Starting phenix.real_space_refine on Thu May 29 22:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t20_40976/05_2025/8t20_40976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t20_40976/05_2025/8t20_40976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t20_40976/05_2025/8t20_40976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t20_40976/05_2025/8t20_40976.map" model { file = "/net/cci-nas-00/data/ceres_data/8t20_40976/05_2025/8t20_40976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t20_40976/05_2025/8t20_40976.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 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 161 5.16 5 C 20836 2.51 5 N 5431 2.21 5 O 6184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32612 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Chain: "B" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7497 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 51, 'TRANS': 910} Chain breaks: 10 Chain: "C" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7497 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 51, 'TRANS': 910} Chain breaks: 10 Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Chain: "E" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Time building chain proxies: 18.87, per 1000 atoms: 0.58 Number of scatterers: 32612 At special positions: 0 Unit cell: (132.09, 166.5, 249.75, 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 161 16.00 O 6184 8.00 N 5431 7.00 C 20836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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 480 " - pdb=" SG CYS B 488 " 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 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: 7.13 Conformation dependent library (CDL) restraints added in 3.8 seconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7730 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 37 sheets defined 36.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.587A pdb=" N TYR A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.022A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.540A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.666A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.663A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.945A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.424A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.589A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 502 through 505 removed outlier: 3.920A pdb=" N TYR B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.518A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.948A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.697A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.939A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.114A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 405 through 409 removed outlier: 4.155A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.918A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.653A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 4.107A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.821A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.309A pdb=" N TYR D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.609A pdb=" N THR D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 83 " --> pdb=" O HIS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.932A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.754A pdb=" N LEU D 278 " --> pdb=" O TRP D 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 279' Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.908A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.545A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 449 Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.529A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 600 Proline residue: D 590 - end of helix Processing helix chain 'E' and resid 20 through 53 Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 109 through 130 removed outlier: 4.572A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.952A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 172 through 193 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 220 through 252 removed outlier: 4.464A pdb=" N GLN E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 292 through 300 removed outlier: 4.145A pdb=" N ALA E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 4.279A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU E 312 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL E 316 " --> pdb=" O GLU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 Processing helix chain 'E' and resid 365 through 385 Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.628A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 442 Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.400A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR E 453 " --> pdb=" O THR E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 534 removed outlier: 3.606A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 Processing helix chain 'E' and resid 565 through 575 removed outlier: 4.426A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.713A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'A' and resid 539 through 540 Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.623A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.697A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.697A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.668A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.625A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.208A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.106A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.891A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.937A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 575 through 577 removed outlier: 3.940A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.522A pdb=" N VAL B 656 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.824A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.619A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.504A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.699A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.651A 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: 7.033A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.573A pdb=" N LEU C 189 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.150A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 355 through 356 removed outlier: 4.218A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.645A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.776A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.859A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.859A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1122 1246 hydrogen bonds defined for protein. 3588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.11 Time building geometry restraints manager: 8.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 1 1.05 - 1.25: 4698 1.25 - 1.45: 10146 1.45 - 1.65: 18338 1.65 - 1.85: 229 Bond restraints: 33412 Sorted by residual: bond pdb=" CG PRO D 583 " pdb=" CD PRO D 583 " ideal model delta sigma weight residual 1.503 0.845 0.658 3.40e-02 8.65e+02 3.74e+02 bond pdb=" CG PRO D 289 " pdb=" CD PRO D 289 " ideal model delta sigma weight residual 1.503 1.223 0.280 3.40e-02 8.65e+02 6.81e+01 bond pdb=" CG PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.79e+01 bond pdb=" N PRO D 583 " pdb=" CD PRO D 583 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.20e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.34e+01 ... (remaining 33407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.84: 45248 5.84 - 11.68: 169 11.68 - 17.53: 20 17.53 - 23.37: 3 23.37 - 29.21: 1 Bond angle restraints: 45441 Sorted by residual: angle pdb=" N PRO D 583 " pdb=" CD PRO D 583 " pdb=" CG PRO D 583 " ideal model delta sigma weight residual 103.20 73.99 29.21 1.50e+00 4.44e-01 3.79e+02 angle pdb=" CA PRO D 426 " pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 112.00 93.72 18.28 1.40e+00 5.10e-01 1.71e+02 angle pdb=" CA PRO D 289 " pdb=" N PRO D 289 " pdb=" CD PRO D 289 " ideal model delta sigma weight residual 112.00 95.29 16.71 1.40e+00 5.10e-01 1.43e+02 angle pdb=" N THR D 608 " pdb=" CA THR D 608 " pdb=" C THR D 608 " ideal model delta sigma weight residual 111.17 127.46 -16.29 1.41e+00 5.03e-01 1.33e+02 angle pdb=" CA PRO D 583 " pdb=" CB PRO D 583 " pdb=" CG PRO D 583 " ideal model delta sigma weight residual 104.50 83.27 21.23 1.90e+00 2.77e-01 1.25e+02 ... (remaining 45436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16565 17.92 - 35.84: 2496 35.84 - 53.75: 653 53.75 - 71.67: 122 71.67 - 89.59: 53 Dihedral angle restraints: 19889 sinusoidal: 7890 harmonic: 11999 Sorted by residual: dihedral pdb=" CA PHE A 55 " pdb=" C PHE A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta harmonic sigma weight residual 180.00 129.95 50.05 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA PHE A 220 " pdb=" C PHE A 220 " pdb=" N SER A 221 " pdb=" CA SER A 221 " ideal model delta harmonic sigma weight residual 180.00 132.59 47.41 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 178.36 -85.36 1 1.00e+01 1.00e-02 8.82e+01 ... (remaining 19886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4387 0.081 - 0.163: 579 0.163 - 0.244: 45 0.244 - 0.326: 11 0.326 - 0.407: 5 Chirality restraints: 5027 Sorted by residual: chirality pdb=" CG LEU A 962 " pdb=" CB LEU A 962 " pdb=" CD1 LEU A 962 " pdb=" CD2 LEU A 962 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" C PRO A 561 " pdb=" CB PRO A 561 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 5024 not shown) Planarity restraints: 5898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 489 " -0.091 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO D 490 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 490 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 490 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.080 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 986 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 288 " -0.082 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO D 289 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " -0.058 5.00e-02 4.00e+02 ... (remaining 5895 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 196 2.45 - 3.06: 22173 3.06 - 3.67: 50154 3.67 - 4.29: 69131 4.29 - 4.90: 112406 Nonbonded interactions: 254060 Sorted by model distance: nonbonded pdb=" N ILE D 484 " pdb=" O ASN D 607 " model vdw 1.836 3.120 nonbonded pdb=" O GLN C1002 " pdb=" OG1 THR C1006 " model vdw 1.893 3.040 nonbonded pdb=" O SER A 46 " pdb=" N ASN A 282 " model vdw 1.935 3.120 nonbonded pdb=" O ASP D 225 " pdb=" OG1 THR D 229 " model vdw 1.970 3.040 nonbonded pdb=" O GLN A1005 " pdb=" OG1 THR A1009 " model vdw 1.971 3.040 ... (remaining 254055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 320 or resid 335 through 366 or resid 376 throu \ gh 527 or resid 544 through 1147)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 8.820 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: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 64.560 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4795 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 : 0.007 0.658 33453 Z= 0.304 Angle : 1.060 29.211 45523 Z= 0.586 Chirality : 0.055 0.407 5027 Planarity : 0.008 0.130 5898 Dihedral : 18.406 89.590 12036 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.88 % Favored : 86.92 % Rotamer: Outliers : 0.67 % Allowed : 29.50 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.12), residues: 4053 helix: -0.09 (0.14), residues: 1325 sheet: -1.47 (0.25), residues: 372 loop : -3.19 (0.11), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 349 HIS 0.015 0.002 HIS D 535 PHE 0.063 0.003 PHE A 275 TYR 0.049 0.002 TYR A 279 ARG 0.011 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.17479 ( 1236) hydrogen bonds : angle 7.57972 ( 3588) SS BOND : bond 0.00648 ( 41) SS BOND : angle 2.50166 ( 82) covalent geometry : bond 0.00730 (33412) covalent geometry : angle 1.05532 (45441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 485 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5841 (p) cc_final: 0.5351 (t) REVERT: B 200 TYR cc_start: 0.2415 (OUTLIER) cc_final: 0.2002 (m-80) REVERT: B 237 ARG cc_start: 0.4922 (mmm160) cc_final: 0.4658 (mmp-170) REVERT: C 237 ARG cc_start: 0.4916 (ptm160) cc_final: 0.4619 (ppt170) REVERT: C 355 ARG cc_start: 0.4983 (OUTLIER) cc_final: 0.4368 (ttm170) REVERT: C 1077 THR cc_start: 0.5046 (t) cc_final: 0.4473 (m) REVERT: D 48 TRP cc_start: 0.1286 (t-100) cc_final: 0.0759 (t-100) REVERT: D 152 MET cc_start: -0.1122 (mmt) cc_final: -0.3592 (ptm) REVERT: D 376 MET cc_start: 0.0469 (tpt) cc_final: 0.0107 (ptm) REVERT: D 400 PHE cc_start: 0.2778 (t80) cc_final: 0.2102 (m-10) REVERT: E 62 MET cc_start: 0.2118 (tmm) cc_final: 0.1592 (tmm) REVERT: E 123 MET cc_start: 0.1290 (tmm) cc_final: 0.0388 (tmm) REVERT: E 190 MET cc_start: 0.3774 (tmm) cc_final: 0.3454 (ptt) REVERT: E 474 MET cc_start: 0.0114 (tmm) cc_final: -0.1133 (mmt) REVERT: E 480 MET cc_start: 0.1229 (mmp) cc_final: 0.0387 (tpp) REVERT: E 557 MET cc_start: -0.1441 (OUTLIER) cc_final: -0.1916 (mtm) outliers start: 24 outliers final: 5 residues processed: 504 average time/residue: 0.4011 time to fit residues: 331.7865 Evaluate side-chains 300 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 292 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 321 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 195 optimal weight: 0.2980 chunk 239 optimal weight: 0.9980 chunk 372 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 690 GLN B 957 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1106 GLN D 33 ASN D 49 ASN D 117 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 265 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS E 49 ASN E 58 ASN ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN E 397 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.244597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.187538 restraints weight = 66679.436| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 4.46 r_work: 0.3902 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 33453 Z= 0.225 Angle : 0.900 15.732 45523 Z= 0.474 Chirality : 0.053 0.348 5027 Planarity : 0.007 0.103 5898 Dihedral : 7.346 59.963 4435 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.04 % Favored : 89.81 % Rotamer: Outliers : 5.94 % Allowed : 25.03 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 4053 helix: -0.09 (0.14), residues: 1346 sheet: -1.04 (0.25), residues: 387 loop : -3.01 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 610 HIS 0.010 0.002 HIS E 373 PHE 0.038 0.002 PHE A 562 TYR 0.029 0.002 TYR A 279 ARG 0.012 0.001 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.06662 ( 1236) hydrogen bonds : angle 6.61705 ( 3588) SS BOND : bond 0.00812 ( 41) SS BOND : angle 1.98856 ( 82) covalent geometry : bond 0.00459 (33412) covalent geometry : angle 0.89652 (45441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 330 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5022 (mtm-85) cc_final: 0.4570 (mtm-85) REVERT: A 197 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5975 (pt) REVERT: A 229 LEU cc_start: 0.3967 (OUTLIER) cc_final: 0.3348 (mp) REVERT: A 492 LEU cc_start: -0.0721 (OUTLIER) cc_final: -0.1008 (mt) REVERT: A 658 ASN cc_start: 0.7543 (m-40) cc_final: 0.7163 (m110) REVERT: A 996 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6872 (tt) REVERT: B 200 TYR cc_start: 0.2832 (OUTLIER) cc_final: 0.2242 (m-80) REVERT: B 237 ARG cc_start: 0.5677 (mmm160) cc_final: 0.5328 (mmp-170) REVERT: B 472 ILE cc_start: -0.1245 (OUTLIER) cc_final: -0.2178 (tt) REVERT: B 568 ASP cc_start: 0.7275 (t0) cc_final: 0.7043 (t0) REVERT: B 582 LEU cc_start: 0.7395 (mt) cc_final: 0.7092 (pt) REVERT: B 740 MET cc_start: 0.7988 (tpt) cc_final: 0.7396 (tpp) REVERT: B 898 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.5630 (m-80) REVERT: B 1000 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8116 (ptm-80) REVERT: C 170 TYR cc_start: 0.6239 (t80) cc_final: 0.5654 (t80) REVERT: C 355 ARG cc_start: 0.5458 (OUTLIER) cc_final: 0.4395 (tpp-160) REVERT: C 492 LEU cc_start: 0.3621 (OUTLIER) cc_final: 0.3264 (pp) REVERT: C 780 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: C 954 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7965 (mp10) REVERT: C 974 SER cc_start: 0.7191 (OUTLIER) cc_final: 0.6985 (p) REVERT: D 44 SER cc_start: 0.1992 (OUTLIER) cc_final: 0.1746 (m) REVERT: D 101 GLN cc_start: 0.2320 (tm-30) cc_final: 0.1763 (mm-40) REVERT: D 400 PHE cc_start: 0.3913 (t80) cc_final: 0.2685 (m-10) REVERT: D 408 MET cc_start: -0.0636 (ptp) cc_final: -0.1254 (mtm) REVERT: E 123 MET cc_start: -0.0797 (tmm) cc_final: -0.1365 (tmm) REVERT: E 176 LEU cc_start: 0.1427 (OUTLIER) cc_final: 0.0874 (mm) REVERT: E 190 MET cc_start: 0.2185 (OUTLIER) cc_final: 0.1832 (ptt) REVERT: E 285 PHE cc_start: -0.1195 (OUTLIER) cc_final: -0.2138 (p90) REVERT: E 297 MET cc_start: -0.0633 (ttp) cc_final: -0.0898 (ptm) REVERT: E 310 GLU cc_start: 0.1319 (OUTLIER) cc_final: 0.0523 (tp30) REVERT: E 480 MET cc_start: 0.0728 (mmp) cc_final: 0.0247 (tpt) outliers start: 214 outliers final: 90 residues processed: 516 average time/residue: 0.4098 time to fit residues: 351.3195 Evaluate side-chains 370 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 263 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 281 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 330 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 397 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 957 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1088 HIS C 498 GLN C 913 GLN C 926 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS E 508 ASN ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.240009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.209554 restraints weight = 63457.691| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 3.05 r_work: 0.4084 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 33453 Z= 0.274 Angle : 0.931 15.053 45523 Z= 0.494 Chirality : 0.054 0.335 5027 Planarity : 0.007 0.085 5898 Dihedral : 7.298 57.161 4429 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.52 % Favored : 88.33 % Rotamer: Outliers : 7.33 % Allowed : 24.04 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.12), residues: 4053 helix: -0.23 (0.14), residues: 1362 sheet: -0.86 (0.26), residues: 373 loop : -3.08 (0.11), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 478 HIS 0.009 0.002 HIS E 373 PHE 0.030 0.003 PHE A 201 TYR 0.033 0.002 TYR A 279 ARG 0.016 0.001 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.08822 ( 1236) hydrogen bonds : angle 6.76901 ( 3588) SS BOND : bond 0.00611 ( 41) SS BOND : angle 2.22990 ( 82) covalent geometry : bond 0.00600 (33412) covalent geometry : angle 0.92725 (45441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 254 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.1822 (OUTLIER) cc_final: 0.0186 (m-80) REVERT: A 207 HIS cc_start: 0.6775 (m90) cc_final: 0.6051 (m90) REVERT: A 241 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5526 (tt) REVERT: A 353 TRP cc_start: 0.4710 (p-90) cc_final: 0.4411 (p-90) REVERT: A 492 LEU cc_start: -0.0679 (OUTLIER) cc_final: -0.0994 (mt) REVERT: A 855 PHE cc_start: 0.5619 (m-10) cc_final: 0.5402 (m-10) REVERT: A 983 ARG cc_start: 0.2822 (OUTLIER) cc_final: 0.2608 (ptt180) REVERT: A 996 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7773 (tt) REVERT: B 191 GLU cc_start: 0.6402 (mt-10) cc_final: 0.5669 (mp0) REVERT: B 210 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5441 (mm) REVERT: B 740 MET cc_start: 0.8835 (tpt) cc_final: 0.8133 (tpp) REVERT: B 918 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: B 935 GLN cc_start: 0.6020 (OUTLIER) cc_final: 0.5564 (tp-100) REVERT: B 1000 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8466 (ptm-80) REVERT: B 1004 LEU cc_start: 0.7113 (tp) cc_final: 0.6258 (tp) REVERT: B 1005 GLN cc_start: 0.6584 (mm-40) cc_final: 0.6074 (tm-30) REVERT: C 115 GLN cc_start: 0.2677 (OUTLIER) cc_final: 0.1971 (tp40) REVERT: C 170 TYR cc_start: 0.6224 (t80) cc_final: 0.5860 (t80) REVERT: C 191 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6511 (mm-30) REVERT: C 237 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5976 (ptm160) REVERT: C 355 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4332 (tpp-160) REVERT: C 358 ILE cc_start: 0.1219 (OUTLIER) cc_final: 0.0503 (mt) REVERT: C 740 MET cc_start: 0.8050 (tpp) cc_final: 0.7559 (ttt) REVERT: C 950 ASP cc_start: 0.8281 (m-30) cc_final: 0.7747 (m-30) REVERT: D 44 SER cc_start: 0.1988 (OUTLIER) cc_final: 0.1642 (m) REVERT: D 123 MET cc_start: 0.2870 (ttp) cc_final: 0.2646 (ttp) REVERT: D 174 LYS cc_start: 0.1058 (mmtt) cc_final: 0.0223 (ptmm) REVERT: D 267 LEU cc_start: 0.0354 (OUTLIER) cc_final: -0.0133 (tt) REVERT: D 297 MET cc_start: 0.1741 (mmm) cc_final: 0.1331 (mmm) REVERT: D 332 MET cc_start: 0.2096 (tmm) cc_final: 0.1572 (tmm) REVERT: D 354 HIS cc_start: 0.3732 (t-90) cc_final: 0.3201 (t-170) REVERT: D 376 MET cc_start: 0.1445 (tpp) cc_final: 0.0418 (ttm) REVERT: D 379 ILE cc_start: -0.0766 (mm) cc_final: -0.1070 (pt) REVERT: D 400 PHE cc_start: 0.3808 (t80) cc_final: 0.2550 (m-10) REVERT: D 408 MET cc_start: -0.0618 (ptp) cc_final: -0.2706 (mtt) REVERT: D 539 LEU cc_start: -0.0520 (OUTLIER) cc_final: -0.0823 (tt) REVERT: D 564 LYS cc_start: 0.2384 (mmmt) cc_final: 0.1919 (ttpp) REVERT: D 579 MET cc_start: -0.1398 (mtm) cc_final: -0.2242 (pmm) REVERT: D 580 ASP cc_start: -0.0373 (OUTLIER) cc_final: -0.0663 (m-30) REVERT: E 123 MET cc_start: 0.0671 (tmm) cc_final: -0.0208 (tmm) REVERT: E 176 LEU cc_start: 0.1082 (OUTLIER) cc_final: -0.0029 (mp) REVERT: E 190 MET cc_start: 0.3271 (OUTLIER) cc_final: 0.2465 (ptt) REVERT: E 285 PHE cc_start: 0.0862 (OUTLIER) cc_final: -0.0748 (p90) REVERT: E 446 ILE cc_start: 0.2887 (OUTLIER) cc_final: 0.2529 (mp) REVERT: E 480 MET cc_start: 0.1434 (mmp) cc_final: 0.0111 (ptt) REVERT: E 536 GLU cc_start: -0.0259 (OUTLIER) cc_final: -0.1998 (mp0) outliers start: 264 outliers final: 126 residues processed: 490 average time/residue: 0.4113 time to fit residues: 330.2966 Evaluate side-chains 365 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 216 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 118 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 369 optimal weight: 7.9990 chunk 305 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 368 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 341 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 353 optimal weight: 10.0000 chunk 164 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 322 ASN D 378 HIS E 380 GLN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.240592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.204392 restraints weight = 64379.568| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 3.58 r_work: 0.4012 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33453 Z= 0.219 Angle : 0.836 16.317 45523 Z= 0.441 Chirality : 0.050 0.338 5027 Planarity : 0.006 0.081 5898 Dihedral : 6.941 51.956 4427 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.36 % Favored : 89.54 % Rotamer: Outliers : 6.11 % Allowed : 25.28 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.13), residues: 4053 helix: 0.05 (0.14), residues: 1335 sheet: -0.82 (0.26), residues: 371 loop : -2.98 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 594 HIS 0.023 0.001 HIS D 555 PHE 0.026 0.002 PHE A 562 TYR 0.038 0.002 TYR A 279 ARG 0.013 0.001 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.07234 ( 1236) hydrogen bonds : angle 6.50417 ( 3588) SS BOND : bond 0.00655 ( 41) SS BOND : angle 1.85244 ( 82) covalent geometry : bond 0.00456 (33412) covalent geometry : angle 0.83314 (45441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 233 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.1546 (OUTLIER) cc_final: 0.0087 (m-80) REVERT: A 207 HIS cc_start: 0.6820 (m90) cc_final: 0.6092 (m90) REVERT: A 241 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5838 (tt) REVERT: A 492 LEU cc_start: -0.0855 (OUTLIER) cc_final: -0.1218 (mt) REVERT: A 533 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6927 (tt) REVERT: A 996 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7759 (tt) REVERT: B 106 PHE cc_start: 0.1475 (OUTLIER) cc_final: 0.1219 (m-80) REVERT: B 117 LEU cc_start: 0.4871 (OUTLIER) cc_final: 0.4551 (mt) REVERT: B 237 ARG cc_start: 0.5627 (mmm160) cc_final: 0.4936 (mmp-170) REVERT: B 740 MET cc_start: 0.9059 (tpt) cc_final: 0.8311 (ttm) REVERT: B 935 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.5997 (tp40) REVERT: B 1000 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8531 (ptm-80) REVERT: B 1105 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8934 (p) REVERT: C 65 PHE cc_start: 0.5962 (m-80) cc_final: 0.5511 (m-80) REVERT: C 115 GLN cc_start: 0.3184 (OUTLIER) cc_final: 0.2744 (mm-40) REVERT: C 170 TYR cc_start: 0.6416 (t80) cc_final: 0.5931 (t80) REVERT: C 237 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6168 (ptm160) REVERT: C 355 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.4186 (tpp-160) REVERT: C 358 ILE cc_start: 0.1376 (OUTLIER) cc_final: 0.0625 (mt) REVERT: C 740 MET cc_start: 0.8264 (tpp) cc_final: 0.7945 (ttt) REVERT: C 950 ASP cc_start: 0.8532 (m-30) cc_final: 0.8254 (m-30) REVERT: D 90 ASP cc_start: 0.1349 (OUTLIER) cc_final: 0.1052 (p0) REVERT: D 376 MET cc_start: 0.1605 (tpp) cc_final: 0.0516 (ttm) REVERT: D 379 ILE cc_start: -0.0926 (mm) cc_final: -0.1283 (pt) REVERT: D 400 PHE cc_start: 0.4213 (t80) cc_final: 0.2911 (m-10) REVERT: D 408 MET cc_start: -0.0764 (ptp) cc_final: -0.2124 (mtm) REVERT: D 564 LYS cc_start: 0.1990 (mmmt) cc_final: 0.1711 (ttpp) REVERT: D 579 MET cc_start: 0.0072 (OUTLIER) cc_final: -0.1363 (pmm) REVERT: E 61 LYS cc_start: 0.1498 (OUTLIER) cc_final: 0.1103 (tptp) REVERT: E 123 MET cc_start: -0.0163 (tmm) cc_final: -0.0554 (tmm) REVERT: E 152 MET cc_start: 0.4962 (tpp) cc_final: 0.4619 (mpp) REVERT: E 190 MET cc_start: 0.3459 (OUTLIER) cc_final: 0.2781 (ptt) REVERT: E 285 PHE cc_start: 0.0734 (OUTLIER) cc_final: -0.0823 (p90) REVERT: E 297 MET cc_start: -0.0027 (ttp) cc_final: -0.0635 (ptm) REVERT: E 446 ILE cc_start: 0.2772 (OUTLIER) cc_final: 0.2400 (mp) REVERT: E 480 MET cc_start: 0.1544 (mmp) cc_final: 0.0227 (ptt) REVERT: E 536 GLU cc_start: 0.0038 (OUTLIER) cc_final: -0.1766 (mp0) outliers start: 220 outliers final: 118 residues processed: 435 average time/residue: 0.4180 time to fit residues: 302.4393 Evaluate side-chains 346 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 207 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 384 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 376 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN D 63 ASN D 117 ASN D 378 HIS D 493 HIS ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.238429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.200706 restraints weight = 63883.070| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 3.52 r_work: 0.3973 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 33453 Z= 0.216 Angle : 0.832 16.748 45523 Z= 0.437 Chirality : 0.051 0.335 5027 Planarity : 0.006 0.080 5898 Dihedral : 6.876 51.847 4427 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.50 % Favored : 88.43 % Rotamer: Outliers : 6.11 % Allowed : 24.81 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.13), residues: 4053 helix: 0.15 (0.14), residues: 1337 sheet: -0.85 (0.26), residues: 375 loop : -2.98 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 594 HIS 0.006 0.001 HIS E 373 PHE 0.034 0.002 PHE A 238 TYR 0.038 0.002 TYR A 279 ARG 0.031 0.001 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.07562 ( 1236) hydrogen bonds : angle 6.45349 ( 3588) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.83884 ( 82) covalent geometry : bond 0.00471 (33412) covalent geometry : angle 0.82858 (45441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 221 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.1826 (OUTLIER) cc_final: 0.1210 (m-80) REVERT: A 241 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5642 (tt) REVERT: A 492 LEU cc_start: -0.0984 (OUTLIER) cc_final: -0.1285 (mt) REVERT: A 533 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6949 (tt) REVERT: A 855 PHE cc_start: 0.6101 (m-10) cc_final: 0.5737 (m-10) REVERT: A 996 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7806 (tt) REVERT: A 1138 TYR cc_start: 0.7802 (t80) cc_final: 0.7505 (t80) REVERT: B 106 PHE cc_start: 0.1805 (OUTLIER) cc_final: 0.0170 (m-80) REVERT: B 206 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6420 (tptt) REVERT: B 210 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5547 (mm) REVERT: B 740 MET cc_start: 0.8980 (tpt) cc_final: 0.8428 (ttm) REVERT: B 935 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6666 (tp-100) REVERT: B 1000 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8383 (ptm-80) REVERT: C 115 GLN cc_start: 0.3474 (OUTLIER) cc_final: 0.2993 (tm-30) REVERT: C 170 TYR cc_start: 0.6603 (t80) cc_final: 0.6044 (t80) REVERT: C 191 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: C 237 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6529 (ptm160) REVERT: C 355 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.4330 (tpp-160) REVERT: C 358 ILE cc_start: 0.1351 (OUTLIER) cc_final: 0.0700 (mt) REVERT: C 740 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8007 (ttt) REVERT: C 950 ASP cc_start: 0.8259 (m-30) cc_final: 0.8030 (m-30) REVERT: D 44 SER cc_start: 0.1436 (OUTLIER) cc_final: 0.1236 (m) REVERT: D 90 ASP cc_start: 0.1691 (OUTLIER) cc_final: 0.1424 (p0) REVERT: D 101 GLN cc_start: 0.2047 (mm-40) cc_final: 0.0579 (mm-40) REVERT: D 190 MET cc_start: 0.1659 (OUTLIER) cc_final: 0.1233 (mtm) REVERT: D 270 MET cc_start: 0.2775 (ttt) cc_final: 0.2523 (ttm) REVERT: D 367 ASP cc_start: 0.3089 (OUTLIER) cc_final: 0.2697 (p0) REVERT: D 376 MET cc_start: 0.1305 (tpp) cc_final: 0.0300 (ttm) REVERT: D 379 ILE cc_start: -0.0862 (mm) cc_final: -0.1289 (pt) REVERT: D 394 ASN cc_start: 0.5168 (OUTLIER) cc_final: 0.3242 (m-40) REVERT: D 400 PHE cc_start: 0.3905 (t80) cc_final: 0.2684 (m-10) REVERT: D 408 MET cc_start: -0.0835 (ptp) cc_final: -0.1816 (mtm) REVERT: D 458 LYS cc_start: 0.1754 (OUTLIER) cc_final: 0.0611 (ttmm) REVERT: D 539 LEU cc_start: -0.0236 (OUTLIER) cc_final: -0.0603 (tt) REVERT: D 564 LYS cc_start: 0.2380 (mmmt) cc_final: 0.1966 (ttpp) REVERT: D 579 MET cc_start: 0.1431 (OUTLIER) cc_final: 0.0280 (pmm) REVERT: E 61 LYS cc_start: 0.1721 (OUTLIER) cc_final: 0.1257 (tptp) REVERT: E 89 GLN cc_start: 0.3802 (tp40) cc_final: 0.1928 (mt0) REVERT: E 190 MET cc_start: 0.3644 (OUTLIER) cc_final: 0.2904 (ptt) REVERT: E 285 PHE cc_start: 0.1281 (OUTLIER) cc_final: -0.0205 (p90) REVERT: E 297 MET cc_start: 0.0539 (ttp) cc_final: -0.0314 (ptm) REVERT: E 310 GLU cc_start: 0.0887 (OUTLIER) cc_final: 0.0137 (tp30) REVERT: E 446 ILE cc_start: 0.2863 (OUTLIER) cc_final: 0.2399 (mp) REVERT: E 480 MET cc_start: 0.1915 (mmp) cc_final: 0.0469 (ptt) REVERT: E 536 GLU cc_start: 0.0099 (OUTLIER) cc_final: -0.1779 (mp0) REVERT: E 600 ARG cc_start: 0.2989 (OUTLIER) cc_final: 0.2561 (tpp-160) outliers start: 220 outliers final: 134 residues processed: 415 average time/residue: 0.4095 time to fit residues: 281.9633 Evaluate side-chains 373 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 208 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 12 optimal weight: 0.9980 chunk 264 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 99 optimal weight: 0.0470 chunk 285 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 239 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN D 378 HIS D 526 GLN D 607 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.241208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.203703 restraints weight = 64366.934| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 3.42 r_work: 0.4028 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33453 Z= 0.174 Angle : 0.778 16.387 45523 Z= 0.407 Chirality : 0.049 0.330 5027 Planarity : 0.006 0.084 5898 Dihedral : 6.593 54.401 4427 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.55 % Favored : 90.35 % Rotamer: Outliers : 5.25 % Allowed : 25.90 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 4053 helix: 0.30 (0.14), residues: 1343 sheet: -0.74 (0.26), residues: 368 loop : -2.91 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 594 HIS 0.007 0.001 HIS E 373 PHE 0.033 0.002 PHE B 106 TYR 0.037 0.001 TYR A 279 ARG 0.015 0.001 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.06349 ( 1236) hydrogen bonds : angle 6.17779 ( 3588) SS BOND : bond 0.00399 ( 41) SS BOND : angle 1.53974 ( 82) covalent geometry : bond 0.00353 (33412) covalent geometry : angle 0.77644 (45441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 216 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6718 (m90) cc_final: 0.6124 (m90) REVERT: A 241 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5397 (tt) REVERT: A 273 ARG cc_start: 0.2542 (OUTLIER) cc_final: 0.1812 (mpt90) REVERT: A 533 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7109 (tt) REVERT: A 855 PHE cc_start: 0.5993 (m-10) cc_final: 0.5706 (m-10) REVERT: A 996 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7502 (tt) REVERT: A 1138 TYR cc_start: 0.7768 (t80) cc_final: 0.7397 (t80) REVERT: B 106 PHE cc_start: 0.1043 (OUTLIER) cc_final: 0.0606 (m-80) REVERT: B 206 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6196 (tptt) REVERT: B 210 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5432 (mm) REVERT: B 237 ARG cc_start: 0.5661 (mmm160) cc_final: 0.5334 (tpt-90) REVERT: B 740 MET cc_start: 0.9022 (tpt) cc_final: 0.8394 (ttm) REVERT: B 935 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6365 (tp-100) REVERT: C 170 TYR cc_start: 0.6441 (t80) cc_final: 0.5862 (t80) REVERT: C 191 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: C 215 ASP cc_start: 0.3001 (OUTLIER) cc_final: 0.2739 (t0) REVERT: C 237 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6171 (ptm160) REVERT: C 355 ARG cc_start: 0.5641 (OUTLIER) cc_final: 0.4028 (tpp-160) REVERT: C 358 ILE cc_start: 0.1075 (OUTLIER) cc_final: 0.0492 (mt) REVERT: C 740 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7902 (ttt) REVERT: C 950 ASP cc_start: 0.8225 (m-30) cc_final: 0.8017 (m-30) REVERT: C 1145 LEU cc_start: 0.4773 (OUTLIER) cc_final: 0.4491 (mp) REVERT: D 90 ASP cc_start: 0.1526 (OUTLIER) cc_final: 0.1295 (p0) REVERT: D 101 GLN cc_start: 0.2148 (mm-40) cc_final: 0.0798 (mm-40) REVERT: D 190 MET cc_start: 0.1921 (ttm) cc_final: 0.1659 (mtm) REVERT: D 270 MET cc_start: 0.2474 (ttt) cc_final: 0.2203 (ttm) REVERT: D 376 MET cc_start: 0.1748 (tpp) cc_final: 0.1364 (mtp) REVERT: D 379 ILE cc_start: -0.1059 (mm) cc_final: -0.1577 (pt) REVERT: D 394 ASN cc_start: 0.5281 (OUTLIER) cc_final: 0.3437 (m-40) REVERT: D 400 PHE cc_start: 0.3968 (t80) cc_final: 0.2381 (m-80) REVERT: D 408 MET cc_start: -0.1079 (ptp) cc_final: -0.2146 (mtm) REVERT: D 539 LEU cc_start: 0.0006 (OUTLIER) cc_final: -0.0324 (tt) REVERT: D 564 LYS cc_start: 0.2158 (mmmt) cc_final: 0.1840 (ttpp) REVERT: D 579 MET cc_start: 0.1404 (mtm) cc_final: 0.0454 (pmm) REVERT: E 61 LYS cc_start: 0.1777 (OUTLIER) cc_final: 0.1388 (tptp) REVERT: E 89 GLN cc_start: 0.3813 (tp40) cc_final: 0.1922 (mt0) REVERT: E 176 LEU cc_start: 0.1075 (OUTLIER) cc_final: 0.0313 (mp) REVERT: E 190 MET cc_start: 0.3228 (OUTLIER) cc_final: 0.2596 (ptt) REVERT: E 285 PHE cc_start: 0.0636 (OUTLIER) cc_final: -0.0658 (p90) REVERT: E 297 MET cc_start: 0.0403 (ttp) cc_final: -0.0365 (ptm) REVERT: E 376 MET cc_start: 0.1474 (ptt) cc_final: 0.1265 (ptm) REVERT: E 446 ILE cc_start: 0.2911 (OUTLIER) cc_final: 0.2501 (mp) REVERT: E 480 MET cc_start: 0.1586 (mmp) cc_final: 0.0297 (ptt) REVERT: E 514 ARG cc_start: 0.2495 (mmp-170) cc_final: -0.0092 (mtt-85) REVERT: E 536 GLU cc_start: 0.0083 (OUTLIER) cc_final: -0.1752 (mp0) REVERT: E 600 ARG cc_start: 0.2893 (OUTLIER) cc_final: 0.2431 (tpp-160) outliers start: 189 outliers final: 117 residues processed: 388 average time/residue: 0.4228 time to fit residues: 272.7690 Evaluate side-chains 344 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 202 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL 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 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 392 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 269 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 340 optimal weight: 7.9990 chunk 57 optimal weight: 0.0870 chunk 72 optimal weight: 0.5980 chunk 237 optimal weight: 0.9980 chunk 178 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 804 GLN B 935 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 913 GLN D 378 HIS D 526 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.242851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.207663 restraints weight = 64990.814| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 3.52 r_work: 0.4085 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33453 Z= 0.164 Angle : 0.760 16.688 45523 Z= 0.396 Chirality : 0.048 0.346 5027 Planarity : 0.006 0.078 5898 Dihedral : 6.348 57.431 4427 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.70 % Favored : 90.20 % Rotamer: Outliers : 4.58 % Allowed : 26.62 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.13), residues: 4053 helix: 0.47 (0.14), residues: 1339 sheet: -0.43 (0.26), residues: 376 loop : -2.87 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP D 594 HIS 0.004 0.001 HIS E 505 PHE 0.049 0.002 PHE A 55 TYR 0.037 0.001 TYR A 279 ARG 0.009 0.001 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.05640 ( 1236) hydrogen bonds : angle 5.94085 ( 3588) SS BOND : bond 0.00342 ( 41) SS BOND : angle 1.39168 ( 82) covalent geometry : bond 0.00323 (33412) covalent geometry : angle 0.75845 (45441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 231 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.2410 (OUTLIER) cc_final: 0.1723 (mt) REVERT: A 241 LEU cc_start: 0.5354 (OUTLIER) cc_final: 0.5143 (tt) REVERT: A 362 VAL cc_start: -0.0751 (OUTLIER) cc_final: -0.1201 (t) REVERT: A 533 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7156 (tt) REVERT: A 855 PHE cc_start: 0.5879 (m-10) cc_final: 0.5581 (m-10) REVERT: A 980 ILE cc_start: 0.3904 (mm) cc_final: 0.3651 (mm) REVERT: A 996 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7530 (tt) REVERT: A 1138 TYR cc_start: 0.7707 (t80) cc_final: 0.7277 (t80) REVERT: B 106 PHE cc_start: 0.1089 (OUTLIER) cc_final: 0.0521 (m-80) REVERT: B 206 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6102 (tptt) REVERT: B 210 ILE cc_start: 0.5986 (OUTLIER) cc_final: 0.5285 (mm) REVERT: B 237 ARG cc_start: 0.5603 (mmm160) cc_final: 0.5277 (tpt-90) REVERT: B 740 MET cc_start: 0.8955 (tpt) cc_final: 0.8374 (ttm) REVERT: B 754 LEU cc_start: 0.9315 (pp) cc_final: 0.9074 (tt) REVERT: B 935 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6008 (tp40) REVERT: C 170 TYR cc_start: 0.6431 (t80) cc_final: 0.5840 (t80) REVERT: C 191 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6653 (mm-30) REVERT: C 215 ASP cc_start: 0.3267 (OUTLIER) cc_final: 0.2951 (t0) REVERT: C 355 ARG cc_start: 0.5253 (OUTLIER) cc_final: 0.3577 (tpp-160) REVERT: C 947 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6697 (mmmm) REVERT: C 954 GLN cc_start: 0.8367 (mt0) cc_final: 0.8161 (mt0) REVERT: C 980 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7383 (mp) REVERT: C 996 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5590 (tp) REVERT: C 1145 LEU cc_start: 0.4752 (OUTLIER) cc_final: 0.4499 (mp) REVERT: D 32 PHE cc_start: 0.1794 (OUTLIER) cc_final: 0.0329 (t80) REVERT: D 78 GLN cc_start: 0.2354 (mm-40) cc_final: 0.1670 (tt0) REVERT: D 90 ASP cc_start: 0.1516 (OUTLIER) cc_final: 0.1271 (p0) REVERT: D 124 SER cc_start: 0.1806 (OUTLIER) cc_final: 0.1340 (p) REVERT: D 190 MET cc_start: 0.1602 (OUTLIER) cc_final: 0.1260 (mtm) REVERT: D 199 TYR cc_start: 0.1235 (OUTLIER) cc_final: -0.0486 (t80) REVERT: D 270 MET cc_start: 0.2923 (ttt) cc_final: 0.2643 (ttm) REVERT: D 366 MET cc_start: 0.1217 (pmm) cc_final: -0.1954 (mmm) REVERT: D 379 ILE cc_start: -0.0915 (mm) cc_final: -0.1430 (pt) REVERT: D 400 PHE cc_start: 0.3821 (t80) cc_final: 0.2342 (m-80) REVERT: D 408 MET cc_start: -0.1068 (ptp) cc_final: -0.1483 (mtm) REVERT: D 474 MET cc_start: 0.1759 (tpt) cc_final: -0.0644 (ttt) REVERT: D 496 THR cc_start: 0.4723 (m) cc_final: 0.4169 (p) REVERT: D 539 LEU cc_start: -0.0119 (OUTLIER) cc_final: -0.0330 (tt) REVERT: D 564 LYS cc_start: 0.2822 (mmmt) cc_final: 0.2244 (ttpp) REVERT: D 579 MET cc_start: 0.1148 (OUTLIER) cc_final: 0.0548 (pmm) REVERT: E 61 LYS cc_start: 0.2094 (OUTLIER) cc_final: 0.1672 (tptp) REVERT: E 89 GLN cc_start: 0.3687 (tp40) cc_final: 0.1762 (mt0) REVERT: E 176 LEU cc_start: 0.1100 (OUTLIER) cc_final: 0.0354 (mp) REVERT: E 270 MET cc_start: -0.0065 (tpp) cc_final: -0.2187 (mmt) REVERT: E 285 PHE cc_start: 0.0449 (OUTLIER) cc_final: -0.0738 (p90) REVERT: E 297 MET cc_start: 0.0578 (ttp) cc_final: 0.0363 (mtp) REVERT: E 310 GLU cc_start: 0.1014 (OUTLIER) cc_final: 0.0291 (tp30) REVERT: E 383 MET cc_start: -0.0380 (OUTLIER) cc_final: -0.0820 (tpt) REVERT: E 446 ILE cc_start: 0.3114 (OUTLIER) cc_final: 0.2651 (mp) REVERT: E 480 MET cc_start: 0.1969 (mmp) cc_final: 0.0520 (ptt) REVERT: E 536 GLU cc_start: 0.0099 (OUTLIER) cc_final: -0.1647 (mp0) REVERT: E 600 ARG cc_start: 0.3003 (OUTLIER) cc_final: 0.2528 (tpp-160) outliers start: 165 outliers final: 100 residues processed: 374 average time/residue: 0.3922 time to fit residues: 243.2445 Evaluate side-chains 343 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 212 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 266 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 288 optimal weight: 0.0370 chunk 120 optimal weight: 0.5980 chunk 221 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 407 optimal weight: 0.7980 chunk 339 optimal weight: 0.5980 chunk 344 optimal weight: 0.2980 chunk 232 optimal weight: 0.4980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B1002 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN D 555 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.243150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.205609 restraints weight = 64764.987| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 3.52 r_work: 0.4074 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.7615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33453 Z= 0.156 Angle : 0.751 16.357 45523 Z= 0.390 Chirality : 0.048 0.335 5027 Planarity : 0.006 0.079 5898 Dihedral : 6.073 58.319 4424 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.88 % Favored : 91.04 % Rotamer: Outliers : 4.08 % Allowed : 27.12 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 4053 helix: 0.57 (0.15), residues: 1335 sheet: -0.40 (0.26), residues: 370 loop : -2.81 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP D 594 HIS 0.004 0.001 HIS E 373 PHE 0.042 0.001 PHE A 55 TYR 0.038 0.001 TYR A 279 ARG 0.009 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.05539 ( 1236) hydrogen bonds : angle 5.83167 ( 3588) SS BOND : bond 0.00346 ( 41) SS BOND : angle 1.34808 ( 82) covalent geometry : bond 0.00311 (33412) covalent geometry : angle 0.74947 (45441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 219 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.2442 (OUTLIER) cc_final: 0.1869 (mt) REVERT: A 235 ILE cc_start: 0.4398 (OUTLIER) cc_final: 0.4188 (mp) REVERT: A 241 LEU cc_start: 0.5312 (OUTLIER) cc_final: 0.5086 (tt) REVERT: A 328 ARG cc_start: 0.7220 (mmm-85) cc_final: 0.6947 (mmm160) REVERT: A 533 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6989 (tt) REVERT: A 855 PHE cc_start: 0.6098 (m-10) cc_final: 0.5736 (m-10) REVERT: A 980 ILE cc_start: 0.4017 (mm) cc_final: 0.3709 (mm) REVERT: A 996 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7503 (tt) REVERT: A 1138 TYR cc_start: 0.7583 (t80) cc_final: 0.7256 (t80) REVERT: B 106 PHE cc_start: 0.1061 (OUTLIER) cc_final: 0.0529 (m-80) REVERT: B 206 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6154 (tptt) REVERT: B 210 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5324 (mm) REVERT: B 740 MET cc_start: 0.8993 (tpt) cc_final: 0.8392 (ttm) REVERT: B 754 LEU cc_start: 0.9295 (pp) cc_final: 0.9051 (tt) REVERT: C 170 TYR cc_start: 0.6542 (t80) cc_final: 0.5916 (t80) REVERT: C 191 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6642 (mm-30) REVERT: C 215 ASP cc_start: 0.3348 (OUTLIER) cc_final: 0.3054 (t0) REVERT: C 355 ARG cc_start: 0.5238 (OUTLIER) cc_final: 0.3208 (ttm170) REVERT: C 947 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6638 (mmmm) REVERT: C 954 GLN cc_start: 0.8268 (mt0) cc_final: 0.8046 (mt0) REVERT: C 996 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5621 (tp) REVERT: C 1145 LEU cc_start: 0.4745 (OUTLIER) cc_final: 0.4476 (mp) REVERT: D 32 PHE cc_start: 0.1774 (OUTLIER) cc_final: -0.0310 (t80) REVERT: D 78 GLN cc_start: 0.2498 (mm-40) cc_final: 0.1805 (tt0) REVERT: D 90 ASP cc_start: 0.1462 (OUTLIER) cc_final: 0.1256 (p0) REVERT: D 199 TYR cc_start: 0.1336 (OUTLIER) cc_final: -0.0391 (t80) REVERT: D 270 MET cc_start: 0.2844 (ttt) cc_final: 0.2586 (ttm) REVERT: D 366 MET cc_start: 0.0716 (pmm) cc_final: -0.1469 (mmm) REVERT: D 400 PHE cc_start: 0.3568 (t80) cc_final: 0.2214 (m-80) REVERT: D 408 MET cc_start: -0.0942 (ptp) cc_final: -0.1806 (mtt) REVERT: D 474 MET cc_start: 0.1492 (tpt) cc_final: -0.0938 (ttt) REVERT: D 496 THR cc_start: 0.4662 (m) cc_final: 0.4139 (p) REVERT: D 564 LYS cc_start: 0.2962 (mmmt) cc_final: 0.2551 (ttpp) REVERT: D 579 MET cc_start: 0.1147 (OUTLIER) cc_final: 0.0604 (pmm) REVERT: E 61 LYS cc_start: 0.2107 (OUTLIER) cc_final: 0.1630 (tptp) REVERT: E 89 GLN cc_start: 0.3602 (tp40) cc_final: 0.1632 (mt0) REVERT: E 176 LEU cc_start: 0.1104 (OUTLIER) cc_final: 0.0347 (mp) REVERT: E 285 PHE cc_start: 0.0566 (OUTLIER) cc_final: -0.0555 (p90) REVERT: E 297 MET cc_start: 0.0517 (ttp) cc_final: -0.0373 (ptm) REVERT: E 480 MET cc_start: 0.1684 (mmp) cc_final: 0.0372 (ptt) REVERT: E 514 ARG cc_start: 0.2090 (mmp-170) cc_final: -0.0079 (mtt-85) REVERT: E 600 ARG cc_start: 0.3092 (OUTLIER) cc_final: 0.2612 (tpp-160) outliers start: 147 outliers final: 101 residues processed: 349 average time/residue: 0.4015 time to fit residues: 230.3859 Evaluate side-chains 333 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 210 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL 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 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 403 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 329 optimal weight: 8.9990 chunk 164 optimal weight: 0.2980 chunk 323 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1113 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN D 194 ASN D 526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.240475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.202346 restraints weight = 63859.336| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 3.63 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.7928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 33453 Z= 0.173 Angle : 0.769 16.184 45523 Z= 0.400 Chirality : 0.049 0.341 5027 Planarity : 0.006 0.076 5898 Dihedral : 6.136 59.694 4424 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.92 % Favored : 90.03 % Rotamer: Outliers : 4.22 % Allowed : 27.01 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 4053 helix: 0.61 (0.15), residues: 1324 sheet: -0.44 (0.26), residues: 377 loop : -2.83 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 594 HIS 0.004 0.001 HIS E 265 PHE 0.039 0.002 PHE A 84 TYR 0.038 0.001 TYR A 279 ARG 0.010 0.001 ARG E 357 Details of bonding type rmsd hydrogen bonds : bond 0.06356 ( 1236) hydrogen bonds : angle 5.87429 ( 3588) SS BOND : bond 0.00386 ( 41) SS BOND : angle 1.49650 ( 82) covalent geometry : bond 0.00366 (33412) covalent geometry : angle 0.76668 (45441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 214 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.2342 (OUTLIER) cc_final: 0.1777 (mt) REVERT: A 533 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6963 (tt) REVERT: A 980 ILE cc_start: 0.4604 (mm) cc_final: 0.4162 (mm) REVERT: A 996 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7379 (tt) REVERT: A 1138 TYR cc_start: 0.7123 (t80) cc_final: 0.6825 (t80) REVERT: B 106 PHE cc_start: 0.1759 (OUTLIER) cc_final: 0.1117 (m-80) REVERT: B 210 ILE cc_start: 0.5010 (OUTLIER) cc_final: 0.4413 (mm) REVERT: B 393 THR cc_start: 0.5150 (OUTLIER) cc_final: 0.4912 (p) REVERT: B 565 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7296 (p90) REVERT: B 754 LEU cc_start: 0.9199 (pp) cc_final: 0.8885 (tt) REVERT: B 776 LYS cc_start: 0.8680 (tppt) cc_final: 0.8426 (tptt) REVERT: C 115 GLN cc_start: 0.3481 (OUTLIER) cc_final: 0.2248 (tt0) REVERT: C 191 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6139 (mm-30) REVERT: C 215 ASP cc_start: 0.3683 (OUTLIER) cc_final: 0.3365 (t0) REVERT: C 355 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.4706 (mtp85) REVERT: C 947 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6898 (mmmm) REVERT: C 954 GLN cc_start: 0.7780 (mt0) cc_final: 0.7549 (mt0) REVERT: C 1145 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.5122 (mp) REVERT: D 32 PHE cc_start: 0.2161 (OUTLIER) cc_final: 0.0459 (t80) REVERT: D 90 ASP cc_start: 0.2572 (OUTLIER) cc_final: 0.2251 (p0) REVERT: D 190 MET cc_start: 0.2132 (OUTLIER) cc_final: 0.1670 (mtm) REVERT: D 199 TYR cc_start: 0.2186 (OUTLIER) cc_final: 0.0196 (t80) REVERT: D 282 MET cc_start: 0.0950 (OUTLIER) cc_final: -0.2546 (pmm) REVERT: D 366 MET cc_start: 0.0805 (pmm) cc_final: 0.0073 (ppp) REVERT: D 400 PHE cc_start: 0.2709 (t80) cc_final: 0.1804 (m-80) REVERT: D 408 MET cc_start: -0.1738 (ptp) cc_final: -0.2580 (mtt) REVERT: D 474 MET cc_start: 0.0988 (tpt) cc_final: -0.1181 (ttt) REVERT: D 496 THR cc_start: 0.5157 (m) cc_final: 0.4461 (t) REVERT: D 527 GLU cc_start: 0.1935 (tm-30) cc_final: 0.1242 (tm-30) REVERT: D 579 MET cc_start: 0.0706 (mtm) cc_final: 0.0202 (pmm) REVERT: E 61 LYS cc_start: 0.2872 (OUTLIER) cc_final: 0.2276 (tptp) REVERT: E 89 GLN cc_start: 0.3884 (tp40) cc_final: 0.2132 (pt0) REVERT: E 176 LEU cc_start: 0.1897 (OUTLIER) cc_final: 0.1187 (mp) REVERT: E 285 PHE cc_start: 0.0610 (OUTLIER) cc_final: -0.0302 (p90) REVERT: E 297 MET cc_start: 0.1745 (ttp) cc_final: 0.0551 (ptm) REVERT: E 480 MET cc_start: 0.2431 (mmp) cc_final: 0.0829 (ptt) REVERT: E 600 ARG cc_start: 0.2622 (OUTLIER) cc_final: 0.2263 (tpp-160) outliers start: 152 outliers final: 112 residues processed: 350 average time/residue: 0.4153 time to fit residues: 239.9181 Evaluate side-chains 341 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 207 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 825 LYS 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 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 391 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 chunk 189 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 331 optimal weight: 7.9990 chunk 234 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.238947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.199408 restraints weight = 61852.042| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 3.47 r_work: 0.3940 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 33453 Z= 0.237 Angle : 0.857 15.750 45523 Z= 0.449 Chirality : 0.052 0.358 5027 Planarity : 0.006 0.097 5898 Dihedral : 6.578 56.407 4424 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.25 % Favored : 88.72 % Rotamer: Outliers : 3.94 % Allowed : 27.48 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.13), residues: 4053 helix: 0.34 (0.14), residues: 1320 sheet: -0.79 (0.27), residues: 363 loop : -2.88 (0.11), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 594 HIS 0.010 0.002 HIS D 354 PHE 0.049 0.003 PHE B 106 TYR 0.034 0.002 TYR A 279 ARG 0.008 0.001 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.08360 ( 1236) hydrogen bonds : angle 6.32704 ( 3588) SS BOND : bond 0.00483 ( 41) SS BOND : angle 1.88893 ( 82) covalent geometry : bond 0.00534 (33412) covalent geometry : angle 0.85446 (45441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 209 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.2017 (OUTLIER) cc_final: 0.1114 (mt) REVERT: A 233 ILE cc_start: 0.2562 (OUTLIER) cc_final: 0.1910 (mt) REVERT: A 237 ARG cc_start: 0.6713 (mpt180) cc_final: 0.6440 (mmp-170) REVERT: A 980 ILE cc_start: 0.3929 (mm) cc_final: 0.3663 (mm) REVERT: A 996 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 1138 TYR cc_start: 0.7731 (t80) cc_final: 0.7398 (t80) REVERT: B 92 PHE cc_start: 0.5753 (m-10) cc_final: 0.5481 (m-10) REVERT: B 106 PHE cc_start: 0.1991 (OUTLIER) cc_final: 0.1228 (m-80) REVERT: B 565 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7341 (p90) REVERT: B 776 LYS cc_start: 0.8818 (tppt) cc_final: 0.8542 (tptt) REVERT: B 966 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6224 (mt) REVERT: C 115 GLN cc_start: 0.3609 (OUTLIER) cc_final: 0.2694 (tt0) REVERT: C 215 ASP cc_start: 0.3519 (OUTLIER) cc_final: 0.3314 (t0) REVERT: C 947 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.6924 (mmmm) REVERT: C 954 GLN cc_start: 0.8399 (mt0) cc_final: 0.8155 (mt0) REVERT: C 1145 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.5004 (mp) REVERT: D 90 ASP cc_start: 0.1417 (OUTLIER) cc_final: 0.1173 (p0) REVERT: D 190 MET cc_start: 0.1769 (OUTLIER) cc_final: 0.1510 (mtm) REVERT: D 199 TYR cc_start: 0.1162 (OUTLIER) cc_final: -0.0297 (t80) REVERT: D 270 MET cc_start: 0.1829 (ttm) cc_final: 0.1185 (ttm) REVERT: D 349 TRP cc_start: 0.1037 (OUTLIER) cc_final: 0.0543 (m-10) REVERT: D 366 MET cc_start: -0.0015 (pmm) cc_final: -0.0498 (ppp) REVERT: D 400 PHE cc_start: 0.3987 (t80) cc_final: 0.2551 (m-80) REVERT: D 408 MET cc_start: -0.0672 (ptp) cc_final: -0.1880 (mtt) REVERT: D 474 MET cc_start: 0.1653 (tpt) cc_final: -0.0378 (ttt) REVERT: D 527 GLU cc_start: 0.0294 (tm-30) cc_final: -0.0024 (tm-30) REVERT: E 61 LYS cc_start: 0.1836 (OUTLIER) cc_final: 0.1567 (tptp) REVERT: E 89 GLN cc_start: 0.3543 (tp40) cc_final: 0.1169 (pt0) REVERT: E 285 PHE cc_start: 0.1051 (OUTLIER) cc_final: -0.0092 (p90) REVERT: E 297 MET cc_start: 0.0559 (ttp) cc_final: 0.0229 (mtm) REVERT: E 332 MET cc_start: 0.0748 (tpt) cc_final: -0.0199 (mmt) REVERT: E 480 MET cc_start: 0.1557 (mmp) cc_final: 0.0243 (ptt) REVERT: E 600 ARG cc_start: 0.2953 (OUTLIER) cc_final: 0.2158 (tpp-160) outliers start: 142 outliers final: 107 residues processed: 339 average time/residue: 0.4054 time to fit residues: 226.9362 Evaluate side-chains 327 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 203 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 825 LYS 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 965 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 356 optimal weight: 6.9990 chunk 396 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 336 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.238535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.199344 restraints weight = 61782.323| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 3.36 r_work: 0.3954 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.8521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.265 33453 Z= 0.271 Angle : 0.952 59.167 45523 Z= 0.508 Chirality : 0.052 0.417 5027 Planarity : 0.006 0.096 5898 Dihedral : 6.584 56.420 4424 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.15 % Favored : 88.80 % Rotamer: Outliers : 3.77 % Allowed : 27.64 % Favored : 68.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.13), residues: 4053 helix: 0.32 (0.14), residues: 1320 sheet: -0.80 (0.27), residues: 363 loop : -2.89 (0.11), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 594 HIS 0.019 0.002 HIS D 228 PHE 0.050 0.002 PHE B 106 TYR 0.131 0.003 TYR D 381 ARG 0.011 0.001 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.08223 ( 1236) hydrogen bonds : angle 6.31743 ( 3588) SS BOND : bond 0.00488 ( 41) SS BOND : angle 1.84853 ( 82) covalent geometry : bond 0.00632 (33412) covalent geometry : angle 0.94987 (45441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17556.31 seconds wall clock time: 304 minutes 38.87 seconds (18278.87 seconds total)