832 (tt) cc_final: 0.8589 (tp) REVERT: C 1029 MET cc_start: 0.9065 (tpp) cc_final: 0.8598 (tmm) REVERT: D 28 PHE cc_start: -0.0626 (OUTLIER) cc_final: -0.0872 (t80) REVERT: D 459 TRP cc_start: -0.1504 (t60) cc_final: -0.2094 (t60) REVERT: D 474 MET cc_start: -0.2150 (mpp) cc_final: -0.2416 (ttp) REVERT: D 478 TRP cc_start: 0.2636 (m100) cc_final: 0.1619 (t60) REVERT: D 489 GLU cc_start: 0.3662 (mm-30) cc_final: 0.2365 (mm-30) outliers start: 115 outliers final: 87 residues processed: 271 average time/residue: 0.3668 time to fit residues: 165.7246 Evaluate side-chains 266 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 171 time to evaluate : 3.164 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain A residue 130 VAL 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 401 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 853 GLN 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 33 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 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 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 374 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS 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 759 PHE Chi-restraints excluded: chain B residue 773 GLU 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 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 C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE 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 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 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 1018 ILE 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 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP 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 261 CYS 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 374 HIS Chi-restraints excluded: chain D residue 392 LEU 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: 0.1980 chunk 166 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 351 optimal weight: 0.9990 chunk 320 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 232 optimal weight: 0.5980 chunk 259 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** 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 = 0.4216 r_free = 0.4216 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092550 restraints weight = 159303.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094945 restraints weight = 80279.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094082 restraints weight = 51812.186| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4900 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= 0.619 Angle : 0.710 45.325 39479 Z= 0.343 Chirality : 0.046 0.892 4423 Planarity : 0.005 0.063 5115 Dihedral : 4.721 27.573 3842 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 3.34 % Allowed : 20.72 % Favored : 75.94 % 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: -1.03 (0.14), residues: 3540 helix: 1.45 (0.17), residues: 952 sheet: -0.24 (0.21), residues: 563 loop : -1.99 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 478 HIS 0.008 0.001 HIS C 655 PHE 0.041 0.001 PHE B 453 TYR 0.027 0.001 TYR B 505 ARG 0.005 0.000 ARG D 460 Details of bonding type rmsd hydrogen bonds : bond 0.06100 ( 1042) hydrogen bonds : angle 4.76993 ( 3035) SS BOND : bond 0.00325 ( 41) SS BOND : angle 1.37267 ( 82) covalent geometry : bond 0.01657 (28947) covalent geometry : angle 0.70775 (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 286 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 181 time to evaluate : 3.205 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 139 PRO cc_start: 0.5690 (Cg_endo) cc_final: 0.5464 (Cg_exo) REVERT: A 200 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7356 (t80) REVERT: A 508 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.4926 (m-10) REVERT: A 853 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: A 855 PHE cc_start: 0.7742 (m-80) cc_final: 0.7473 (m-80) REVERT: A 1029 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8282 (tpp) REVERT: B 33 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7276 (p) REVERT: B 115 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5305 (mm-40) REVERT: B 226 LEU cc_start: 0.7967 (tp) cc_final: 0.7652 (tp) REVERT: B 386 LYS cc_start: 0.9262 (tptt) cc_final: 0.8861 (tptp) REVERT: B 755 GLN cc_start: 0.7774 (mp10) cc_final: 0.7491 (mp10) REVERT: B 759 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7415 (t80) REVERT: C 14 GLN cc_start: 0.4915 (mp10) cc_final: 0.4293 (tp40) REVERT: C 190 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7152 (mmt180) REVERT: C 916 LEU cc_start: 0.8820 (tt) cc_final: 0.8610 (tp) REVERT: C 1029 MET cc_start: 0.9029 (tpp) cc_final: 0.8564 (tmm) REVERT: D 28 PHE cc_start: 0.0057 (OUTLIER) cc_final: -0.0339 (t80) REVERT: D 243 TYR cc_start: 0.5201 (t80) cc_final: 0.4924 (t80) REVERT: D 273 ARG cc_start: 0.2103 (ttt180) cc_final: 0.1326 (tmt170) REVERT: D 474 MET cc_start: -0.1245 (mpp) cc_final: -0.2156 (ttt) REVERT: D 478 TRP cc_start: 0.2134 (m100) cc_final: 0.0787 (t60) REVERT: D 489 GLU cc_start: 0.2911 (mm-30) cc_final: 0.1530 (mm-30) REVERT: D 494 ASP cc_start: 0.3926 (p0) cc_final: 0.3043 (m-30) outliers start: 105 outliers final: 85 residues processed: 268 average time/residue: 0.3826 time to fit residues: 169.1527 Evaluate side-chains 263 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 170 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL 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 312 ILE 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 508 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 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 853 GLN 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 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE 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 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 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS 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 759 PHE Chi-restraints excluded: chain B residue 773 GLU 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 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 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 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 140 PHE 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 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 991 VAL 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 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 69 TRP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS 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 374 HIS Chi-restraints excluded: chain D residue 392 LEU 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: 1.9990 chunk 282 optimal weight: 0.7980 chunk 299 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 326 optimal weight: 6.9990 chunk 338 optimal weight: 0.0980 chunk 194 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 43 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.134248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095733 restraints weight = 159254.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096480 restraints weight = 88560.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095078 restraints weight = 57265.858| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5013 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= 0.617 Angle : 0.702 45.297 39479 Z= 0.338 Chirality : 0.046 0.896 4423 Planarity : 0.005 0.064 5115 Dihedral : 4.637 27.481 3842 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 2.86 % Allowed : 21.17 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3540 helix: 1.57 (0.17), residues: 952 sheet: -0.25 (0.21), residues: 573 loop : -1.95 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 478 HIS 0.004 0.001 HIS C 655 PHE 0.031 0.001 PHE B 453 TYR 0.035 0.001 TYR B 505 ARG 0.013 0.000 ARG C 634 Details of bonding type rmsd hydrogen bonds : bond 0.05729 ( 1042) hydrogen bonds : angle 4.68400 ( 3035) SS BOND : bond 0.00395 ( 41) SS BOND : angle 1.31611 ( 82) covalent geometry : bond 0.01653 (28947) covalent geometry : angle 0.70024 (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 269 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 179 time to evaluate : 3.278 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 200 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 508 TYR cc_start: 0.5703 (OUTLIER) cc_final: 0.4936 (m-10) REVERT: A 853 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: A 855 PHE cc_start: 0.7745 (m-80) cc_final: 0.7467 (m-80) REVERT: A 1029 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8189 (tpp) REVERT: B 33 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7155 (p) REVERT: B 115 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.5211 (mm-40) REVERT: B 226 LEU cc_start: 0.7991 (tp) cc_final: 0.7652 (tp) REVERT: B 386 LYS cc_start: 0.9242 (tptt) cc_final: 0.8850 (tptp) REVERT: B 755 GLN cc_start: 0.7837 (mp10) cc_final: 0.7522 (mp10) REVERT: B 759 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7240 (t80) REVERT: C 14 GLN cc_start: 0.4898 (mp10) cc_final: 0.4289 (tp40) REVERT: C 190 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7202 (mmt180) REVERT: C 1029 MET cc_start: 0.8959 (tpp) cc_final: 0.8471 (tmm) REVERT: D 28 PHE cc_start: 0.0192 (OUTLIER) cc_final: -0.0167 (t80) REVERT: D 243 TYR cc_start: 0.5281 (t80) cc_final: 0.4978 (t80) REVERT: D 373 HIS cc_start: 0.2698 (OUTLIER) cc_final: 0.2140 (t-90) REVERT: D 474 MET cc_start: -0.1046 (mpp) cc_final: -0.2233 (ttp) REVERT: D 478 TRP cc_start: 0.1784 (m100) cc_final: 0.0427 (t60) REVERT: D 489 GLU cc_start: 0.2881 (mm-30) cc_final: 0.1709 (mm-30) REVERT: D 494 ASP cc_start: 0.3644 (p0) cc_final: 0.2671 (m-30) outliers start: 90 outliers final: 76 residues processed: 256 average time/residue: 0.3876 time to fit residues: 166.3296 Evaluate side-chains 253 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 168 time to evaluate : 3.057 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain A residue 130 VAL 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 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE 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 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 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS 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 759 PHE 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 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 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 130 VAL Chi-restraints excluded: chain C residue 131 CYS 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 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 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS 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 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS 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 374 HIS Chi-restraints excluded: chain D residue 392 LEU 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: 0.8980 chunk 147 optimal weight: 0.0970 chunk 261 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 109 optimal weight: 0.0870 chunk 338 optimal weight: 0.0670 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** 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 = 0.4199 r_free = 0.4199 target = 0.130250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092328 restraints weight = 136116.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.094258 restraints weight = 74754.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094085 restraints weight = 44503.575| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5028 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= 0.619 Angle : 0.802 59.197 39479 Z= 0.415 Chirality : 0.046 0.945 4423 Planarity : 0.005 0.088 5115 Dihedral : 4.637 27.472 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 2.92 % Allowed : 21.17 % Favored : 75.91 % Cbeta Deviations : 0.03 % 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: -0.95 (0.14), residues: 3540 helix: 1.55 (0.17), residues: 952 sheet: -0.25 (0.21), residues: 573 loop : -1.95 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 478 HIS 0.004 0.001 HIS C 655 PHE 0.034 0.001 PHE D 512 TYR 0.028 0.001 TYR B 505 ARG 0.010 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.05744 ( 1042) hydrogen bonds : angle 4.68723 ( 3035) SS BOND : bond 0.00295 ( 41) SS BOND : angle 1.29514 ( 82) covalent geometry : bond 0.01655 (28947) covalent geometry : angle 0.80017 (39397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14678.33 seconds wall clock time: 264 minutes 24.13 seconds (15864.13 seconds total)