Starting phenix.real_space_refine on Mon Aug 25 13:42:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8taz_41143/08_2025/8taz_41143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8taz_41143/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8taz_41143/08_2025/8taz_41143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8taz_41143/08_2025/8taz_41143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8taz_41143/08_2025/8taz_41143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8taz_41143/08_2025/8taz_41143.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.33, per 1000 atoms: 0.22 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: 1.76 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.00 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: 4.92 Time building geometry restraints manager: 2.51 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: 11.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 23.370 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG D 169 TYR 0.032 0.002 TYR D 279 PHE 0.055 0.002 PHE D 464 TRP 0.060 0.003 TRP D 165 HIS 0.010 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.01735 (28947) covalent geometry : angle 0.93797 (39397) SS BOND : bond 0.00730 ( 41) SS BOND : angle 1.93292 ( 82) hydrogen bonds : bond 0.20196 ( 1042) hydrogen bonds : angle 7.59857 ( 3035) *********************** 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 : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7010 (t80) cc_final: 0.6687 (t80) REVERT: A 190 ARG cc_start: 0.7307 (mpt-90) cc_final: 0.6815 (mtm180) REVERT: A 204 TYR cc_start: 0.7518 (m-10) cc_final: 0.7188 (m-10) REVERT: A 394 ASN cc_start: 0.7342 (m-40) cc_final: 0.6934 (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: 0.7653 (t0) REVERT: B 159 VAL cc_start: 0.7193 (t) cc_final: 0.6682 (t) REVERT: B 202 LYS cc_start: 0.8010 (mttp) cc_final: 0.7692 (mppt) REVERT: B 226 LEU cc_start: 0.8039 (tt) cc_final: 0.7531 (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: 0.8224 (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: 0.8213 (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: 0.8080 (m-10) REVERT: C 190 ARG cc_start: 0.6580 (mtt180) cc_final: 0.6042 (mpt-90) REVERT: C 984 LEU cc_start: 0.7164 (mm) cc_final: 0.6906 (mm) REVERT: D 85 LEU cc_start: 0.3459 (mm) cc_final: 0.3043 (tp) REVERT: D 306 ARG cc_start: 0.4085 (tpt90) cc_final: 0.3254 (tpt170) REVERT: D 360 MET cc_start: -0.1694 (pmm) cc_final: -0.3076 (ttm) REVERT: D 455 MET cc_start: -0.4098 (tmm) cc_final: -0.4616 (tmm) REVERT: D 483 ASP cc_start: 0.5453 (m-30) cc_final: 0.5200 (t0) REVERT: D 608 THR cc_start: 0.7478 (m) cc_final: 0.6946 (p) outliers start: 1 outliers final: 0 residues processed: 423 average time/residue: 0.1571 time to fit residues: 105.3373 Evaluate side-chains 213 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 30.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 164 ASN A 564 GLN A 675 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 644 GLN C 17 ASN C 121 ASN 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 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 607 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.131949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094407 restraints weight = 120943.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096479 restraints weight = 64583.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096188 restraints weight = 36963.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096540 restraints weight = 39559.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.096744 restraints weight = 33572.650| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 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 = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.892 28988 Z= 0.638 Angle : 0.842 45.473 39479 Z= 0.424 Chirality : 0.050 0.931 4423 Planarity : 0.006 0.120 5115 Dihedral : 5.761 42.751 3842 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.00 % Favored : 91.83 % Rotamer: Outliers : 3.08 % Allowed : 16.31 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.14), residues: 3540 helix: 0.67 (0.17), residues: 945 sheet: -0.53 (0.22), residues: 547 loop : -2.28 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 169 TYR 0.030 0.002 TYR D 279 PHE 0.036 0.002 PHE D 464 TRP 0.039 0.003 TRP D 165 HIS 0.010 0.002 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.01692 (28947) covalent geometry : angle 0.83789 (39397) SS BOND : bond 0.00476 ( 41) SS BOND : angle 1.94662 ( 82) hydrogen bonds : bond 0.07876 ( 1042) hydrogen bonds : angle 5.98849 ( 3035) *********************** 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 324 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 227 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7314 (t80) cc_final: 0.7071 (t80) REVERT: A 190 ARG cc_start: 0.7378 (mpt-90) cc_final: 0.6915 (mtm180) REVERT: A 200 TYR cc_start: 0.8493 (m-80) cc_final: 0.8176 (t80) REVERT: A 223 LEU cc_start: 0.7724 (mt) cc_final: 0.6793 (tt) REVERT: A 393 THR cc_start: 0.3705 (p) cc_final: 0.3370 (p) REVERT: A 505 TYR cc_start: 0.4095 (OUTLIER) cc_final: 0.3507 (t80) REVERT: A 641 ASN cc_start: 0.7709 (m110) cc_final: 0.7351 (t0) REVERT: A 740 MET cc_start: 0.8253 (tmm) cc_final: 0.7137 (tmm) REVERT: B 16 VAL cc_start: 0.2382 (OUTLIER) cc_final: 0.2105 (m) REVERT: B 65 PHE cc_start: 0.7245 (t80) cc_final: 0.6724 (t80) REVERT: B 226 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7625 (tp) REVERT: B 229 LEU cc_start: 0.8144 (tp) cc_final: 0.7392 (mp) REVERT: B 265 TYR cc_start: 0.6294 (p90) cc_final: 0.5964 (p90) REVERT: B 787 GLN cc_start: 0.8900 (mp10) cc_final: 0.8628 (mm110) REVERT: C 14 GLN cc_start: 0.6027 (mp10) cc_final: 0.5112 (tp40) REVERT: C 15 CYS cc_start: -0.1809 (OUTLIER) cc_final: -0.2317 (t) REVERT: C 64 TRP cc_start: 0.7166 (t60) cc_final: 0.6154 (t60) REVERT: C 79 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7382 (m-40) REVERT: C 118 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8794 (mp) REVERT: C 133 PHE cc_start: 0.8395 (m-80) cc_final: 0.8151 (m-80) REVERT: C 190 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6360 (mpt-90) REVERT: D 56 ASP cc_start: 0.6799 (p0) cc_final: 0.6410 (m-30) REVERT: D 266 LEU cc_start: 0.4796 (mm) cc_final: 0.3996 (tp) REVERT: D 335 GLU cc_start: 0.1585 (mt-10) cc_final: 0.0545 (pp20) REVERT: D 345 HIS cc_start: 0.4992 (t-170) cc_final: 0.4471 (m90) REVERT: D 360 MET cc_start: -0.0551 (pmm) cc_final: -0.2752 (ttm) REVERT: D 516 TYR cc_start: 0.0330 (t80) cc_final: 0.0011 (t80) outliers start: 97 outliers final: 48 residues processed: 308 average time/residue: 0.1436 time to fit residues: 73.0557 Evaluate side-chains 236 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 140 PHE 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 770 ILE 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 16 VAL 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 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU 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 649 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 858 LEU 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 105 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 165 ASN 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 32 PHE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 190 MET 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 392 LEU Chi-restraints excluded: chain D residue 449 THR 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 96 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 276 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1135 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.130348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092080 restraints weight = 110450.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094301 restraints weight = 59065.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093957 restraints weight = 35046.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094461 restraints weight = 34708.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094255 restraints weight = 32755.228| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.881 28988 Z= 0.636 Angle : 0.798 45.305 39479 Z= 0.402 Chirality : 0.049 0.923 4423 Planarity : 0.006 0.090 5115 Dihedral : 5.575 29.040 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.21 % Favored : 92.65 % Rotamer: Outliers : 4.32 % Allowed : 16.88 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.14), residues: 3540 helix: 0.61 (0.17), residues: 961 sheet: -0.50 (0.21), residues: 574 loop : -2.29 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 305 TYR 0.029 0.002 TYR D 41 PHE 0.031 0.002 PHE D 464 TRP 0.034 0.003 TRP D 165 HIS 0.011 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.01691 (28947) covalent geometry : angle 0.79459 (39397) SS BOND : bond 0.00403 ( 41) SS BOND : angle 1.81335 ( 82) hydrogen bonds : bond 0.07924 ( 1042) hydrogen bonds : angle 5.65661 ( 3035) *********************** 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 335 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 199 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7276 (t80) cc_final: 0.6959 (t80) REVERT: A 104 TRP cc_start: 0.6459 (m-10) cc_final: 0.6245 (m-10) REVERT: A 131 CYS cc_start: -0.2777 (OUTLIER) cc_final: -0.3260 (p) REVERT: A 200 TYR cc_start: 0.8538 (m-80) cc_final: 0.8181 (t80) REVERT: A 505 TYR cc_start: 0.4024 (OUTLIER) cc_final: 0.3423 (t80) REVERT: B 33 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7344 (p) REVERT: B 65 PHE cc_start: 0.7543 (t80) cc_final: 0.7094 (t80) REVERT: B 115 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5568 (mm-40) REVERT: B 265 TYR cc_start: 0.6260 (p90) cc_final: 0.5894 (p90) REVERT: C 14 GLN cc_start: 0.5940 (mp10) cc_final: 0.5106 (tp40) REVERT: C 66 HIS cc_start: 0.6522 (OUTLIER) cc_final: 0.5707 (t70) REVERT: C 126 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 190 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6460 (mpt-90) REVERT: D 56 ASP cc_start: 0.6711 (p0) cc_final: 0.6332 (m-30) REVERT: D 158 TYR cc_start: -0.0064 (OUTLIER) cc_final: -0.0455 (t80) REVERT: D 333 LEU cc_start: -0.1002 (OUTLIER) cc_final: -0.1256 (pp) REVERT: D 335 GLU cc_start: 0.1599 (mt-10) cc_final: 0.0654 (pp20) REVERT: D 345 HIS cc_start: 0.5801 (t-170) cc_final: 0.5397 (m90) REVERT: D 360 MET cc_start: -0.0510 (pmm) cc_final: -0.3010 (ttm) REVERT: D 455 MET cc_start: -0.2374 (tmm) cc_final: -0.3432 (tmm) outliers start: 136 outliers final: 72 residues processed: 312 average time/residue: 0.1391 time to fit residues: 72.3041 Evaluate side-chains 249 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 169 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 176 LEU 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 512 VAL Chi-restraints excluded: chain A residue 524 VAL 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 58 PHE Chi-restraints excluded: chain B residue 66 HIS 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 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 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET 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 C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP 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 48 TRP Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 158 TYR 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 333 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 454 TYR 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 115 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 346 optimal weight: 0.1980 chunk 290 optimal weight: 1.9990 chunk 196 optimal weight: 0.4980 chunk 140 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 261 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 66 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 901 GLN C 52 GLN C 79 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.133649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095613 restraints weight = 119372.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097358 restraints weight = 69579.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096843 restraints weight = 42084.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097182 restraints weight = 45101.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097752 restraints weight = 37238.507| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 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 = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.882 28988 Z= 0.619 Angle : 0.726 45.276 39479 Z= 0.356 Chirality : 0.047 0.914 4423 Planarity : 0.005 0.083 5115 Dihedral : 5.135 27.249 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.44 % Rotamer: Outliers : 2.77 % Allowed : 18.66 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.14), residues: 3540 helix: 0.93 (0.17), residues: 953 sheet: -0.23 (0.21), residues: 555 loop : -2.19 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 305 TYR 0.049 0.002 TYR D 381 PHE 0.026 0.001 PHE D 464 TRP 0.033 0.002 TRP D 165 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.01655 (28947) covalent geometry : angle 0.72291 (39397) SS BOND : bond 0.00421 ( 41) SS BOND : angle 1.55111 ( 82) hydrogen bonds : bond 0.06219 ( 1042) hydrogen bonds : angle 5.18167 ( 3035) *********************** 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 297 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 210 time to evaluate : 0.737 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 131 CYS cc_start: -0.2605 (OUTLIER) cc_final: -0.3129 (p) REVERT: A 505 TYR cc_start: 0.3871 (OUTLIER) cc_final: 0.3187 (t80) REVERT: A 508 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.5070 (m-10) REVERT: A 853 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: B 33 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7136 (p) REVERT: B 65 PHE cc_start: 0.7499 (t80) cc_final: 0.7147 (t80) REVERT: B 265 TYR cc_start: 0.6174 (p90) cc_final: 0.5947 (p90) REVERT: B 374 PHE cc_start: 0.7385 (p90) cc_final: 0.6930 (p90) REVERT: B 417 LYS cc_start: 0.9091 (mttt) cc_final: 0.8789 (ttpt) REVERT: B 740 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7443 (ppp) REVERT: B 759 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7373 (t80) REVERT: B 787 GLN cc_start: 0.8871 (mp10) cc_final: 0.8524 (mm110) REVERT: C 14 GLN cc_start: 0.5569 (mp10) cc_final: 0.4920 (tp40) REVERT: C 126 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8589 (t) REVERT: C 190 ARG cc_start: 0.6980 (mtt180) cc_final: 0.6651 (mpt-90) REVERT: C 869 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7874 (pmm) REVERT: C 1019 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8380 (tpt-90) REVERT: C 1029 MET cc_start: 0.9066 (tpp) cc_final: 0.8642 (tmm) REVERT: D 56 ASP cc_start: 0.6663 (p0) cc_final: 0.6289 (m-30) REVERT: D 305 ARG cc_start: 0.3361 (OUTLIER) cc_final: 0.3149 (tpt170) REVERT: D 335 GLU cc_start: 0.1424 (mt-10) cc_final: 0.0743 (pp20) REVERT: D 345 HIS cc_start: 0.5772 (t-170) cc_final: 0.5370 (m90) REVERT: D 360 MET cc_start: -0.0526 (pmm) cc_final: -0.3078 (ttm) REVERT: D 449 THR cc_start: 0.4278 (t) cc_final: 0.3910 (m) REVERT: D 455 MET cc_start: -0.2619 (tmm) cc_final: -0.2980 (tmm) REVERT: D 459 TRP cc_start: -0.0959 (t60) cc_final: -0.1400 (t60) REVERT: D 462 MET cc_start: 0.3639 (mmp) cc_final: 0.3320 (ptt) REVERT: D 512 PHE cc_start: 0.2624 (OUTLIER) cc_final: 0.1769 (m-80) outliers start: 87 outliers final: 51 residues processed: 284 average time/residue: 0.1424 time to fit residues: 67.0185 Evaluate side-chains 239 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 176 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 176 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL 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 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 451 TYR 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 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER 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 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 454 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 338 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 29 optimal weight: 0.2980 chunk 283 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 339 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 B 901 GLN ** C 755 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 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.131658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092674 restraints weight = 136773.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094496 restraints weight = 67473.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096555 restraints weight = 41888.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095388 restraints weight = 37454.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095632 restraints weight = 36070.174| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.881 28988 Z= 0.618 Angle : 0.710 45.351 39479 Z= 0.345 Chirality : 0.046 0.893 4423 Planarity : 0.005 0.074 5115 Dihedral : 4.905 27.060 3842 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.30 % Favored : 93.56 % Rotamer: Outliers : 3.24 % Allowed : 19.04 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.14), residues: 3540 helix: 1.11 (0.17), residues: 958 sheet: -0.18 (0.22), residues: 532 loop : -2.04 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 305 TYR 0.026 0.001 TYR D 279 PHE 0.021 0.001 PHE D 464 TRP 0.036 0.002 TRP D 165 HIS 0.018 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.01654 (28947) covalent geometry : angle 0.70837 (39397) SS BOND : bond 0.00336 ( 41) SS BOND : angle 1.36032 ( 82) hydrogen bonds : bond 0.05767 ( 1042) hydrogen bonds : angle 4.97689 ( 3035) *********************** 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 299 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 197 time to evaluate : 0.869 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 131 CYS cc_start: -0.3077 (OUTLIER) cc_final: -0.3564 (p) REVERT: A 200 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 505 TYR cc_start: 0.3801 (OUTLIER) cc_final: 0.3151 (t80) REVERT: A 508 TYR cc_start: 0.5914 (OUTLIER) cc_final: 0.5099 (m-10) REVERT: A 853 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: A 855 PHE cc_start: 0.7860 (m-80) cc_final: 0.7524 (m-80) REVERT: B 33 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7097 (p) REVERT: B 65 PHE cc_start: 0.7659 (t80) cc_final: 0.7328 (t80) REVERT: B 115 GLN cc_start: 0.5950 (OUTLIER) cc_final: 0.5630 (mm-40) REVERT: B 369 TYR cc_start: 0.8500 (m-10) cc_final: 0.8296 (m-10) REVERT: B 374 PHE cc_start: 0.7372 (p90) cc_final: 0.6936 (p90) REVERT: B 458 LYS cc_start: 0.8122 (tppt) cc_final: 0.7340 (ptmt) REVERT: B 759 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7363 (t80) REVERT: B 787 GLN cc_start: 0.8839 (mp10) cc_final: 0.8460 (mm110) REVERT: C 14 GLN cc_start: 0.5174 (mp10) cc_final: 0.4638 (tp40) REVERT: C 190 ARG cc_start: 0.6983 (mtt180) cc_final: 0.6666 (mmt180) REVERT: C 869 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7838 (pmm) REVERT: C 1029 MET cc_start: 0.8917 (tpp) cc_final: 0.8312 (tmm) REVERT: D 305 ARG cc_start: 0.3359 (OUTLIER) cc_final: 0.3089 (tpt170) REVERT: D 335 GLU cc_start: 0.0898 (mt-10) cc_final: 0.0313 (pp20) REVERT: D 345 HIS cc_start: 0.5677 (t-170) cc_final: 0.5384 (m90) REVERT: D 347 THR cc_start: 0.3346 (OUTLIER) cc_final: 0.2954 (m) REVERT: D 349 TRP cc_start: 0.5374 (m100) cc_final: 0.5134 (m100) REVERT: D 360 MET cc_start: -0.0269 (pmm) cc_final: -0.3103 (ttm) REVERT: D 449 THR cc_start: 0.4411 (t) cc_final: 0.4066 (m) REVERT: D 455 MET cc_start: -0.2062 (tmm) cc_final: -0.2847 (tmm) REVERT: D 459 TRP cc_start: -0.0677 (t60) cc_final: -0.1340 (t60) REVERT: D 462 MET cc_start: 0.3576 (mmp) cc_final: 0.3132 (mmp) REVERT: D 510 TYR cc_start: 0.4029 (t80) cc_final: 0.3620 (t80) REVERT: D 512 PHE cc_start: 0.2364 (OUTLIER) cc_final: 0.1628 (m-80) REVERT: D 572 ARG cc_start: 0.2430 (tpp-160) cc_final: 0.1015 (mmt180) outliers start: 102 outliers final: 62 residues processed: 284 average time/residue: 0.1437 time to fit residues: 67.6930 Evaluate side-chains 251 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 177 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 853 GLN Chi-restraints excluded: chain A residue 869 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 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 329 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 645 THR 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 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 131 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 738 CYS 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 32 PHE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 ARG 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 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 374 HIS Chi-restraints excluded: chain D residue 454 TYR 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 606 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 269 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 134 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.128309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.082179 restraints weight = 120762.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081288 restraints weight = 65885.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082030 restraints weight = 43314.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082775 restraints weight = 34388.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083597 restraints weight = 26630.624| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.873 28988 Z= 0.693 Angle : 0.937 45.879 39479 Z= 0.477 Chirality : 0.053 0.877 4423 Planarity : 0.006 0.072 5115 Dihedral : 5.811 25.103 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.41 % Favored : 90.53 % Rotamer: Outliers : 4.51 % Allowed : 19.33 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.13), residues: 3540 helix: 0.23 (0.16), residues: 965 sheet: -0.59 (0.21), residues: 586 loop : -2.39 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 995 TYR 0.037 0.003 TYR D 381 PHE 0.032 0.003 PHE B1089 TRP 0.043 0.004 TRP D 478 HIS 0.024 0.003 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.01806 (28947) covalent geometry : angle 0.93288 (39397) SS BOND : bond 0.00989 ( 41) SS BOND : angle 2.10543 ( 82) hydrogen bonds : bond 0.10228 ( 1042) hydrogen bonds : angle 5.94995 ( 3035) *********************** 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 311 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 169 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.4413 (m-80) cc_final: 0.3997 (m-80) REVERT: A 104 TRP cc_start: 0.7528 (OUTLIER) cc_final: 0.7031 (m-10) REVERT: A 131 CYS cc_start: -0.3486 (OUTLIER) cc_final: -0.4140 (p) REVERT: A 200 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7507 (t80) REVERT: A 204 TYR cc_start: 0.8269 (m-80) cc_final: 0.7954 (m-10) REVERT: A 505 TYR cc_start: 0.1926 (OUTLIER) cc_final: 0.1703 (t80) REVERT: A 740 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8284 (tpp) REVERT: A 755 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 853 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: A 855 PHE cc_start: 0.7671 (m-80) cc_final: 0.7406 (m-80) REVERT: A 869 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7767 (mtm) REVERT: B 115 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.5553 (mm-40) REVERT: B 236 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 374 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.7049 (p90) REVERT: B 386 LYS cc_start: 0.9151 (tptp) cc_final: 0.8931 (tptp) REVERT: B 409 GLN cc_start: 0.7591 (mt0) cc_final: 0.7313 (tp40) REVERT: B 464 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: B 759 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8152 (t80) REVERT: B 900 MET cc_start: 0.8599 (mmm) cc_final: 0.8383 (mmm) REVERT: B 1111 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: C 14 GLN cc_start: 0.4681 (mp10) cc_final: 0.4115 (tp40) REVERT: C 190 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6967 (mtt-85) REVERT: C 1029 MET cc_start: 0.9222 (tpp) cc_final: 0.8919 (tmm) REVERT: D 455 MET cc_start: -0.3295 (tmm) cc_final: -0.3567 (tmm) REVERT: D 474 MET cc_start: -0.3024 (mpp) cc_final: -0.3289 (ttt) REVERT: D 478 TRP cc_start: 0.2708 (m100) cc_final: 0.1849 (t60) REVERT: D 562 ARG cc_start: 0.4364 (mtt180) cc_final: 0.3348 (tpt170) outliers start: 142 outliers final: 83 residues processed: 287 average time/residue: 0.1541 time to fit residues: 72.8219 Evaluate side-chains 250 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 153 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 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 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 755 GLN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 THR 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 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 553 THR 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 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 254 SER 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 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 606 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 1 optimal weight: 6.9990 chunk 302 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 355 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 288 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 655 HIS ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091624 restraints weight = 140218.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.090842 restraints weight = 74081.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.091091 restraints weight = 50390.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091904 restraints weight = 37515.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091777 restraints weight = 26870.206| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4841 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= 0.622 Angle : 0.746 45.481 39479 Z= 0.366 Chirality : 0.047 0.899 4423 Planarity : 0.005 0.084 5115 Dihedral : 5.178 27.201 3842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 3.37 % Allowed : 20.79 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.14), residues: 3540 helix: 0.93 (0.17), residues: 961 sheet: -0.32 (0.21), residues: 554 loop : -2.25 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 161 TYR 0.041 0.002 TYR D 381 PHE 0.042 0.001 PHE B 453 TRP 0.036 0.002 TRP D 478 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.01659 (28947) covalent geometry : angle 0.74348 (39397) SS BOND : bond 0.00580 ( 41) SS BOND : angle 1.56402 ( 82) hydrogen bonds : bond 0.07075 ( 1042) hydrogen bonds : angle 5.13652 ( 3035) *********************** 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 277 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 171 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.4251 (m-80) cc_final: 0.3846 (m-80) REVERT: A 104 TRP cc_start: 0.7224 (OUTLIER) cc_final: 0.6836 (m-10) REVERT: A 131 CYS cc_start: -0.3599 (OUTLIER) cc_final: -0.4109 (p) REVERT: A 204 TYR cc_start: 0.8118 (m-80) cc_final: 0.7902 (m-10) REVERT: A 505 TYR cc_start: 0.2810 (OUTLIER) cc_final: 0.2340 (t80) REVERT: A 697 MET cc_start: 0.7785 (pmm) cc_final: 0.7580 (ptt) REVERT: A 853 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: A 855 PHE cc_start: 0.7689 (m-80) cc_final: 0.7412 (m-80) REVERT: A 1029 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8278 (tpp) REVERT: B 115 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.5917 (mm-40) REVERT: B 378 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7537 (pttt) REVERT: B 386 LYS cc_start: 0.9108 (tptp) cc_final: 0.8874 (tptp) REVERT: B 740 MET cc_start: 0.8381 (ttp) cc_final: 0.8138 (ttp) REVERT: B 759 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7803 (t80) REVERT: B 900 MET cc_start: 0.8370 (mmm) cc_final: 0.7939 (mtp) REVERT: C 14 GLN cc_start: 0.4637 (mp10) cc_final: 0.4343 (tp40) REVERT: C 190 ARG cc_start: 0.7423 (mtt180) cc_final: 0.6926 (mmt180) REVERT: C 1029 MET cc_start: 0.9198 (tpp) cc_final: 0.8810 (tmm) REVERT: D 28 PHE cc_start: 0.0203 (OUTLIER) cc_final: -0.0116 (t80) REVERT: D 51 ASN cc_start: 0.5088 (m-40) cc_final: 0.4876 (m110) REVERT: D 176 LEU cc_start: 0.1850 (OUTLIER) cc_final: 0.1565 (pt) REVERT: D 265 HIS cc_start: -0.1009 (OUTLIER) cc_final: -0.1431 (p90) REVERT: D 347 THR cc_start: 0.2064 (OUTLIER) cc_final: 0.1698 (p) REVERT: D 455 MET cc_start: -0.1706 (tmm) cc_final: -0.2606 (tmm) REVERT: D 474 MET cc_start: -0.2375 (mpp) cc_final: -0.2875 (ttp) REVERT: D 478 TRP cc_start: 0.2502 (m100) cc_final: 0.1246 (t60) REVERT: D 489 GLU cc_start: 0.2955 (mm-30) cc_final: 0.1373 (mm-30) outliers start: 106 outliers final: 65 residues processed: 262 average time/residue: 0.1421 time to fit residues: 62.0183 Evaluate side-chains 242 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 165 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 LYS 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 505 TYR 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 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1029 MET 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 226 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR 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 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 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 963 VAL Chi-restraints excluded: chain C residue 991 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 163 optimal weight: 0.0060 chunk 212 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 319 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 755 GLN A1088 HIS B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.127479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085162 restraints weight = 116486.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086775 restraints weight = 65720.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086179 restraints weight = 43213.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086423 restraints weight = 43228.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086523 restraints weight = 38690.039| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.873 28988 Z= 0.693 Angle : 0.926 45.451 39479 Z= 0.469 Chirality : 0.053 0.917 4423 Planarity : 0.006 0.094 5115 Dihedral : 5.846 28.036 3842 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.29 % Favored : 89.63 % Rotamer: Outliers : 4.10 % Allowed : 20.44 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.13), residues: 3540 helix: 0.34 (0.16), residues: 973 sheet: -0.86 (0.21), residues: 552 loop : -2.49 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 518 TYR 0.053 0.003 TYR D 521 PHE 0.034 0.002 PHE B 453 TRP 0.031 0.003 TRP D 459 HIS 0.010 0.002 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.01807 (28947) covalent geometry : angle 0.92149 (39397) SS BOND : bond 0.00609 ( 41) SS BOND : angle 2.18288 ( 82) hydrogen bonds : bond 0.09911 ( 1042) hydrogen bonds : angle 5.91101 ( 3035) *********************** 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 285 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 156 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6627 (mmt180) REVERT: A 104 TRP cc_start: 0.6535 (OUTLIER) cc_final: 0.6137 (m-10) REVERT: A 131 CYS cc_start: -0.3272 (OUTLIER) cc_final: -0.3552 (p) REVERT: A 204 TYR cc_start: 0.8145 (m-80) cc_final: 0.7893 (m-10) REVERT: A 421 TYR cc_start: 0.4945 (OUTLIER) cc_final: 0.4600 (m-80) REVERT: A 505 TYR cc_start: 0.2579 (OUTLIER) cc_final: 0.2166 (t80) REVERT: A 697 MET cc_start: 0.8020 (pmm) cc_final: 0.7780 (ptt) REVERT: A 853 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: A 855 PHE cc_start: 0.7781 (m-80) cc_final: 0.7526 (m-80) REVERT: A 869 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7831 (mtm) REVERT: A 1029 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8497 (tpp) REVERT: B 115 GLN cc_start: 0.6045 (OUTLIER) cc_final: 0.5193 (mm-40) REVERT: B 236 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9037 (p) REVERT: B 409 GLN cc_start: 0.7387 (mt0) cc_final: 0.6607 (tp40) REVERT: B 464 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: B 759 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8270 (t80) REVERT: B 1111 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: C 14 GLN cc_start: 0.4756 (mp10) cc_final: 0.3864 (tp40) REVERT: C 15 CYS cc_start: -0.1455 (OUTLIER) cc_final: -0.2514 (t) REVERT: C 190 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6916 (mmt180) REVERT: C 1019 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8315 (tpt-90) REVERT: D 28 PHE cc_start: 0.0224 (OUTLIER) cc_final: -0.0135 (t80) REVERT: D 265 HIS cc_start: -0.0987 (OUTLIER) cc_final: -0.1361 (p90) REVERT: D 455 MET cc_start: -0.2268 (tmm) cc_final: -0.3040 (tmm) REVERT: D 474 MET cc_start: -0.3127 (mpp) cc_final: -0.3400 (ttp) REVERT: D 478 TRP cc_start: 0.2416 (m100) cc_final: 0.1393 (t60) REVERT: D 489 GLU cc_start: 0.2996 (mm-30) cc_final: 0.1732 (mm-30) REVERT: D 562 ARG cc_start: 0.4476 (mtt180) cc_final: 0.3362 (tpt170) outliers start: 129 outliers final: 88 residues processed: 266 average time/residue: 0.1399 time to fit residues: 62.0838 Evaluate side-chains 251 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 146 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain 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 226 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1067 TYR 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 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 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 352 optimal weight: 0.0170 chunk 306 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 335 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.130374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090617 restraints weight = 121999.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092700 restraints weight = 67980.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091421 restraints weight = 49340.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092377 restraints weight = 37162.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092314 restraints weight = 30781.302| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.876 28988 Z= 0.627 Angle : 0.771 45.471 39479 Z= 0.382 Chirality : 0.048 0.905 4423 Planarity : 0.005 0.089 5115 Dihedral : 5.372 29.099 3842 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.57 % Favored : 92.37 % Rotamer: Outliers : 3.27 % Allowed : 21.20 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.14), residues: 3540 helix: 0.87 (0.17), residues: 966 sheet: -0.60 (0.21), residues: 563 loop : -2.38 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 177 TYR 0.031 0.002 TYR D 381 PHE 0.024 0.001 PHE B 453 TRP 0.029 0.002 TRP D 165 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.01671 (28947) covalent geometry : angle 0.76797 (39397) SS BOND : bond 0.00410 ( 41) SS BOND : angle 1.72414 ( 82) hydrogen bonds : bond 0.07725 ( 1042) hydrogen bonds : angle 5.29032 ( 3035) *********************** 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 266 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 163 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6869 (mmt180) REVERT: A 104 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: A 131 CYS cc_start: -0.4185 (OUTLIER) cc_final: -0.4607 (p) REVERT: A 200 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 505 TYR cc_start: 0.3254 (OUTLIER) cc_final: 0.2613 (t80) REVERT: A 508 TYR cc_start: 0.5775 (t80) cc_final: 0.5214 (m-10) REVERT: A 697 MET cc_start: 0.7998 (pmm) cc_final: 0.7712 (ptt) REVERT: A 853 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: A 855 PHE cc_start: 0.7710 (m-80) cc_final: 0.7468 (m-80) REVERT: A 1029 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8254 (tpp) REVERT: B 115 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.5480 (mm-40) REVERT: B 236 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9081 (p) REVERT: B 386 LYS cc_start: 0.9157 (tptp) cc_final: 0.8827 (tptp) REVERT: B 759 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7965 (t80) REVERT: B 900 MET cc_start: 0.8464 (mmm) cc_final: 0.8029 (mtp) REVERT: C 14 GLN cc_start: 0.4696 (mp10) cc_final: 0.4028 (tp40) REVERT: C 543 PHE cc_start: 0.2925 (OUTLIER) cc_final: 0.2617 (t80) REVERT: C 1019 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8390 (tpt-90) REVERT: C 1029 MET cc_start: 0.9241 (tpp) cc_final: 0.8834 (tmm) REVERT: D 28 PHE cc_start: 0.0721 (OUTLIER) cc_final: 0.0196 (t80) REVERT: D 51 ASN cc_start: 0.5198 (m-40) cc_final: 0.4875 (m110) REVERT: D 265 HIS cc_start: -0.1176 (OUTLIER) cc_final: -0.1639 (p90) REVERT: D 455 MET cc_start: -0.2214 (tmm) cc_final: -0.3178 (tmm) REVERT: D 474 MET cc_start: -0.2259 (mpp) cc_final: -0.3059 (ttp) REVERT: D 478 TRP cc_start: 0.2134 (m100) cc_final: 0.0879 (t60) REVERT: D 489 GLU cc_start: 0.2471 (mm-30) cc_final: 0.1389 (mm-30) outliers start: 103 outliers final: 81 residues processed: 250 average time/residue: 0.1488 time to fit residues: 61.1472 Evaluate side-chains 254 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 159 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1029 MET 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 226 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 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 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 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 991 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain 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 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 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 107 optimal weight: 0.0570 chunk 260 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 265 optimal weight: 0.0270 chunk 274 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 355 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.126971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090605 restraints weight = 116910.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.092011 restraints weight = 67535.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091397 restraints weight = 44422.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091861 restraints weight = 44404.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092094 restraints weight = 38464.736| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.876 28988 Z= 0.629 Angle : 0.858 59.198 39479 Z= 0.449 Chirality : 0.048 0.829 4423 Planarity : 0.005 0.062 5115 Dihedral : 5.364 29.135 3842 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.91 % Favored : 92.03 % Rotamer: Outliers : 3.40 % Allowed : 21.14 % Favored : 75.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.14), residues: 3540 helix: 0.88 (0.17), residues: 966 sheet: -0.58 (0.21), residues: 563 loop : -2.37 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 177 TYR 0.027 0.002 TYR D 381 PHE 0.019 0.001 PHE D 464 TRP 0.028 0.002 TRP D 165 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.01673 (28947) covalent geometry : angle 0.85587 (39397) SS BOND : bond 0.00407 ( 41) SS BOND : angle 1.68514 ( 82) hydrogen bonds : bond 0.07691 ( 1042) hydrogen bonds : angle 5.28406 ( 3035) ********************** 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 265 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 158 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6915 (mmt180) REVERT: A 104 TRP cc_start: 0.7330 (OUTLIER) cc_final: 0.7012 (m-10) REVERT: A 131 CYS cc_start: -0.4106 (OUTLIER) cc_final: -0.4537 (p) REVERT: A 200 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 421 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.4276 (m-80) REVERT: A 505 TYR cc_start: 0.3607 (OUTLIER) cc_final: 0.2729 (t80) REVERT: A 508 TYR cc_start: 0.5900 (t80) cc_final: 0.5256 (m-10) REVERT: A 697 MET cc_start: 0.8065 (pmm) cc_final: 0.7738 (ptt) REVERT: A 853 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: A 855 PHE cc_start: 0.7852 (m-80) cc_final: 0.7618 (m-80) REVERT: A 1029 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8313 (tpp) REVERT: B 115 GLN cc_start: 0.5882 (OUTLIER) cc_final: 0.5349 (mm-40) REVERT: B 236 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9052 (p) REVERT: B 386 LYS cc_start: 0.9179 (tptp) cc_final: 0.8826 (tptp) REVERT: B 759 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7976 (t80) REVERT: B 900 MET cc_start: 0.8566 (mmm) cc_final: 0.8157 (mtp) REVERT: C 14 GLN cc_start: 0.4752 (mp10) cc_final: 0.4006 (tp40) REVERT: C 190 ARG cc_start: 0.7582 (mtt180) cc_final: 0.6885 (mmt180) REVERT: C 543 PHE cc_start: 0.2873 (OUTLIER) cc_final: 0.2563 (t80) REVERT: C 1019 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8398 (tpt-90) REVERT: C 1029 MET cc_start: 0.9241 (tpp) cc_final: 0.8823 (tmm) REVERT: D 28 PHE cc_start: 0.1246 (OUTLIER) cc_final: 0.0592 (t80) REVERT: D 51 ASN cc_start: 0.5366 (m-40) cc_final: 0.4883 (m110) REVERT: D 265 HIS cc_start: -0.0675 (OUTLIER) cc_final: -0.1370 (p90) REVERT: D 455 MET cc_start: -0.2730 (tmm) cc_final: -0.3889 (tmm) REVERT: D 474 MET cc_start: -0.1172 (mpp) cc_final: -0.2936 (ttp) REVERT: D 478 TRP cc_start: 0.1894 (m100) cc_final: 0.0997 (t60) REVERT: D 489 GLU cc_start: 0.3333 (mm-30) cc_final: 0.2797 (mm-30) outliers start: 107 outliers final: 86 residues processed: 250 average time/residue: 0.1379 time to fit residues: 57.2224 Evaluate side-chains 258 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 157 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1029 MET 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 226 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 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 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 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 543 PHE 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 991 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain 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 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 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 62 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 chunk 286 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.126804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089964 restraints weight = 110350.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092043 restraints weight = 61373.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091772 restraints weight = 38173.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.092072 restraints weight = 42226.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092128 restraints weight = 33755.945| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.876 28988 Z= 0.633 Angle : 0.862 59.198 39479 Z= 0.450 Chirality : 0.048 0.829 4423 Planarity : 0.005 0.062 5115 Dihedral : 5.364 29.135 3842 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.91 % Favored : 92.03 % Rotamer: Outliers : 3.21 % Allowed : 21.23 % Favored : 75.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.14), residues: 3540 helix: 0.88 (0.17), residues: 966 sheet: -0.58 (0.21), residues: 563 loop : -2.37 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 177 TYR 0.027 0.002 TYR D 381 PHE 0.019 0.001 PHE D 464 TRP 0.028 0.002 TRP D 165 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.01673 (28947) covalent geometry : angle 0.85587 (39397) SS BOND : bond 0.03746 ( 41) SS BOND : angle 2.41255 ( 82) hydrogen bonds : bond 0.07691 ( 1042) hydrogen bonds : angle 5.28406 ( 3035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5908.83 seconds wall clock time: 102 minutes 9.49 seconds (6129.49 seconds total)