Starting phenix.real_space_refine on Wed Jun 25 19:44:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9c_32364/06_2025/7w9c_32364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9c_32364/06_2025/7w9c_32364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w9c_32364/06_2025/7w9c_32364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9c_32364/06_2025/7w9c_32364.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9c_32364/06_2025/7w9c_32364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9c_32364/06_2025/7w9c_32364.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.102 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 143 5.16 5 C 18970 2.51 5 N 4982 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 235 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 18.75, per 1000 atoms: 0.63 Number of scatterers: 29737 At special positions: 0 Unit cell: (156.299, 173.787, 241.553, 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 143 16.00 O 5642 8.00 N 4982 7.00 C 18970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.02 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 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=2.03 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 A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 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: 7.59 Conformation dependent library (CDL) restraints added in 3.9 seconds 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7076 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 51 sheets defined 29.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.550A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.532A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.322A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.613A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.565A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 780 removed outlier: 3.593A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.583A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.556A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) 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 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.359A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.527A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.067A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.549A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.719A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.779A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.736A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.507A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.984A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.288A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.837A pdb=" N ALA A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.658A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.563A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.579A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix removed outlier: 3.668A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 4.007A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.828A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.317A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.596A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.528A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.792A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.600A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.529A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.534A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.585A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.144A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.809A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.882A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.692A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.185A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.564A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.573A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.626A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.503A pdb=" N TYR D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.627A pdb=" N ASN D 764 " --> pdb=" O CYS D 760 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 823 removed outlier: 3.636A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.517A pdb=" N GLN D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.133A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.849A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.909A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.567A pdb=" N LYS D 933 " --> pdb=" O SER D 929 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.986A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 958 " --> pdb=" O GLN D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.184A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 removed outlier: 4.182A pdb=" N ASP D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.553A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.997A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.624A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.512A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 327 removed outlier: 4.440A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.671A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.576A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.688A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.191A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.463A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.678A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.689A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.067A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.792A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.275A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.608A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.796A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.180A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.751A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (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 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AD8, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.381A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.073A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.722A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.925A pdb=" N VAL D 47 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS D 49 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.266A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 319 removed outlier: 3.543A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.039A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AE7, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.511A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.260A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 673 " --> pdb=" O ILE D 693 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.580A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'D' and resid 718 through 722 removed outlier: 7.059A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'D' and resid 1121 through 1125 removed outlier: 4.001A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3141 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: 14.47 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9635 1.35 - 1.47: 7583 1.47 - 1.59: 13032 1.59 - 1.71: 0 1.71 - 1.83: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" C LYS D 424 " pdb=" N LEU D 425 " ideal model delta sigma weight residual 1.327 1.354 -0.027 1.39e-02 5.18e+03 3.87e+00 bond pdb=" C VAL B 860 " pdb=" N LEU B 861 " ideal model delta sigma weight residual 1.330 1.304 0.026 1.47e-02 4.63e+03 3.19e+00 bond pdb=" N SER A 19 " pdb=" CA SER A 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N GLN D 14 " pdb=" CA GLN D 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 41213 3.55 - 7.11: 180 7.11 - 10.66: 1 10.66 - 14.21: 0 14.21 - 17.76: 2 Bond angle restraints: 41396 Sorted by residual: angle pdb=" CA CYS C 166 " pdb=" CB CYS C 166 " pdb=" SG CYS C 166 " ideal model delta sigma weight residual 114.40 132.16 -17.76 2.30e+00 1.89e-01 5.97e+01 angle pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 114.40 131.46 -17.06 2.30e+00 1.89e-01 5.50e+01 angle pdb=" CA VAL A 491 " pdb=" C VAL A 491 " pdb=" N PRO A 492 " ideal model delta sigma weight residual 116.57 119.90 -3.33 9.80e-01 1.04e+00 1.15e+01 angle pdb=" CA LEU C 582 " pdb=" CB LEU C 582 " pdb=" CG LEU C 582 " ideal model delta sigma weight residual 116.30 125.00 -8.70 3.50e+00 8.16e-02 6.17e+00 angle pdb=" N ASP D 215 " pdb=" CA ASP D 215 " pdb=" CB ASP D 215 " ideal model delta sigma weight residual 113.65 110.03 3.62 1.47e+00 4.63e-01 6.06e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 16792 17.89 - 35.78: 1094 35.78 - 53.67: 164 53.67 - 71.56: 65 71.56 - 89.46: 21 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 45.19 47.81 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -128.82 42.82 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -123.52 37.52 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2822 0.031 - 0.063: 1264 0.063 - 0.094: 236 0.094 - 0.125: 260 0.125 - 0.156: 34 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE D 714 " pdb=" N ILE D 714 " pdb=" C ILE D 714 " pdb=" CB ILE D 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE C 712 " pdb=" N ILE C 712 " pdb=" C ILE C 712 " pdb=" CB ILE C 712 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 84 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO B 85 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 927 " -0.001 2.00e-02 2.50e+03 1.37e-02 3.30e+00 pdb=" CG PHE B 927 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 927 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 927 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 927 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 927 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 927 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 800 " -0.012 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE B 800 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 800 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 800 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 800 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 800 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 800 " -0.016 2.00e-02 2.50e+03 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 304 2.64 - 3.21: 26566 3.21 - 3.77: 43240 3.77 - 4.34: 63173 4.34 - 4.90: 104024 Nonbonded interactions: 237307 Sorted by model distance: nonbonded pdb=" O GLN B 755 " pdb=" OG SER D 968 " model vdw 2.079 3.040 nonbonded pdb=" O SER B 937 " pdb=" OG1 THR B 941 " model vdw 2.084 3.040 nonbonded pdb=" O GLN C 755 " pdb=" OG SER B 968 " model vdw 2.088 3.040 nonbonded pdb=" O VAL D 367 " pdb=" OG SER D 371 " model vdw 2.097 3.040 nonbonded pdb=" OG SER C 708 " pdb=" OG SER C 711 " model vdw 2.132 3.040 ... (remaining 237302 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 74.290 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 : 0.004 0.047 30486 Z= 0.180 Angle : 0.614 17.764 41480 Z= 0.340 Chirality : 0.042 0.156 4616 Planarity : 0.003 0.052 5375 Dihedral : 12.685 89.456 10934 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.11), residues: 3733 helix: -2.94 (0.10), residues: 1017 sheet: -2.34 (0.16), residues: 695 loop : -2.23 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 152 HIS 0.007 0.001 HIS C 519 PHE 0.025 0.001 PHE B 800 TYR 0.011 0.001 TYR D 707 ARG 0.006 0.000 ARG D1039 Details of bonding type rmsd hydrogen bonds : bond 0.26966 ( 1107) hydrogen bonds : angle 9.57067 ( 3141) SS BOND : bond 0.00244 ( 42) SS BOND : angle 0.97586 ( 84) covalent geometry : bond 0.00409 (30444) covalent geometry : angle 0.61300 (41396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 730 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.3616 (mmt) cc_final: -0.3963 (mmt) REVERT: C 226 LEU cc_start: 0.7483 (tp) cc_final: 0.7218 (tp) REVERT: C 229 LEU cc_start: 0.7000 (mt) cc_final: 0.6781 (mp) REVERT: C 562 PHE cc_start: 0.4290 (m-80) cc_final: 0.4052 (m-80) REVERT: B 117 LEU cc_start: 0.8357 (tp) cc_final: 0.7945 (mp) REVERT: B 133 PHE cc_start: 0.7469 (m-80) cc_final: 0.6592 (m-80) REVERT: B 135 PHE cc_start: 0.5881 (m-80) cc_final: 0.5600 (m-80) REVERT: B 335 LEU cc_start: 0.6099 (mt) cc_final: 0.5656 (pt) REVERT: A 27 THR cc_start: 0.5135 (m) cc_final: 0.4644 (t) REVERT: A 34 HIS cc_start: 0.7317 (t70) cc_final: 0.6626 (m90) REVERT: A 74 LYS cc_start: 0.4914 (mmmt) cc_final: 0.4665 (ptpt) REVERT: A 225 ASP cc_start: 0.5011 (m-30) cc_final: 0.4703 (t0) REVERT: A 366 MET cc_start: 0.2196 (tpt) cc_final: 0.0379 (ttt) REVERT: A 555 PHE cc_start: 0.5144 (t80) cc_final: 0.4943 (t80) REVERT: A 557 MET cc_start: 0.5465 (ttp) cc_final: 0.4634 (tmm) REVERT: A 579 MET cc_start: 0.1514 (mtm) cc_final: 0.1289 (mtm) REVERT: D 129 LYS cc_start: 0.7884 (mttt) cc_final: 0.7480 (mmmt) REVERT: D 140 PHE cc_start: 0.4018 (p90) cc_final: 0.3802 (p90) REVERT: D 346 ARG cc_start: 0.7525 (mmt-90) cc_final: 0.7111 (mmm-85) REVERT: D 643 PHE cc_start: 0.5081 (m-80) cc_final: 0.4878 (m-80) REVERT: D 697 MET cc_start: 0.7101 (ptm) cc_final: 0.6810 (ptm) outliers start: 0 outliers final: 0 residues processed: 730 average time/residue: 0.4419 time to fit residues: 501.8734 Evaluate side-chains 364 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 295 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 519 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 787 GLN C1071 GLN B 66 HIS B 87 ASN B 196 ASN B 501 ASN B 536 ASN B 709 ASN B 755 GLN B 804 GLN B 926 GLN B 935 GLN B 965 GLN B1074 ASN B1101 HIS A 117 ASN A 149 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN D 188 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 334 ASN D 607 GLN D 703 ASN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D1101 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.187084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.152251 restraints weight = 64695.691| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.05 r_work: 0.3856 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30486 Z= 0.151 Angle : 0.572 9.753 41480 Z= 0.299 Chirality : 0.045 0.201 4616 Planarity : 0.004 0.045 5375 Dihedral : 4.052 26.094 4050 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.91 % Allowed : 8.90 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 3733 helix: -0.45 (0.15), residues: 993 sheet: -1.50 (0.17), residues: 731 loop : -1.44 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 258 HIS 0.006 0.001 HIS A 535 PHE 0.023 0.002 PHE C 55 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.001 ARG C 454 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 1107) hydrogen bonds : angle 5.81036 ( 3141) SS BOND : bond 0.00503 ( 42) SS BOND : angle 2.06022 ( 84) covalent geometry : bond 0.00345 (30444) covalent geometry : angle 0.56531 (41396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 420 time to evaluate : 3.469 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: C 92 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7438 (t80) REVERT: C 187 LYS cc_start: 0.4501 (mmtt) cc_final: 0.4167 (ttmm) REVERT: C 516 GLU cc_start: 0.3862 (mm-30) cc_final: 0.3147 (mm-30) REVERT: C 562 PHE cc_start: 0.4950 (m-80) cc_final: 0.4546 (m-80) REVERT: C 904 TYR cc_start: 0.7314 (t80) cc_final: 0.6954 (t80) REVERT: B 135 PHE cc_start: 0.5798 (m-80) cc_final: 0.5438 (m-80) REVERT: B 335 LEU cc_start: 0.5979 (mt) cc_final: 0.5476 (pt) REVERT: A 225 ASP cc_start: 0.5324 (m-30) cc_final: 0.4796 (t0) REVERT: A 328 TRP cc_start: 0.6164 (m100) cc_final: 0.5879 (m100) REVERT: A 366 MET cc_start: 0.2065 (tpt) cc_final: 0.0630 (ttt) REVERT: A 430 GLU cc_start: 0.4482 (mm-30) cc_final: 0.4159 (mm-30) REVERT: A 514 ARG cc_start: 0.5853 (ptm160) cc_final: 0.5636 (mmt180) REVERT: A 557 MET cc_start: 0.6198 (ttp) cc_final: 0.5831 (ppp) REVERT: A 579 MET cc_start: 0.1169 (mtm) cc_final: 0.0259 (mtm) REVERT: D 140 PHE cc_start: 0.4459 (p90) cc_final: 0.4211 (p90) REVERT: D 346 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7280 (mmm-85) REVERT: D 643 PHE cc_start: 0.5835 (m-80) cc_final: 0.5552 (m-80) REVERT: D 1119 ASN cc_start: 0.7701 (m-40) cc_final: 0.7486 (m110) outliers start: 63 outliers final: 32 residues processed: 462 average time/residue: 0.4256 time to fit residues: 319.8361 Evaluate side-chains 358 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 325 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 703 ASN Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 316 optimal weight: 0.0270 chunk 370 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 655 HIS C 751 ASN B 121 ASN B 188 ASN B 540 ASN B 709 ASN B 774 GLN B 914 ASN A 34 HIS ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 774 GLN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.181403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.146639 restraints weight = 64458.329| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.00 r_work: 0.3775 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30486 Z= 0.190 Angle : 0.590 8.382 41480 Z= 0.310 Chirality : 0.046 0.216 4616 Planarity : 0.004 0.044 5375 Dihedral : 4.367 21.018 4050 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.18 % Allowed : 11.21 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3733 helix: 0.31 (0.16), residues: 999 sheet: -1.17 (0.17), residues: 736 loop : -1.25 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 64 HIS 0.006 0.001 HIS C 655 PHE 0.019 0.002 PHE C 186 TYR 0.017 0.002 TYR C1067 ARG 0.008 0.001 ARG D 452 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 1107) hydrogen bonds : angle 5.42628 ( 3141) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.80427 ( 84) covalent geometry : bond 0.00447 (30444) covalent geometry : angle 0.58522 (41396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 358 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7855 (t80) REVERT: C 187 LYS cc_start: 0.4899 (mmtt) cc_final: 0.4528 (ttmm) REVERT: C 904 TYR cc_start: 0.7481 (t80) cc_final: 0.7037 (t80) REVERT: C 1041 ASP cc_start: 0.7876 (t0) cc_final: 0.7675 (t0) REVERT: B 177 MET cc_start: 0.0026 (ttp) cc_final: -0.0199 (ttp) REVERT: B 335 LEU cc_start: 0.5761 (mt) cc_final: 0.5230 (pt) REVERT: A 23 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6922 (mp0) REVERT: A 34 HIS cc_start: 0.7341 (t-90) cc_final: 0.6916 (m90) REVERT: A 225 ASP cc_start: 0.5345 (m-30) cc_final: 0.5061 (m-30) REVERT: A 366 MET cc_start: 0.2305 (tpt) cc_final: 0.0864 (ttt) REVERT: D 140 PHE cc_start: 0.4497 (p90) cc_final: 0.4198 (p90) REVERT: D 342 PHE cc_start: 0.7095 (m-80) cc_final: 0.6830 (m-80) REVERT: D 346 ARG cc_start: 0.7908 (mmt-90) cc_final: 0.7290 (mmm-85) REVERT: D 498 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: D 737 ASP cc_start: 0.8394 (t0) cc_final: 0.8146 (t0) REVERT: D 754 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9126 (tp) outliers start: 72 outliers final: 49 residues processed: 415 average time/residue: 0.3976 time to fit residues: 267.6659 Evaluate side-chains 357 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 373 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 252 optimal weight: 8.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 914 ASN C 965 GLN C1074 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 556 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 703 ASN D 762 GLN D 914 ASN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.179428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143065 restraints weight = 64335.303| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.54 r_work: 0.3773 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30486 Z= 0.181 Angle : 0.579 13.964 41480 Z= 0.303 Chirality : 0.045 0.176 4616 Planarity : 0.004 0.046 5375 Dihedral : 4.515 27.306 4050 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.94 % Allowed : 12.78 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3733 helix: 0.67 (0.16), residues: 990 sheet: -0.97 (0.17), residues: 742 loop : -1.20 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 275 HIS 0.005 0.001 HIS A 374 PHE 0.020 0.002 PHE C 186 TYR 0.027 0.002 TYR B 91 ARG 0.005 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 1107) hydrogen bonds : angle 5.26972 ( 3141) SS BOND : bond 0.00363 ( 42) SS BOND : angle 2.01944 ( 84) covalent geometry : bond 0.00429 (30444) covalent geometry : angle 0.57265 (41396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 341 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.8024 (t80) REVERT: C 187 LYS cc_start: 0.4931 (mmtt) cc_final: 0.4553 (ttmm) REVERT: C 353 TRP cc_start: -0.0518 (p-90) cc_final: -0.0744 (p-90) REVERT: C 745 ASP cc_start: 0.7967 (t0) cc_final: 0.7742 (t0) REVERT: C 904 TYR cc_start: 0.7630 (t80) cc_final: 0.7197 (t80) REVERT: C 1041 ASP cc_start: 0.8095 (t0) cc_final: 0.7840 (t0) REVERT: C 1107 ARG cc_start: 0.7652 (mtt-85) cc_final: 0.6117 (tpt170) REVERT: B 135 PHE cc_start: 0.5689 (m-80) cc_final: 0.5057 (m-80) REVERT: B 335 LEU cc_start: 0.5728 (mt) cc_final: 0.5189 (pt) REVERT: B 546 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7966 (mp) REVERT: B 787 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8111 (mm-40) REVERT: B 1019 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8392 (ttp80) REVERT: A 23 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6905 (mp0) REVERT: A 366 MET cc_start: 0.2254 (tpt) cc_final: 0.0738 (ttt) REVERT: A 555 PHE cc_start: 0.5858 (t80) cc_final: 0.5543 (t80) REVERT: D 92 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: D 140 PHE cc_start: 0.4268 (p90) cc_final: 0.4039 (p90) REVERT: D 346 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.7343 (mmm-85) REVERT: D 408 ARG cc_start: 0.7738 (ppt170) cc_final: 0.7152 (ppt170) REVERT: D 412 PRO cc_start: 0.7072 (Cg_exo) cc_final: 0.6690 (Cg_endo) REVERT: D 498 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: D 754 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9131 (tp) REVERT: D 918 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7586 (mp0) outliers start: 97 outliers final: 66 residues processed: 408 average time/residue: 0.3945 time to fit residues: 264.1265 Evaluate side-chains 372 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 300 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 362 optimal weight: 4.9990 chunk 296 optimal weight: 0.1980 chunk 272 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 556 ASN D 188 ASN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.181384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.145678 restraints weight = 63886.272| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.57 r_work: 0.3810 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30486 Z= 0.116 Angle : 0.509 9.320 41480 Z= 0.265 Chirality : 0.043 0.150 4616 Planarity : 0.004 0.044 5375 Dihedral : 4.192 32.340 4050 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.70 % Allowed : 13.60 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 3733 helix: 1.06 (0.17), residues: 994 sheet: -0.87 (0.17), residues: 768 loop : -1.04 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.019 0.001 PHE A 369 TYR 0.027 0.001 TYR B 365 ARG 0.009 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1107) hydrogen bonds : angle 5.01363 ( 3141) SS BOND : bond 0.00359 ( 42) SS BOND : angle 1.78937 ( 84) covalent geometry : bond 0.00266 (30444) covalent geometry : angle 0.50299 (41396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 336 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.8050 (t80) REVERT: C 187 LYS cc_start: 0.4748 (mmtt) cc_final: 0.4401 (ttmm) REVERT: C 745 ASP cc_start: 0.7762 (t0) cc_final: 0.7538 (t0) REVERT: C 779 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: C 904 TYR cc_start: 0.7687 (t80) cc_final: 0.7282 (t80) REVERT: C 1041 ASP cc_start: 0.8086 (t0) cc_final: 0.7824 (t0) REVERT: C 1107 ARG cc_start: 0.7538 (mtt-85) cc_final: 0.6052 (tpt170) REVERT: B 135 PHE cc_start: 0.5894 (m-80) cc_final: 0.5242 (m-80) REVERT: B 335 LEU cc_start: 0.5859 (mt) cc_final: 0.5365 (pt) REVERT: B 505 TYR cc_start: 0.4186 (m-80) cc_final: 0.3941 (t80) REVERT: B 546 LEU cc_start: 0.8189 (mt) cc_final: 0.7820 (mp) REVERT: A 23 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6665 (mp0) REVERT: A 313 LYS cc_start: 0.6383 (mttp) cc_final: 0.5636 (tttt) REVERT: A 366 MET cc_start: 0.2166 (tpt) cc_final: 0.0559 (ttt) REVERT: A 402 GLU cc_start: 0.4659 (OUTLIER) cc_final: 0.4358 (mm-30) REVERT: A 555 PHE cc_start: 0.6075 (t80) cc_final: 0.5776 (t80) REVERT: D 92 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: D 346 ARG cc_start: 0.7984 (mmt-90) cc_final: 0.7341 (mmm-85) REVERT: D 408 ARG cc_start: 0.7777 (ppt170) cc_final: 0.7340 (ppt170) REVERT: D 412 PRO cc_start: 0.7068 (Cg_exo) cc_final: 0.6693 (Cg_endo) REVERT: D 498 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: D 754 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9049 (tp) REVERT: D 918 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: D 1114 ILE cc_start: 0.9392 (mm) cc_final: 0.9177 (mm) outliers start: 89 outliers final: 50 residues processed: 402 average time/residue: 0.4659 time to fit residues: 312.2591 Evaluate side-chains 359 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 302 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 366 optimal weight: 0.3980 chunk 238 optimal weight: 0.5980 chunk 226 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 275 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 542 ASN C1142 GLN B 81 ASN B 239 GLN A 34 HIS ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS D 779 GLN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.181906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.146815 restraints weight = 64332.451| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.69 r_work: 0.3797 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30486 Z= 0.113 Angle : 0.501 11.033 41480 Z= 0.259 Chirality : 0.043 0.150 4616 Planarity : 0.003 0.045 5375 Dihedral : 4.058 22.943 4050 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.51 % Allowed : 14.48 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 3733 helix: 1.24 (0.17), residues: 995 sheet: -0.67 (0.17), residues: 772 loop : -0.95 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 275 HIS 0.007 0.001 HIS A 373 PHE 0.020 0.001 PHE D 338 TYR 0.016 0.001 TYR C1067 ARG 0.007 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 1107) hydrogen bonds : angle 4.87595 ( 3141) SS BOND : bond 0.00564 ( 42) SS BOND : angle 1.31213 ( 84) covalent geometry : bond 0.00256 (30444) covalent geometry : angle 0.49832 (41396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 330 time to evaluate : 3.348 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: C 92 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7920 (t80) REVERT: C 187 LYS cc_start: 0.4328 (mmtt) cc_final: 0.4062 (ttmm) REVERT: C 779 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: C 904 TYR cc_start: 0.7401 (t80) cc_final: 0.7041 (t80) REVERT: C 1041 ASP cc_start: 0.7927 (t0) cc_final: 0.7675 (t0) REVERT: B 135 PHE cc_start: 0.5821 (m-80) cc_final: 0.5355 (m-80) REVERT: B 335 LEU cc_start: 0.5812 (mt) cc_final: 0.5294 (pt) REVERT: A 23 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6713 (mp0) REVERT: A 34 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6671 (m90) REVERT: A 366 MET cc_start: 0.2038 (tpt) cc_final: 0.0479 (ttt) REVERT: A 402 GLU cc_start: 0.4534 (OUTLIER) cc_final: 0.4219 (mm-30) REVERT: A 555 PHE cc_start: 0.6074 (t80) cc_final: 0.5736 (t80) REVERT: D 92 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6683 (m-80) REVERT: D 346 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7383 (mmm-85) REVERT: D 408 ARG cc_start: 0.7716 (ppt170) cc_final: 0.7309 (ppt170) REVERT: D 412 PRO cc_start: 0.7017 (Cg_exo) cc_final: 0.6650 (Cg_endo) REVERT: D 498 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: D 918 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: D 1114 ILE cc_start: 0.9389 (mm) cc_final: 0.9180 (mm) outliers start: 83 outliers final: 59 residues processed: 392 average time/residue: 0.4180 time to fit residues: 275.9519 Evaluate side-chains 364 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 129 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 301 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN B 81 ASN B 239 GLN B 955 ASN A 34 HIS ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN D 655 HIS ** D1106 GLN ** 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 = 0.4385 r_free = 0.4385 target = 0.178244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.142148 restraints weight = 63891.291| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.31 r_work: 0.3763 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30486 Z= 0.182 Angle : 0.579 10.660 41480 Z= 0.301 Chirality : 0.045 0.196 4616 Planarity : 0.004 0.046 5375 Dihedral : 4.473 21.243 4050 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.91 % Allowed : 14.99 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3733 helix: 1.04 (0.17), residues: 1005 sheet: -0.70 (0.17), residues: 773 loop : -1.05 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 275 HIS 0.035 0.001 HIS A 34 PHE 0.027 0.002 PHE D 541 TYR 0.019 0.002 TYR C 396 ARG 0.007 0.001 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1107) hydrogen bonds : angle 5.03614 ( 3141) SS BOND : bond 0.00445 ( 42) SS BOND : angle 1.43359 ( 84) covalent geometry : bond 0.00430 (30444) covalent geometry : angle 0.57607 (41396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 305 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8106 (t80) REVERT: C 187 LYS cc_start: 0.4741 (mmtt) cc_final: 0.4433 (ttmm) REVERT: C 904 TYR cc_start: 0.7866 (t80) cc_final: 0.7405 (t80) REVERT: C 1107 ARG cc_start: 0.7619 (mtt-85) cc_final: 0.6184 (tpt170) REVERT: B 153 MET cc_start: -0.1530 (ptm) cc_final: -0.2392 (ptt) REVERT: A 23 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6904 (mp0) REVERT: A 34 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.6904 (m170) REVERT: A 313 LYS cc_start: 0.6197 (mttp) cc_final: 0.5721 (tttt) REVERT: A 327 PHE cc_start: 0.5435 (t80) cc_final: 0.5193 (t80) REVERT: A 402 GLU cc_start: 0.4357 (OUTLIER) cc_final: 0.4134 (mm-30) REVERT: D 92 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: D 346 ARG cc_start: 0.8197 (mmt-90) cc_final: 0.7480 (mmm-85) REVERT: D 408 ARG cc_start: 0.7753 (ppt170) cc_final: 0.7379 (ppt170) REVERT: D 412 PRO cc_start: 0.6920 (Cg_exo) cc_final: 0.6547 (Cg_endo) REVERT: D 498 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: D 918 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: D 1114 ILE cc_start: 0.9434 (mm) cc_final: 0.9184 (mm) REVERT: D 1123 SER cc_start: 0.8665 (m) cc_final: 0.8436 (m) outliers start: 96 outliers final: 77 residues processed: 382 average time/residue: 0.4013 time to fit residues: 256.1320 Evaluate side-chains 371 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 288 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 151 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 335 optimal weight: 0.7980 chunk 257 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN B 774 GLN A 34 HIS ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN D 394 ASN ** D 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** 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 = 0.4426 r_free = 0.4426 target = 0.181110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148739 restraints weight = 64086.455| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.68 r_work: 0.3808 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30486 Z= 0.116 Angle : 0.514 9.000 41480 Z= 0.267 Chirality : 0.043 0.166 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.175 20.756 4050 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 15.90 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 3733 helix: 1.29 (0.17), residues: 997 sheet: -0.60 (0.17), residues: 773 loop : -0.94 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 275 HIS 0.029 0.001 HIS A 34 PHE 0.037 0.001 PHE D 541 TYR 0.032 0.001 TYR D 473 ARG 0.007 0.000 ARG D1107 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1107) hydrogen bonds : angle 4.84636 ( 3141) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.52700 ( 84) covalent geometry : bond 0.00267 (30444) covalent geometry : angle 0.50981 (41396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 307 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8113 (t80) REVERT: C 140 PHE cc_start: 0.6327 (p90) cc_final: 0.5715 (p90) REVERT: C 187 LYS cc_start: 0.4542 (mmtt) cc_final: 0.4288 (ttmm) REVERT: C 904 TYR cc_start: 0.7787 (t80) cc_final: 0.7321 (t80) REVERT: B 153 MET cc_start: -0.1882 (ptm) cc_final: -0.2664 (ptt) REVERT: A 34 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6742 (m-70) REVERT: A 366 MET cc_start: 0.2060 (tpt) cc_final: 0.0444 (ttt) REVERT: A 402 GLU cc_start: 0.4364 (OUTLIER) cc_final: 0.4095 (mm-30) REVERT: D 92 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: D 346 ARG cc_start: 0.8225 (mmt-90) cc_final: 0.7561 (mmm-85) REVERT: D 408 ARG cc_start: 0.7739 (ppt170) cc_final: 0.7336 (ppt170) REVERT: D 412 PRO cc_start: 0.6926 (Cg_exo) cc_final: 0.6542 (Cg_endo) REVERT: D 498 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: D 918 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: D 1114 ILE cc_start: 0.9413 (mm) cc_final: 0.9178 (mm) REVERT: D 1123 SER cc_start: 0.8585 (m) cc_final: 0.8358 (m) outliers start: 82 outliers final: 61 residues processed: 366 average time/residue: 0.3831 time to fit residues: 234.1910 Evaluate side-chains 357 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 77 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 337 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 764 ASN B 540 ASN A 34 HIS ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** D1106 GLN ** 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 = 0.4413 r_free = 0.4413 target = 0.179910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148203 restraints weight = 63916.954| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.12 r_work: 0.3857 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30486 Z= 0.137 Angle : 0.538 9.501 41480 Z= 0.279 Chirality : 0.044 0.187 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.269 20.009 4050 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.63 % Allowed : 16.32 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 3733 helix: 1.24 (0.17), residues: 1001 sheet: -0.53 (0.18), residues: 765 loop : -0.97 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 275 HIS 0.030 0.001 HIS A 34 PHE 0.026 0.002 PHE C 541 TYR 0.022 0.001 TYR D 473 ARG 0.012 0.000 ARG D1107 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1107) hydrogen bonds : angle 4.85431 ( 3141) SS BOND : bond 0.00379 ( 42) SS BOND : angle 1.66681 ( 84) covalent geometry : bond 0.00321 (30444) covalent geometry : angle 0.53302 (41396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 296 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.8009 (t80) REVERT: C 904 TYR cc_start: 0.7588 (t80) cc_final: 0.7150 (t80) REVERT: B 153 MET cc_start: -0.1596 (ptm) cc_final: -0.2470 (ptt) REVERT: A 34 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6691 (m90) REVERT: A 366 MET cc_start: 0.2271 (tpt) cc_final: 0.0583 (ttt) REVERT: A 402 GLU cc_start: 0.4649 (OUTLIER) cc_final: 0.4268 (mm-30) REVERT: D 92 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: D 346 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7575 (mmm-85) REVERT: D 408 ARG cc_start: 0.7731 (ppt170) cc_final: 0.7347 (ppt170) REVERT: D 412 PRO cc_start: 0.6847 (Cg_exo) cc_final: 0.6486 (Cg_endo) REVERT: D 498 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: D 918 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: D 1114 ILE cc_start: 0.9389 (mm) cc_final: 0.9161 (mm) REVERT: D 1123 SER cc_start: 0.8557 (m) cc_final: 0.8325 (m) outliers start: 87 outliers final: 75 residues processed: 361 average time/residue: 0.3834 time to fit residues: 231.2838 Evaluate side-chains 359 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 278 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 266 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 246 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 107 optimal weight: 0.1980 chunk 151 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 51 ASN A 556 ASN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.179775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.148282 restraints weight = 63927.227| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.02 r_work: 0.3849 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30486 Z= 0.143 Angle : 0.544 10.221 41480 Z= 0.283 Chirality : 0.044 0.195 4616 Planarity : 0.004 0.048 5375 Dihedral : 4.304 21.016 4050 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.54 % Allowed : 16.69 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 3733 helix: 1.15 (0.17), residues: 1014 sheet: -0.52 (0.18), residues: 747 loop : -0.97 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 275 HIS 0.029 0.001 HIS A 34 PHE 0.024 0.002 PHE A 327 TYR 0.019 0.001 TYR D 473 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 1107) hydrogen bonds : angle 4.85020 ( 3141) SS BOND : bond 0.00358 ( 42) SS BOND : angle 1.31961 ( 84) covalent geometry : bond 0.00335 (30444) covalent geometry : angle 0.54162 (41396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 285 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.8009 (t80) REVERT: C 738 CYS cc_start: 0.6877 (t) cc_final: 0.6564 (t) REVERT: C 904 TYR cc_start: 0.7557 (t80) cc_final: 0.7189 (t80) REVERT: C 1041 ASP cc_start: 0.8322 (t0) cc_final: 0.8118 (t0) REVERT: B 153 MET cc_start: -0.1345 (ptm) cc_final: -0.2212 (ptt) REVERT: A 34 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6829 (m-70) REVERT: A 332 MET cc_start: -0.3137 (ppp) cc_final: -0.3508 (ppp) REVERT: A 366 MET cc_start: 0.2385 (tpt) cc_final: 0.0666 (ttt) REVERT: A 402 GLU cc_start: 0.4821 (OUTLIER) cc_final: 0.4434 (mm-30) REVERT: D 346 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7561 (mmm-85) REVERT: D 408 ARG cc_start: 0.7762 (ppt170) cc_final: 0.7372 (ppt170) REVERT: D 498 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: D 918 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: D 1114 ILE cc_start: 0.9400 (mm) cc_final: 0.9168 (mm) REVERT: D 1123 SER cc_start: 0.8566 (m) cc_final: 0.8336 (m) outliers start: 84 outliers final: 76 residues processed: 350 average time/residue: 0.4364 time to fit residues: 256.2059 Evaluate side-chains 354 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 273 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 366 optimal weight: 0.9980 chunk 292 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 342 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 354 optimal weight: 0.9990 chunk 376 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.179455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.148162 restraints weight = 63644.700| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.10 r_work: 0.3852 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 30486 Z= 0.169 Angle : 0.663 59.200 41480 Z= 0.374 Chirality : 0.048 1.267 4616 Planarity : 0.004 0.104 5375 Dihedral : 4.302 20.838 4050 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.67 % Allowed : 16.51 % Favored : 80.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 3733 helix: 1.13 (0.17), residues: 1014 sheet: -0.53 (0.18), residues: 748 loop : -0.97 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 275 HIS 0.150 0.002 HIS A 34 PHE 0.026 0.002 PHE D 92 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1107) hydrogen bonds : angle 4.86384 ( 3141) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.33716 ( 84) covalent geometry : bond 0.00384 (30444) covalent geometry : angle 0.66075 (41396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21878.53 seconds wall clock time: 380 minutes 5.82 seconds (22805.82 seconds total)