Starting phenix.real_space_refine on Tue Aug 26 02:38:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t20_40976/08_2025/8t20_40976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t20_40976/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t20_40976/08_2025/8t20_40976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t20_40976/08_2025/8t20_40976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t20_40976/08_2025/8t20_40976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t20_40976/08_2025/8t20_40976.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.88, per 1000 atoms: 0.21 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.26 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: 8.15 Time building geometry restraints manager: 3.95 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: 0.010 Normalize map: mean=0, sd=1: 13.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.310 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- 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 : 25.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.81 (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 ARG 0.011 0.001 ARG E 177 TYR 0.049 0.002 TYR A 279 PHE 0.063 0.003 PHE A 275 TRP 0.043 0.003 TRP E 349 HIS 0.015 0.002 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00730 (33412) covalent geometry : angle 1.05532 (45441) SS BOND : bond 0.00648 ( 41) SS BOND : angle 2.50166 ( 82) hydrogen bonds : bond 0.17479 ( 1236) hydrogen bonds : angle 7.57972 ( 3588) *********************** 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 : 1.253 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: 0.5365 (t) REVERT: A 237 ARG cc_start: 0.4763 (mmt180) cc_final: 0.2605 (mmm160) REVERT: B 200 TYR cc_start: 0.2415 (OUTLIER) cc_final: 0.2003 (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: 0.4469 (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: 0.2101 (m-10) REVERT: E 62 MET cc_start: 0.2118 (tmm) cc_final: 0.1593 (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: -0.1132 (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: -0.1915 (mtm) outliers start: 24 outliers final: 5 residues processed: 504 average time/residue: 0.1962 time to fit residues: 163.5840 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 : 1.400 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 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 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN D 33 ASN D 49 ASN D 228 HIS D 535 HIS E 49 ASN E 58 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.244104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.213811 restraints weight = 64362.974| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 3.21 r_work: 0.4091 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 33453 Z= 0.214 Angle : 0.883 16.060 45523 Z= 0.467 Chirality : 0.051 0.358 5027 Planarity : 0.007 0.085 5898 Dihedral : 7.327 53.570 4435 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.29 % Favored : 89.59 % Rotamer: Outliers : 5.11 % Allowed : 26.31 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.79 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.13), residues: 4053 helix: -0.01 (0.14), residues: 1346 sheet: -0.99 (0.25), residues: 393 loop : -3.00 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1000 TYR 0.035 0.002 TYR A 279 PHE 0.035 0.002 PHE A 562 TRP 0.024 0.002 TRP E 168 HIS 0.009 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00438 (33412) covalent geometry : angle 0.87984 (45441) SS BOND : bond 0.01203 ( 41) SS BOND : angle 2.01638 ( 82) hydrogen bonds : bond 0.06842 ( 1236) hydrogen bonds : angle 6.65681 ( 3588) *********************** 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 505 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 321 time to evaluate : 1.188 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: A 102 ARG cc_start: 0.5827 (mtm-85) cc_final: 0.5572 (mtm-85) REVERT: A 237 ARG cc_start: 0.5427 (mmt180) cc_final: 0.3191 (mmm160) REVERT: A 492 LEU cc_start: -0.1183 (OUTLIER) cc_final: -0.1503 (mt) REVERT: A 781 VAL cc_start: 0.8807 (p) cc_final: 0.8571 (t) REVERT: A 995 ARG cc_start: 0.7778 (tmm160) cc_final: 0.7411 (ptp-170) REVERT: A 996 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6933 (tt) REVERT: B 200 TYR cc_start: 0.2792 (OUTLIER) cc_final: 0.2305 (m-80) REVERT: B 237 ARG cc_start: 0.5404 (mmm160) cc_final: 0.5123 (mmp-170) REVERT: B 472 ILE cc_start: -0.1558 (OUTLIER) cc_final: -0.2360 (tt) REVERT: B 740 MET cc_start: 0.7526 (tpt) cc_final: 0.7078 (tpp) REVERT: B 898 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: C 170 TYR cc_start: 0.5383 (t80) cc_final: 0.4951 (t80) REVERT: C 355 ARG cc_start: 0.5578 (OUTLIER) cc_final: 0.4105 (ttm170) REVERT: D 101 GLN cc_start: 0.1912 (tm-30) cc_final: 0.1675 (mm-40) REVERT: D 131 LYS cc_start: -0.0274 (OUTLIER) cc_final: -0.0501 (pttt) REVERT: D 376 MET cc_start: 0.1502 (tpt) cc_final: 0.1001 (ttm) REVERT: D 400 PHE cc_start: 0.3727 (t80) cc_final: 0.2584 (m-10) REVERT: D 480 MET cc_start: -0.0738 (mmm) cc_final: -0.0947 (mtm) REVERT: D 523 PHE cc_start: -0.0577 (OUTLIER) cc_final: -0.0897 (t80) REVERT: E 62 MET cc_start: 0.0905 (tmm) cc_final: 0.0654 (tmm) REVERT: E 123 MET cc_start: 0.0188 (tmm) cc_final: -0.0611 (tmm) REVERT: E 176 LEU cc_start: 0.1282 (OUTLIER) cc_final: 0.0921 (mm) REVERT: E 190 MET cc_start: 0.3466 (tmm) cc_final: 0.3070 (ptt) REVERT: E 285 PHE cc_start: -0.0195 (OUTLIER) cc_final: -0.1334 (p90) REVERT: E 297 MET cc_start: 0.0849 (ttp) cc_final: -0.0018 (ptm) REVERT: E 310 GLU cc_start: 0.1304 (OUTLIER) cc_final: 0.0482 (tp30) REVERT: E 480 MET cc_start: 0.1442 (mmp) cc_final: 0.0657 (tpt) outliers start: 184 outliers final: 83 residues processed: 478 average time/residue: 0.1883 time to fit residues: 149.5847 Evaluate side-chains 348 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 254 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 130 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 316 SER 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 530 SER 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 693 ILE 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 85 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 303 LEU 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 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain C residue 36 VAL 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 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 436 TRP 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 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 968 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 D residue 32 PHE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 523 PHE 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 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 38 optimal weight: 20.0000 chunk 297 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 373 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 198 optimal weight: 0.0670 overall best weight: 1.1724 ------------------------------------------------------------------------------- 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 354 ASN ** 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** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B1002 GLN B1088 HIS C 498 GLN C 935 GLN D 117 ASN D 265 HIS D 378 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.243706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.210377 restraints weight = 63900.446| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 3.35 r_work: 0.4087 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33453 Z= 0.231 Angle : 0.877 14.877 45523 Z= 0.463 Chirality : 0.052 0.339 5027 Planarity : 0.006 0.082 5898 Dihedral : 7.057 53.581 4429 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.03 % Favored : 88.85 % Rotamer: Outliers : 7.02 % Allowed : 24.40 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.13), residues: 4053 helix: -0.00 (0.14), residues: 1352 sheet: -0.64 (0.25), residues: 380 loop : -2.99 (0.12), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C1000 TYR 0.025 0.002 TYR A 91 PHE 0.038 0.002 PHE B 43 TRP 0.021 0.002 TRP D 478 HIS 0.039 0.002 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00492 (33412) covalent geometry : angle 0.87300 (45441) SS BOND : bond 0.00503 ( 41) SS BOND : angle 2.12309 ( 82) hydrogen bonds : bond 0.07313 ( 1236) hydrogen bonds : angle 6.45303 ( 3588) *********************** 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 519 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 266 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.1416 (OUTLIER) cc_final: 0.0007 (m-80) REVERT: A 131 CYS cc_start: 0.4718 (OUTLIER) cc_final: 0.4341 (p) REVERT: A 194 PHE cc_start: 0.6246 (m-10) cc_final: 0.5909 (m-10) REVERT: A 241 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5769 (tt) REVERT: A 312 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7599 (tt) REVERT: A 492 LEU cc_start: -0.0838 (OUTLIER) cc_final: -0.1160 (mt) REVERT: A 533 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6922 (tt) REVERT: A 598 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 855 PHE cc_start: 0.5724 (m-10) cc_final: 0.5404 (m-10) REVERT: A 983 ARG cc_start: 0.2790 (OUTLIER) cc_final: 0.2480 (ptt-90) REVERT: A 996 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7687 (tt) REVERT: B 210 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5566 (mm) REVERT: B 237 ARG cc_start: 0.5470 (mmm160) cc_final: 0.5090 (mmp-170) REVERT: B 402 ILE cc_start: 0.2587 (OUTLIER) cc_final: 0.2238 (pt) REVERT: B 472 ILE cc_start: -0.1915 (OUTLIER) cc_final: -0.2621 (tt) REVERT: B 740 MET cc_start: 0.8510 (tpt) cc_final: 0.7850 (tpp) REVERT: B 900 MET cc_start: 0.7675 (mtp) cc_final: 0.7464 (mtp) REVERT: B 918 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 935 GLN cc_start: 0.5408 (OUTLIER) cc_final: 0.4622 (tp40) REVERT: B 962 LEU cc_start: 0.1990 (OUTLIER) cc_final: 0.1733 (tt) REVERT: B 994 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8014 (p0) REVERT: B 1000 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8267 (ptm-80) REVERT: C 65 PHE cc_start: 0.5702 (m-80) cc_final: 0.5429 (m-80) REVERT: C 115 GLN cc_start: 0.2064 (OUTLIER) cc_final: 0.1461 (tp40) REVERT: C 170 TYR cc_start: 0.6014 (t80) cc_final: 0.5678 (t80) REVERT: C 191 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.6076 (mm-30) REVERT: C 204 TYR cc_start: 0.6469 (m-80) cc_final: 0.6217 (m-80) REVERT: C 355 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.4602 (tpp-160) REVERT: C 358 ILE cc_start: 0.0898 (OUTLIER) cc_final: 0.0147 (mt) REVERT: C 950 ASP cc_start: 0.8463 (m-30) cc_final: 0.8100 (m-30) REVERT: C 990 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 1115 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7638 (mt) REVERT: C 1145 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.5151 (mp) REVERT: D 131 LYS cc_start: 0.0066 (OUTLIER) cc_final: -0.0138 (pttt) REVERT: D 174 LYS cc_start: 0.0576 (mmtt) cc_final: 0.0024 (ptmm) REVERT: D 342 VAL cc_start: -0.0717 (OUTLIER) cc_final: -0.0934 (p) REVERT: D 400 PHE cc_start: 0.3504 (t80) cc_final: 0.2278 (m-10) REVERT: D 564 LYS cc_start: 0.2348 (mmmt) cc_final: 0.2007 (ttpp) REVERT: D 579 MET cc_start: -0.0604 (mtm) cc_final: -0.2304 (tmm) REVERT: E 62 MET cc_start: 0.0905 (tmm) cc_final: 0.0679 (tmm) REVERT: E 123 MET cc_start: 0.0571 (tmm) cc_final: -0.0174 (tmm) REVERT: E 176 LEU cc_start: 0.1202 (OUTLIER) cc_final: 0.0711 (mm) REVERT: E 190 MET cc_start: 0.3653 (OUTLIER) cc_final: 0.2862 (ptt) REVERT: E 285 PHE cc_start: 0.0585 (OUTLIER) cc_final: -0.1047 (p90) REVERT: E 297 MET cc_start: 0.0620 (ttp) cc_final: -0.0203 (ptm) REVERT: E 446 ILE cc_start: 0.2820 (OUTLIER) cc_final: 0.2443 (mp) REVERT: E 480 MET cc_start: 0.1754 (mmp) cc_final: 0.0793 (tpt) REVERT: E 536 GLU cc_start: -0.0295 (OUTLIER) cc_final: -0.1871 (mp0) outliers start: 253 outliers final: 103 residues processed: 492 average time/residue: 0.2023 time to fit residues: 164.1207 Evaluate side-chains 356 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 223 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain A residue 131 CYS 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 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 312 ILE 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 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 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL 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 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 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 210 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 472 ILE 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 698 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 898 PHE 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 962 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1132 ILE 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 115 GLN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU 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 436 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL 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 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 342 VAL 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 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 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 316 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 409 optimal weight: 0.9990 chunk 404 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 214 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 405 optimal weight: 4.9990 chunk 339 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 327 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 804 GLN C1002 GLN D 63 ASN D 194 ASN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.242710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.208171 restraints weight = 64820.300| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 3.47 r_work: 0.4082 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33453 Z= 0.202 Angle : 0.826 16.863 45523 Z= 0.432 Chirality : 0.050 0.343 5027 Planarity : 0.006 0.079 5898 Dihedral : 6.801 55.070 4427 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.80 % Favored : 90.11 % Rotamer: Outliers : 5.88 % Allowed : 25.26 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.13), residues: 4053 helix: 0.18 (0.14), residues: 1345 sheet: -0.70 (0.25), residues: 388 loop : -2.94 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1000 TYR 0.040 0.002 TYR A 279 PHE 0.042 0.002 PHE E 512 TRP 0.022 0.002 TRP D 349 HIS 0.006 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00421 (33412) covalent geometry : angle 0.82313 (45441) SS BOND : bond 0.00485 ( 41) SS BOND : angle 1.71302 ( 82) hydrogen bonds : bond 0.06733 ( 1236) hydrogen bonds : angle 6.34957 ( 3588) *********************** 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 457 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 245 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.1125 (OUTLIER) cc_final: -0.0506 (m-80) REVERT: A 241 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5423 (tt) REVERT: A 312 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7699 (tt) REVERT: A 492 LEU cc_start: -0.0850 (OUTLIER) cc_final: -0.1136 (mt) REVERT: A 533 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6931 (tt) REVERT: A 855 PHE cc_start: 0.5757 (m-10) cc_final: 0.5495 (m-10) REVERT: A 962 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8665 (pt) REVERT: A 996 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 237 ARG cc_start: 0.5435 (mmm160) cc_final: 0.4997 (mmp-170) REVERT: B 402 ILE cc_start: 0.2819 (OUTLIER) cc_final: 0.2462 (pt) REVERT: B 740 MET cc_start: 0.8830 (tpt) cc_final: 0.8141 (tpp) REVERT: B 935 GLN cc_start: 0.5782 (OUTLIER) cc_final: 0.5337 (tp40) REVERT: B 1000 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8349 (ptm-80) REVERT: C 65 PHE cc_start: 0.5705 (m-80) cc_final: 0.5363 (m-80) REVERT: C 97 LYS cc_start: 0.5467 (tptp) cc_final: 0.4479 (mmmt) REVERT: C 170 TYR cc_start: 0.6028 (t80) cc_final: 0.5705 (t80) REVERT: C 237 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5707 (ptm160) REVERT: C 355 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.4512 (tpp-160) REVERT: C 358 ILE cc_start: 0.0782 (OUTLIER) cc_final: 0.0026 (mt) REVERT: C 740 MET cc_start: 0.7957 (tpp) cc_final: 0.7551 (ttt) REVERT: C 950 ASP cc_start: 0.8567 (m-30) cc_final: 0.7813 (m-30) REVERT: C 1054 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7661 (mm110) REVERT: C 1115 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7989 (mt) REVERT: D 32 PHE cc_start: 0.1629 (OUTLIER) cc_final: -0.1582 (t80) REVERT: D 297 MET cc_start: 0.2174 (mmm) cc_final: 0.1690 (mmm) REVERT: D 400 PHE cc_start: 0.3671 (t80) cc_final: 0.2684 (m-10) REVERT: D 408 MET cc_start: -0.0724 (ptp) cc_final: -0.2395 (mtm) REVERT: D 564 LYS cc_start: 0.2424 (mmmt) cc_final: 0.2041 (ttpp) REVERT: D 579 MET cc_start: 0.0774 (mtm) cc_final: -0.0262 (pmm) REVERT: E 62 MET cc_start: 0.0795 (tmm) cc_final: 0.0592 (tmm) REVERT: E 123 MET cc_start: 0.0596 (tmm) cc_final: -0.0205 (tmm) REVERT: E 176 LEU cc_start: 0.1163 (OUTLIER) cc_final: 0.0644 (mm) REVERT: E 190 MET cc_start: 0.3505 (OUTLIER) cc_final: 0.2858 (ptt) REVERT: E 285 PHE cc_start: 0.0394 (OUTLIER) cc_final: -0.1159 (p90) REVERT: E 297 MET cc_start: 0.0647 (ttp) cc_final: -0.0197 (ptm) REVERT: E 332 MET cc_start: 0.0608 (tpt) cc_final: 0.0335 (tpt) REVERT: E 446 ILE cc_start: 0.2775 (OUTLIER) cc_final: 0.2367 (mp) REVERT: E 480 MET cc_start: 0.1551 (mmp) cc_final: 0.0353 (tpt) REVERT: E 536 GLU cc_start: -0.0018 (OUTLIER) cc_final: -0.1769 (mp0) outliers start: 212 outliers final: 116 residues processed: 430 average time/residue: 0.1762 time to fit residues: 126.0914 Evaluate side-chains 352 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 215 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 231 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 276 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE 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 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 791 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 966 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 B residue 62 VAL Chi-restraints excluded: chain B residue 64 TRP 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 303 LEU Chi-restraints excluded: chain B residue 312 ILE 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 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 726 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 898 PHE 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 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL 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 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU 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 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 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 615 VAL Chi-restraints excluded: chain C residue 645 THR 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 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 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 402 GLU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 552 GLN 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 97 LEU 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 365 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 91 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 chunk 348 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 256 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 367 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 935 GLN D 117 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.243175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.207124 restraints weight = 65223.664| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 3.49 r_work: 0.4060 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 33453 Z= 0.181 Angle : 0.797 16.521 45523 Z= 0.414 Chirality : 0.049 0.336 5027 Planarity : 0.006 0.073 5898 Dihedral : 6.617 54.866 4427 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.41 % Favored : 89.49 % Rotamer: Outliers : 5.50 % Allowed : 25.73 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.13), residues: 4053 helix: 0.28 (0.14), residues: 1352 sheet: -0.53 (0.26), residues: 376 loop : -2.92 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C1000 TYR 0.040 0.001 TYR A 279 PHE 0.033 0.002 PHE B 106 TRP 0.034 0.002 TRP D 594 HIS 0.007 0.001 HIS D 555 Details of bonding type rmsd covalent geometry : bond 0.00375 (33412) covalent geometry : angle 0.79456 (45441) SS BOND : bond 0.00400 ( 41) SS BOND : angle 1.73894 ( 82) hydrogen bonds : bond 0.06458 ( 1236) hydrogen bonds : angle 6.22419 ( 3588) *********************** 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 432 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 234 time to evaluate : 1.128 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 37 TYR cc_start: 0.1105 (OUTLIER) cc_final: -0.0065 (m-80) REVERT: A 241 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5767 (tt) REVERT: A 312 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 492 LEU cc_start: -0.0607 (OUTLIER) cc_final: -0.0936 (mt) REVERT: A 533 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7004 (tt) REVERT: A 658 ASN cc_start: 0.7464 (m-40) cc_final: 0.7207 (m110) REVERT: A 855 PHE cc_start: 0.5820 (m-10) cc_final: 0.5508 (m-10) REVERT: A 962 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8708 (pt) REVERT: A 996 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7731 (tt) REVERT: A 1002 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: B 210 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5514 (mm) REVERT: B 237 ARG cc_start: 0.5337 (mmm160) cc_final: 0.4974 (mmp-170) REVERT: B 402 ILE cc_start: 0.2553 (OUTLIER) cc_final: 0.2236 (pt) REVERT: B 740 MET cc_start: 0.8870 (tpt) cc_final: 0.8143 (ttm) REVERT: B 918 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: B 935 GLN cc_start: 0.6154 (OUTLIER) cc_final: 0.5653 (tp40) REVERT: B 1000 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8424 (ptm-80) REVERT: B 1105 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8807 (p) REVERT: C 65 PHE cc_start: 0.5762 (m-80) cc_final: 0.5362 (m-80) REVERT: C 97 LYS cc_start: 0.5640 (tptp) cc_final: 0.4774 (mmmt) REVERT: C 115 GLN cc_start: 0.2883 (OUTLIER) cc_final: 0.1966 (tp40) REVERT: C 170 TYR cc_start: 0.6318 (t80) cc_final: 0.5856 (t80) REVERT: C 191 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6462 (mm-30) REVERT: C 237 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5888 (ptm160) REVERT: C 355 ARG cc_start: 0.5533 (OUTLIER) cc_final: 0.4349 (tpp-160) REVERT: C 358 ILE cc_start: 0.0808 (OUTLIER) cc_final: 0.0188 (mt) REVERT: C 563 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6775 (mp10) REVERT: C 740 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7844 (ttt) REVERT: C 950 ASP cc_start: 0.8542 (m-30) cc_final: 0.7953 (m-30) REVERT: C 1054 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7848 (mm110) REVERT: D 32 PHE cc_start: 0.1697 (OUTLIER) cc_final: -0.1629 (t80) REVERT: D 190 MET cc_start: 0.0155 (ttt) cc_final: -0.0213 (ttm) REVERT: D 270 MET cc_start: 0.2461 (ttt) cc_final: 0.2215 (ttm) REVERT: D 297 MET cc_start: 0.1957 (mmm) cc_final: 0.1580 (mmm) REVERT: D 400 PHE cc_start: 0.3883 (t80) cc_final: 0.2729 (m-10) REVERT: D 408 MET cc_start: -0.0566 (ptp) cc_final: -0.2113 (mtm) REVERT: D 474 MET cc_start: 0.0288 (OUTLIER) cc_final: -0.1262 (ttt) REVERT: D 564 LYS cc_start: 0.2598 (mmmt) cc_final: 0.2238 (ttpp) REVERT: D 579 MET cc_start: 0.0517 (mtm) cc_final: -0.0256 (pmm) REVERT: E 57 GLU cc_start: 0.3331 (OUTLIER) cc_final: 0.2124 (pt0) REVERT: E 61 LYS cc_start: 0.1315 (OUTLIER) cc_final: 0.0964 (tptp) REVERT: E 123 MET cc_start: 0.0023 (tmm) cc_final: -0.0407 (tmm) REVERT: E 190 MET cc_start: 0.3031 (OUTLIER) cc_final: 0.2380 (ptt) REVERT: E 285 PHE cc_start: 0.0340 (OUTLIER) cc_final: -0.1204 (p90) REVERT: E 297 MET cc_start: 0.0225 (ttp) cc_final: -0.0454 (ptm) REVERT: E 446 ILE cc_start: 0.2748 (OUTLIER) cc_final: 0.2343 (mp) REVERT: E 480 MET cc_start: 0.1178 (mmp) cc_final: 0.0166 (tpt) REVERT: E 536 GLU cc_start: -0.0063 (OUTLIER) cc_final: -0.1748 (mp0) REVERT: E 600 ARG cc_start: 0.2852 (OUTLIER) cc_final: 0.2543 (tpp-160) outliers start: 198 outliers final: 117 residues processed: 405 average time/residue: 0.1873 time to fit residues: 125.9414 Evaluate side-chains 355 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 207 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG 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 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 231 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 285 ILE Chi-restraints excluded: chain A residue 312 ILE 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 727 LEU 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 998 THR Chi-restraints excluded: chain A residue 1002 GLN 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 B residue 62 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE 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 698 SER 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 898 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU 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 1043 CYS 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 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 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 308 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 393 THR 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 563 GLN 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 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 172 VAL 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 282 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 474 MET 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 543 ASP Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 152 MET 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 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 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 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 138 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 361 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 397 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 540 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN D 221 GLN D 397 ASN D 493 HIS ** D 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 417 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.241546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.202140 restraints weight = 64545.123| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 3.45 r_work: 0.4018 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33453 Z= 0.190 Angle : 0.793 16.555 45523 Z= 0.414 Chirality : 0.049 0.328 5027 Planarity : 0.006 0.097 5898 Dihedral : 6.554 57.576 4427 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.49 % Favored : 89.49 % Rotamer: Outliers : 5.86 % Allowed : 25.53 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.13), residues: 4053 helix: 0.34 (0.14), residues: 1341 sheet: -0.52 (0.26), residues: 366 loop : -2.91 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.040 0.002 TYR A 279 PHE 0.051 0.002 PHE A 55 TRP 0.039 0.002 TRP D 594 HIS 0.004 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00401 (33412) covalent geometry : angle 0.79098 (45441) SS BOND : bond 0.00415 ( 41) SS BOND : angle 1.65801 ( 82) hydrogen bonds : bond 0.06667 ( 1236) hydrogen bonds : angle 6.19463 ( 3588) *********************** 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 436 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 225 time to evaluate : 1.239 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 37 TYR cc_start: 0.1672 (OUTLIER) cc_final: 0.1044 (m-80) REVERT: A 241 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5498 (tt) REVERT: A 273 ARG cc_start: 0.2066 (OUTLIER) cc_final: 0.1781 (mpt90) REVERT: A 279 TYR cc_start: 0.2916 (m-80) cc_final: 0.2640 (m-80) REVERT: A 492 LEU cc_start: -0.0646 (OUTLIER) cc_final: -0.0942 (mt) REVERT: A 533 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7066 (tt) REVERT: A 855 PHE cc_start: 0.5860 (m-10) cc_final: 0.5563 (m-10) REVERT: A 996 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7597 (tt) REVERT: A 1138 TYR cc_start: 0.7596 (t80) cc_final: 0.7340 (t80) REVERT: B 206 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6183 (tptt) REVERT: B 210 ILE cc_start: 0.6174 (OUTLIER) cc_final: 0.5621 (mm) REVERT: B 237 ARG cc_start: 0.5426 (mmm160) cc_final: 0.4888 (mmp-170) REVERT: B 402 ILE cc_start: 0.2550 (OUTLIER) cc_final: 0.2102 (pt) REVERT: B 740 MET cc_start: 0.8956 (tpt) cc_final: 0.8303 (ttm) REVERT: B 918 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: B 935 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.5960 (tp40) REVERT: B 1000 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8392 (ptm-80) REVERT: C 65 PHE cc_start: 0.5911 (m-80) cc_final: 0.5426 (m-80) REVERT: C 97 LYS cc_start: 0.5900 (tptp) cc_final: 0.5129 (mmmt) REVERT: C 115 GLN cc_start: 0.3553 (OUTLIER) cc_final: 0.3172 (mm-40) REVERT: C 170 TYR cc_start: 0.6473 (t80) cc_final: 0.5912 (t80) REVERT: C 191 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: C 237 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5981 (ptm160) REVERT: C 355 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.4489 (tpp-160) REVERT: C 358 ILE cc_start: 0.0844 (OUTLIER) cc_final: 0.0279 (mt) REVERT: C 740 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8006 (ttt) REVERT: C 950 ASP cc_start: 0.8375 (m-30) cc_final: 0.7973 (m-30) REVERT: C 1054 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7903 (mm110) REVERT: C 1145 LEU cc_start: 0.4459 (OUTLIER) cc_final: 0.4108 (mp) REVERT: D 90 ASP cc_start: 0.2037 (OUTLIER) cc_final: 0.1764 (p0) REVERT: D 124 SER cc_start: 0.2068 (OUTLIER) cc_final: 0.1578 (p) REVERT: D 190 MET cc_start: 0.0957 (ttt) cc_final: 0.0637 (ttm) REVERT: D 199 TYR cc_start: 0.1018 (OUTLIER) cc_final: -0.0636 (t80) REVERT: D 220 ASN cc_start: 0.3309 (OUTLIER) cc_final: 0.2597 (t0) REVERT: D 270 MET cc_start: 0.2511 (ttt) cc_final: 0.2275 (ttt) REVERT: D 297 MET cc_start: 0.1847 (mmm) cc_final: 0.1536 (mmm) REVERT: D 367 ASP cc_start: 0.2744 (OUTLIER) cc_final: 0.2431 (p0) REVERT: D 368 ASP cc_start: 0.2194 (t0) cc_final: 0.1891 (t0) REVERT: D 400 PHE cc_start: 0.3979 (t80) cc_final: 0.2847 (m-10) REVERT: D 408 MET cc_start: -0.0586 (ptp) cc_final: -0.1915 (mtm) REVERT: D 474 MET cc_start: 0.0720 (OUTLIER) cc_final: -0.1176 (ttt) REVERT: D 480 MET cc_start: -0.2326 (mmm) cc_final: -0.2898 (mtp) REVERT: D 564 LYS cc_start: 0.2797 (mmmt) cc_final: 0.2148 (ttpp) REVERT: D 579 MET cc_start: 0.0794 (mtm) cc_final: -0.0389 (pmm) REVERT: E 61 LYS cc_start: 0.1515 (OUTLIER) cc_final: 0.1182 (tptp) REVERT: E 89 GLN cc_start: 0.3305 (tp40) cc_final: 0.1774 (mt0) REVERT: E 190 MET cc_start: 0.2977 (OUTLIER) cc_final: 0.2354 (ptt) REVERT: E 285 PHE cc_start: 0.0315 (OUTLIER) cc_final: -0.1146 (p90) REVERT: E 297 MET cc_start: 0.0263 (ttp) cc_final: -0.0500 (ptm) REVERT: E 446 ILE cc_start: 0.2733 (OUTLIER) cc_final: 0.2364 (mp) REVERT: E 480 MET cc_start: 0.1415 (mmp) cc_final: 0.0329 (tpt) REVERT: E 514 ARG cc_start: 0.1699 (mmp-170) cc_final: -0.0427 (mtt-85) REVERT: E 536 GLU cc_start: -0.0061 (OUTLIER) cc_final: -0.1758 (mp0) outliers start: 211 outliers final: 134 residues processed: 407 average time/residue: 0.2020 time to fit residues: 136.7056 Evaluate side-chains 371 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 206 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG 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 82 LEU Chi-restraints excluded: chain A residue 110 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 229 LEU Chi-restraints excluded: chain A residue 231 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 273 ARG Chi-restraints excluded: chain A residue 285 ILE 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 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 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 791 THR Chi-restraints excluded: chain A residue 962 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 1060 VAL 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 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 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS 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 656 VAL 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 898 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1043 CYS 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 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 208 THR Chi-restraints excluded: chain C residue 229 LEU 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 312 ILE 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 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 724 THR 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 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1054 GLN 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 C residue 1145 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 220 ASN 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 367 ASP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 474 MET 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 552 GLN 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 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 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 588 PHE 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 235 optimal weight: 9.9990 chunk 324 optimal weight: 0.0370 chunk 192 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 305 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 351 optimal weight: 0.8980 chunk 348 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.242552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.207081 restraints weight = 66799.253| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 3.64 r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33453 Z= 0.168 Angle : 0.762 16.252 45523 Z= 0.397 Chirality : 0.048 0.324 5027 Planarity : 0.006 0.078 5898 Dihedral : 6.373 55.249 4427 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.65 % Favored : 90.33 % Rotamer: Outliers : 5.41 % Allowed : 25.70 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.13), residues: 4053 helix: 0.42 (0.14), residues: 1341 sheet: -0.43 (0.26), residues: 364 loop : -2.88 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 995 TYR 0.036 0.001 TYR A 279 PHE 0.032 0.001 PHE B 106 TRP 0.046 0.002 TRP D 594 HIS 0.004 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00339 (33412) covalent geometry : angle 0.75960 (45441) SS BOND : bond 0.00363 ( 41) SS BOND : angle 1.49699 ( 82) hydrogen bonds : bond 0.06052 ( 1236) hydrogen bonds : angle 6.05942 ( 3588) *********************** 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 420 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 225 time to evaluate : 1.323 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 218 GLN cc_start: 0.5902 (OUTLIER) cc_final: 0.5629 (tp40) REVERT: A 362 VAL cc_start: -0.0649 (OUTLIER) cc_final: -0.1149 (t) REVERT: A 492 LEU cc_start: -0.0885 (OUTLIER) cc_final: -0.1168 (mp) REVERT: A 533 LEU cc_start: 0.7349 (pt) cc_final: 0.7047 (tt) REVERT: A 996 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7507 (tt) REVERT: A 1138 TYR cc_start: 0.7020 (t80) cc_final: 0.6760 (t80) REVERT: B 106 PHE cc_start: 0.2043 (OUTLIER) cc_final: 0.1482 (m-80) REVERT: B 210 ILE cc_start: 0.4861 (OUTLIER) cc_final: 0.4493 (mm) REVERT: B 740 MET cc_start: 0.8346 (tpt) cc_final: 0.8067 (ttm) REVERT: B 918 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: B 935 GLN cc_start: 0.6552 (OUTLIER) cc_final: 0.5857 (tp40) REVERT: B 1000 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7947 (ptm-80) REVERT: C 97 LYS cc_start: 0.5383 (tptp) cc_final: 0.4714 (tptt) REVERT: C 115 GLN cc_start: 0.3611 (OUTLIER) cc_final: 0.3244 (mm-40) REVERT: C 237 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.5357 (ptm160) REVERT: C 983 ARG cc_start: 0.3950 (mmm160) cc_final: 0.3552 (mmm160) REVERT: C 1145 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4733 (mp) REVERT: D 90 ASP cc_start: 0.3509 (OUTLIER) cc_final: 0.3254 (p0) REVERT: D 199 TYR cc_start: 0.2185 (OUTLIER) cc_final: 0.0032 (t80) REVERT: D 270 MET cc_start: 0.3012 (ttt) cc_final: 0.2797 (ttm) REVERT: D 297 MET cc_start: 0.2639 (mmm) cc_final: 0.2264 (mmm) REVERT: D 366 MET cc_start: 0.2648 (pmm) cc_final: -0.1114 (mmm) REVERT: D 400 PHE cc_start: 0.2732 (t80) cc_final: 0.2331 (m-10) REVERT: D 408 MET cc_start: -0.1791 (ptp) cc_final: -0.2956 (mtm) REVERT: D 474 MET cc_start: 0.0238 (OUTLIER) cc_final: -0.1536 (ttm) REVERT: D 480 MET cc_start: -0.0887 (mmm) cc_final: -0.1916 (ttm) REVERT: D 579 MET cc_start: 0.0080 (mtm) cc_final: -0.0508 (pmm) REVERT: E 61 LYS cc_start: 0.2756 (OUTLIER) cc_final: 0.2113 (tptp) REVERT: E 89 GLN cc_start: 0.3675 (tp40) cc_final: 0.2384 (mt0) REVERT: E 190 MET cc_start: 0.4037 (OUTLIER) cc_final: 0.3425 (ptt) REVERT: E 285 PHE cc_start: 0.0313 (OUTLIER) cc_final: -0.0839 (p90) REVERT: E 297 MET cc_start: 0.1689 (ttp) cc_final: 0.0885 (mtp) REVERT: E 332 MET cc_start: 0.1263 (tpt) cc_final: 0.1003 (tpt) REVERT: E 446 ILE cc_start: 0.2937 (OUTLIER) cc_final: 0.2207 (mp) REVERT: E 480 MET cc_start: 0.2119 (mmp) cc_final: 0.0872 (tpt) REVERT: E 514 ARG cc_start: 0.2270 (mmp-170) cc_final: 0.0224 (mtp85) REVERT: E 536 GLU cc_start: -0.0035 (OUTLIER) cc_final: -0.1859 (mp0) outliers start: 195 outliers final: 122 residues processed: 388 average time/residue: 0.1944 time to fit residues: 125.6547 Evaluate side-chains 347 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 205 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG 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 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 218 GLN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 362 VAL 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 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 617 CYS 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 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 1060 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 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS 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 551 VAL 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 705 VAL Chi-restraints excluded: chain B residue 780 GLU 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 918 GLU 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 998 THR Chi-restraints excluded: chain B residue 1000 ARG 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 115 GLN Chi-restraints excluded: chain C residue 127 VAL 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 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 393 THR 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 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 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER 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 134 ASN Chi-restraints excluded: chain D residue 172 VAL 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 343 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 552 GLN 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 152 MET 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 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 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 606 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 358 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 315 optimal weight: 6.9990 chunk 335 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 965 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 220 ASN D 607 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.239733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.202552 restraints weight = 64303.934| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 3.55 r_work: 0.3995 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 33453 Z= 0.199 Angle : 0.809 15.683 45523 Z= 0.423 Chirality : 0.050 0.336 5027 Planarity : 0.006 0.070 5898 Dihedral : 6.345 53.140 4424 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.44 % Favored : 89.54 % Rotamer: Outliers : 4.88 % Allowed : 26.12 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.13), residues: 4053 helix: 0.38 (0.14), residues: 1336 sheet: -0.32 (0.26), residues: 357 loop : -2.92 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.032 0.002 TYR A 279 PHE 0.037 0.002 PHE B 106 TRP 0.049 0.002 TRP D 594 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00431 (33412) covalent geometry : angle 0.80658 (45441) SS BOND : bond 0.00424 ( 41) SS BOND : angle 1.70146 ( 82) hydrogen bonds : bond 0.07069 ( 1236) hydrogen bonds : angle 6.16782 ( 3588) *********************** 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 386 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 210 time to evaluate : 0.749 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 52 GLN cc_start: 0.5306 (OUTLIER) cc_final: 0.3840 (tm-30) REVERT: A 218 GLN cc_start: 0.6066 (OUTLIER) cc_final: 0.5777 (tt0) REVERT: A 235 ILE cc_start: 0.4431 (OUTLIER) cc_final: 0.3930 (mt) REVERT: A 492 LEU cc_start: -0.0680 (OUTLIER) cc_final: -0.1012 (mp) REVERT: A 533 LEU cc_start: 0.7775 (pt) cc_final: 0.7174 (tt) REVERT: A 598 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9045 (mp) REVERT: A 855 PHE cc_start: 0.5961 (m-10) cc_final: 0.5748 (m-10) REVERT: A 996 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7498 (tt) REVERT: A 1138 TYR cc_start: 0.7683 (t80) cc_final: 0.7367 (t80) REVERT: B 92 PHE cc_start: 0.5230 (m-10) cc_final: 0.5010 (m-10) REVERT: B 106 PHE cc_start: 0.1792 (OUTLIER) cc_final: 0.1246 (m-80) REVERT: B 210 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5390 (mm) REVERT: B 740 MET cc_start: 0.8994 (tpt) cc_final: 0.8418 (ttm) REVERT: B 918 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: B 1000 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8391 (ptm-80) REVERT: B 1105 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8993 (p) REVERT: C 115 GLN cc_start: 0.3545 (OUTLIER) cc_final: 0.2993 (tm-30) REVERT: C 191 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6699 (mm-30) REVERT: C 237 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6342 (ptm160) REVERT: C 1145 LEU cc_start: 0.4785 (OUTLIER) cc_final: 0.4455 (mp) REVERT: D 90 ASP cc_start: 0.2272 (OUTLIER) cc_final: 0.1994 (p0) REVERT: D 199 TYR cc_start: 0.1182 (OUTLIER) cc_final: -0.0473 (t80) REVERT: D 270 MET cc_start: 0.2821 (ttt) cc_final: 0.2572 (ttm) REVERT: D 325 GLU cc_start: -0.1451 (OUTLIER) cc_final: -0.1695 (mt-10) REVERT: D 366 MET cc_start: 0.0687 (pmm) cc_final: -0.1818 (mmm) REVERT: D 400 PHE cc_start: 0.3634 (t80) cc_final: 0.2732 (m-10) REVERT: D 408 MET cc_start: -0.1070 (ptp) cc_final: -0.2260 (mtm) REVERT: D 474 MET cc_start: -0.0004 (OUTLIER) cc_final: -0.1205 (ttm) REVERT: D 480 MET cc_start: -0.2439 (mmm) cc_final: -0.2876 (ttm) REVERT: D 579 MET cc_start: 0.1546 (mtm) cc_final: 0.0799 (pmm) REVERT: E 54 ILE cc_start: 0.0554 (mm) cc_final: 0.0142 (mm) REVERT: E 61 LYS cc_start: 0.2225 (OUTLIER) cc_final: 0.1769 (tptp) REVERT: E 89 GLN cc_start: 0.3634 (tp40) cc_final: 0.1640 (mt0) REVERT: E 176 LEU cc_start: 0.1031 (OUTLIER) cc_final: 0.0237 (mp) REVERT: E 190 MET cc_start: 0.3147 (OUTLIER) cc_final: 0.2491 (ptt) REVERT: E 267 LEU cc_start: 0.2923 (OUTLIER) cc_final: 0.2467 (mt) REVERT: E 282 MET cc_start: 0.3017 (ptp) cc_final: 0.2483 (ppp) REVERT: E 285 PHE cc_start: 0.0730 (OUTLIER) cc_final: -0.0584 (p90) REVERT: E 297 MET cc_start: 0.0295 (ttp) cc_final: -0.0402 (ptm) REVERT: E 446 ILE cc_start: 0.3373 (OUTLIER) cc_final: 0.2918 (mp) REVERT: E 480 MET cc_start: 0.1743 (mmp) cc_final: 0.0211 (tpt) REVERT: E 536 GLU cc_start: 0.0046 (OUTLIER) cc_final: -0.1737 (mp0) outliers start: 176 outliers final: 124 residues processed: 364 average time/residue: 0.1683 time to fit residues: 102.1772 Evaluate side-chains 351 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 201 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 GLN 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 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 218 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 270 LEU 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 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 617 CYS 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 791 THR 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 998 THR 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 B residue 79 ASN 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 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 361 CYS 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 551 VAL 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 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 918 GLU Chi-restraints excluded: chain B residue 926 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 1043 CYS Chi-restraints excluded: chain B residue 1100 THR 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 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 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL 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 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 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER 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 161 ARG Chi-restraints excluded: chain D residue 172 VAL 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 325 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 29 LEU 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 152 MET 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 267 LEU Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 300 GLN 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 434 THR Chi-restraints excluded: chain E residue 440 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 588 PHE 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 19 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 397 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.240365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.206142 restraints weight = 64346.732| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 3.38 r_work: 0.4068 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 33453 Z= 0.182 Angle : 0.792 15.893 45523 Z= 0.413 Chirality : 0.049 0.329 5027 Planarity : 0.006 0.081 5898 Dihedral : 6.221 57.359 4420 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.40 % Favored : 90.55 % Rotamer: Outliers : 4.75 % Allowed : 26.20 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.13), residues: 4053 helix: 0.47 (0.14), residues: 1325 sheet: -0.32 (0.26), residues: 360 loop : -2.90 (0.11), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 995 TYR 0.033 0.002 TYR A 279 PHE 0.032 0.002 PHE B 106 TRP 0.050 0.002 TRP D 594 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00386 (33412) covalent geometry : angle 0.79027 (45441) SS BOND : bond 0.00450 ( 41) SS BOND : angle 1.51609 ( 82) hydrogen bonds : bond 0.06494 ( 1236) hydrogen bonds : angle 6.05437 ( 3588) *********************** 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 386 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 215 time to evaluate : 1.137 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 52 GLN cc_start: 0.5340 (OUTLIER) cc_final: 0.3859 (tm-30) REVERT: A 218 GLN cc_start: 0.6116 (OUTLIER) cc_final: 0.5807 (tt0) REVERT: A 235 ILE cc_start: 0.4185 (OUTLIER) cc_final: 0.3740 (mt) REVERT: A 237 ARG cc_start: 0.6931 (mpt180) cc_final: 0.6653 (mmp-170) REVERT: A 533 LEU cc_start: 0.7725 (pt) cc_final: 0.7091 (tt) REVERT: A 598 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8926 (mp) REVERT: A 855 PHE cc_start: 0.6163 (m-10) cc_final: 0.5918 (m-10) REVERT: A 996 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7488 (tt) REVERT: A 1138 TYR cc_start: 0.7606 (t80) cc_final: 0.7213 (t80) REVERT: B 106 PHE cc_start: 0.1996 (OUTLIER) cc_final: 0.1546 (m-80) REVERT: B 210 ILE cc_start: 0.5791 (OUTLIER) cc_final: 0.5122 (mm) REVERT: B 740 MET cc_start: 0.8954 (tpt) cc_final: 0.8463 (ttm) REVERT: B 1000 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8120 (ptm-80) REVERT: C 115 GLN cc_start: 0.3549 (OUTLIER) cc_final: 0.2435 (tt0) REVERT: C 191 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: C 237 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6241 (ptm160) REVERT: C 1145 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4702 (mp) REVERT: D 90 ASP cc_start: 0.2564 (OUTLIER) cc_final: 0.2307 (p0) REVERT: D 199 TYR cc_start: 0.1756 (OUTLIER) cc_final: -0.0155 (t80) REVERT: D 270 MET cc_start: 0.3304 (ttt) cc_final: 0.3040 (ttm) REVERT: D 325 GLU cc_start: -0.1244 (OUTLIER) cc_final: -0.1930 (mt-10) REVERT: D 364 VAL cc_start: 0.1614 (p) cc_final: 0.1343 (m) REVERT: D 366 MET cc_start: 0.0387 (pmm) cc_final: -0.1390 (mmm) REVERT: D 400 PHE cc_start: 0.3326 (t80) cc_final: 0.2627 (m-10) REVERT: D 408 MET cc_start: -0.1108 (ptp) cc_final: -0.2618 (mtt) REVERT: D 474 MET cc_start: 0.0202 (OUTLIER) cc_final: -0.0943 (ttt) REVERT: D 496 THR cc_start: 0.4915 (m) cc_final: 0.4222 (p) REVERT: D 527 GLU cc_start: 0.0959 (tm-30) cc_final: 0.0296 (tm-30) REVERT: D 579 MET cc_start: 0.1938 (mtm) cc_final: 0.1296 (pmm) REVERT: E 61 LYS cc_start: 0.2308 (OUTLIER) cc_final: 0.1818 (tptp) REVERT: E 89 GLN cc_start: 0.3472 (tp40) cc_final: 0.1591 (pt0) REVERT: E 176 LEU cc_start: 0.1133 (OUTLIER) cc_final: 0.0366 (mp) REVERT: E 267 LEU cc_start: 0.2694 (OUTLIER) cc_final: 0.2491 (mt) REVERT: E 270 MET cc_start: 0.0370 (tpp) cc_final: -0.1498 (mmt) REVERT: E 282 MET cc_start: 0.3239 (ptp) cc_final: 0.2751 (ppp) REVERT: E 285 PHE cc_start: 0.0923 (OUTLIER) cc_final: -0.0462 (p90) REVERT: E 297 MET cc_start: 0.0778 (ttp) cc_final: -0.0019 (ptm) REVERT: E 446 ILE cc_start: 0.3383 (OUTLIER) cc_final: 0.3047 (mp) REVERT: E 480 MET cc_start: 0.2169 (mmp) cc_final: 0.0656 (tpt) outliers start: 171 outliers final: 123 residues processed: 362 average time/residue: 0.1714 time to fit residues: 104.3612 Evaluate side-chains 345 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 201 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 52 GLN 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 110 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 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL 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 617 CYS 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 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 962 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 A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 106 PHE 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 277 LEU 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 303 LEU Chi-restraints excluded: chain B residue 361 CYS 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 551 VAL 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 705 VAL Chi-restraints excluded: chain B residue 754 LEU 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 965 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 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 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 237 ARG 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 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL 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 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 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER 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 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 325 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 48 TRP 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 152 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 267 LEU 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 434 THR Chi-restraints excluded: chain E residue 440 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 542 CYS Chi-restraints excluded: chain E residue 588 PHE 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 367 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 280 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 318 optimal weight: 0.0970 chunk 390 optimal weight: 1.9990 chunk 141 optimal weight: 0.0020 chunk 334 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 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 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** 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 = 0.4849 r_free = 0.4849 target = 0.240041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.205880 restraints weight = 65058.648| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 3.36 r_work: 0.4059 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.317 33453 Z= 0.216 Angle : 0.884 59.200 45523 Z= 0.473 Chirality : 0.049 0.324 5027 Planarity : 0.006 0.084 5898 Dihedral : 6.218 57.391 4420 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.55 % Favored : 90.40 % Rotamer: Outliers : 4.22 % Allowed : 26.67 % Favored : 69.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.13), residues: 4053 helix: 0.47 (0.14), residues: 1325 sheet: -0.31 (0.26), residues: 360 loop : -2.90 (0.11), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 34 TYR 0.035 0.001 TYR A 279 PHE 0.076 0.002 PHE A 559 TRP 0.050 0.002 TRP D 594 HIS 0.013 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00501 (33412) covalent geometry : angle 0.88222 (45441) SS BOND : bond 0.00383 ( 41) SS BOND : angle 1.65295 ( 82) hydrogen bonds : bond 0.06440 ( 1236) hydrogen bonds : angle 6.04777 ( 3588) ********************** 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 355 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 203 time to evaluate : 0.882 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 52 GLN cc_start: 0.5366 (OUTLIER) cc_final: 0.3900 (tm-30) REVERT: A 218 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5801 (tt0) REVERT: A 235 ILE cc_start: 0.4193 (OUTLIER) cc_final: 0.3731 (mt) REVERT: A 533 LEU cc_start: 0.7732 (pt) cc_final: 0.7100 (tt) REVERT: A 598 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8917 (mp) REVERT: A 855 PHE cc_start: 0.6098 (m-10) cc_final: 0.5871 (m-10) REVERT: A 996 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7459 (tt) REVERT: A 1138 TYR cc_start: 0.7622 (t80) cc_final: 0.7223 (t80) REVERT: B 106 PHE cc_start: 0.1751 (OUTLIER) cc_final: 0.1394 (m-80) REVERT: B 210 ILE cc_start: 0.5830 (OUTLIER) cc_final: 0.5168 (mm) REVERT: B 740 MET cc_start: 0.8937 (tpt) cc_final: 0.8455 (ttm) REVERT: B 1000 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8114 (ptm-80) REVERT: C 191 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6561 (mm-30) REVERT: C 237 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6266 (ptm160) REVERT: C 1145 LEU cc_start: 0.4995 (OUTLIER) cc_final: 0.4697 (mp) REVERT: D 90 ASP cc_start: 0.2528 (OUTLIER) cc_final: 0.2279 (p0) REVERT: D 199 TYR cc_start: 0.1790 (OUTLIER) cc_final: -0.0139 (t80) REVERT: D 270 MET cc_start: 0.3344 (ttt) cc_final: 0.3083 (ttm) REVERT: D 325 GLU cc_start: -0.1301 (OUTLIER) cc_final: -0.1976 (mt-10) REVERT: D 364 VAL cc_start: 0.1670 (p) cc_final: 0.1359 (m) REVERT: D 366 MET cc_start: 0.0347 (pmm) cc_final: -0.1404 (mmm) REVERT: D 400 PHE cc_start: 0.3331 (t80) cc_final: 0.2633 (m-10) REVERT: D 408 MET cc_start: -0.1137 (ptp) cc_final: -0.2629 (mtt) REVERT: D 474 MET cc_start: 0.0224 (OUTLIER) cc_final: -0.0925 (ttt) REVERT: D 496 THR cc_start: 0.4894 (m) cc_final: 0.4206 (p) REVERT: D 527 GLU cc_start: 0.0921 (tm-30) cc_final: 0.0294 (tm-30) REVERT: D 579 MET cc_start: 0.1919 (mtm) cc_final: 0.1277 (pmm) REVERT: E 61 LYS cc_start: 0.2333 (OUTLIER) cc_final: 0.1823 (tptp) REVERT: E 89 GLN cc_start: 0.3442 (tp40) cc_final: 0.1559 (pt0) REVERT: E 176 LEU cc_start: 0.1147 (OUTLIER) cc_final: 0.0381 (mp) REVERT: E 270 MET cc_start: 0.0390 (tpp) cc_final: -0.1504 (mmt) REVERT: E 282 MET cc_start: 0.3260 (ptp) cc_final: 0.2767 (ppp) REVERT: E 285 PHE cc_start: 0.0913 (OUTLIER) cc_final: -0.0472 (p90) REVERT: E 297 MET cc_start: 0.0850 (ttp) cc_final: 0.0043 (ptm) REVERT: E 446 ILE cc_start: 0.3387 (OUTLIER) cc_final: 0.3058 (mp) REVERT: E 480 MET cc_start: 0.2161 (mmp) cc_final: 0.0660 (tpt) outliers start: 152 outliers final: 125 residues processed: 337 average time/residue: 0.1627 time to fit residues: 92.5788 Evaluate side-chains 344 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 200 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 52 GLN 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 82 LEU Chi-restraints excluded: chain A residue 110 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 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 461 LEU 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 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 617 CYS 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 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 962 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 A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 106 PHE 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 277 LEU Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 361 CYS 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 551 VAL 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 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 780 GLU 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 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1043 CYS 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 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU 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 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL 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 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 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER 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 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 325 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 48 TRP 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 152 MET Chi-restraints excluded: chain E residue 176 LEU 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 434 THR Chi-restraints excluded: chain E residue 440 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 542 CYS Chi-restraints excluded: chain E residue 588 PHE 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 127 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 394 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 296 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 364 optimal weight: 0.7980 chunk 390 optimal weight: 0.0070 chunk 387 optimal weight: 4.9990 chunk 401 optimal weight: 0.9980 chunk 271 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 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 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** 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 = 0.4844 r_free = 0.4844 target = 0.239993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.205249 restraints weight = 66263.543| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 3.49 r_work: 0.4038 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.7741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.326 33453 Z= 0.233 Angle : 0.884 59.200 45523 Z= 0.473 Chirality : 0.049 0.324 5027 Planarity : 0.006 0.084 5898 Dihedral : 6.218 57.391 4420 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.55 % Favored : 90.40 % Rotamer: Outliers : 4.00 % Allowed : 26.78 % Favored : 69.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.13), residues: 4053 helix: 0.47 (0.14), residues: 1325 sheet: -0.31 (0.26), residues: 360 loop : -2.90 (0.11), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 34 TYR 0.035 0.001 TYR A 279 PHE 0.076 0.002 PHE A 559 TRP 0.050 0.002 TRP D 594 HIS 0.013 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00501 (33412) covalent geometry : angle 0.88222 (45441) SS BOND : bond 0.05106 ( 41) SS BOND : angle 1.70481 ( 82) hydrogen bonds : bond 0.06440 ( 1236) hydrogen bonds : angle 6.04777 ( 3588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8055.10 seconds wall clock time: 139 minutes 1.84 seconds (8341.84 seconds total)