Starting phenix.real_space_refine on Sat Jun 28 05:44:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t20_40976/06_2025/8t20_40976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t20_40976/06_2025/8t20_40976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t20_40976/06_2025/8t20_40976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t20_40976/06_2025/8t20_40976.map" model { file = "/net/cci-nas-00/data/ceres_data/8t20_40976/06_2025/8t20_40976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t20_40976/06_2025/8t20_40976.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 161 5.16 5 C 20836 2.51 5 N 5431 2.21 5 O 6184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32612 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Chain: "B" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7497 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 51, 'TRANS': 910} Chain breaks: 10 Chain: "C" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7497 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 51, 'TRANS': 910} Chain breaks: 10 Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Chain: "E" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Time building chain proxies: 18.79, per 1000 atoms: 0.58 Number of scatterers: 32612 At special positions: 0 Unit cell: (132.09, 166.5, 249.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 161 16.00 O 6184 8.00 N 5431 7.00 C 20836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.00 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 3.9 seconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7730 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 37 sheets defined 36.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 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: 10.70 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 1 1.05 - 1.25: 4698 1.25 - 1.45: 10146 1.45 - 1.65: 18338 1.65 - 1.85: 229 Bond restraints: 33412 Sorted by residual: bond pdb=" CG PRO D 583 " pdb=" CD PRO D 583 " ideal model delta sigma weight residual 1.503 0.845 0.658 3.40e-02 8.65e+02 3.74e+02 bond pdb=" CG PRO D 289 " pdb=" CD PRO D 289 " ideal model delta sigma weight residual 1.503 1.223 0.280 3.40e-02 8.65e+02 6.81e+01 bond pdb=" CG PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.79e+01 bond pdb=" N PRO D 583 " pdb=" CD PRO D 583 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.20e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.34e+01 ... (remaining 33407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.84: 45248 5.84 - 11.68: 169 11.68 - 17.53: 20 17.53 - 23.37: 3 23.37 - 29.21: 1 Bond angle restraints: 45441 Sorted by residual: angle pdb=" N PRO D 583 " pdb=" CD PRO D 583 " pdb=" CG PRO D 583 " ideal model delta sigma weight residual 103.20 73.99 29.21 1.50e+00 4.44e-01 3.79e+02 angle pdb=" CA PRO D 426 " pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 112.00 93.72 18.28 1.40e+00 5.10e-01 1.71e+02 angle pdb=" CA PRO D 289 " pdb=" N PRO D 289 " pdb=" CD PRO D 289 " ideal model delta sigma weight residual 112.00 95.29 16.71 1.40e+00 5.10e-01 1.43e+02 angle pdb=" N THR D 608 " pdb=" CA THR D 608 " pdb=" C THR D 608 " ideal model delta sigma weight residual 111.17 127.46 -16.29 1.41e+00 5.03e-01 1.33e+02 angle pdb=" CA PRO D 583 " pdb=" CB PRO D 583 " pdb=" CG PRO D 583 " ideal model delta sigma weight residual 104.50 83.27 21.23 1.90e+00 2.77e-01 1.25e+02 ... (remaining 45436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16565 17.92 - 35.84: 2496 35.84 - 53.75: 653 53.75 - 71.67: 122 71.67 - 89.59: 53 Dihedral angle restraints: 19889 sinusoidal: 7890 harmonic: 11999 Sorted by residual: dihedral pdb=" CA PHE A 55 " pdb=" C PHE A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta harmonic sigma weight residual 180.00 129.95 50.05 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA PHE A 220 " pdb=" C PHE A 220 " pdb=" N SER A 221 " pdb=" CA SER A 221 " ideal model delta harmonic sigma weight residual 180.00 132.59 47.41 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 178.36 -85.36 1 1.00e+01 1.00e-02 8.82e+01 ... (remaining 19886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4387 0.081 - 0.163: 579 0.163 - 0.244: 45 0.244 - 0.326: 11 0.326 - 0.407: 5 Chirality restraints: 5027 Sorted by residual: chirality pdb=" CG LEU A 962 " pdb=" CB LEU A 962 " pdb=" CD1 LEU A 962 " pdb=" CD2 LEU A 962 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" C PRO A 561 " pdb=" CB PRO A 561 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 5024 not shown) Planarity restraints: 5898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 489 " -0.091 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO D 490 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 490 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 490 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.080 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 986 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 288 " -0.082 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO D 289 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " -0.058 5.00e-02 4.00e+02 ... (remaining 5895 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 196 2.45 - 3.06: 22173 3.06 - 3.67: 50154 3.67 - 4.29: 69131 4.29 - 4.90: 112406 Nonbonded interactions: 254060 Sorted by model distance: nonbonded pdb=" N ILE D 484 " pdb=" O ASN D 607 " model vdw 1.836 3.120 nonbonded pdb=" O GLN C1002 " pdb=" OG1 THR C1006 " model vdw 1.893 3.040 nonbonded pdb=" O SER A 46 " pdb=" N ASN A 282 " model vdw 1.935 3.120 nonbonded pdb=" O ASP D 225 " pdb=" OG1 THR D 229 " model vdw 1.970 3.040 nonbonded pdb=" O GLN A1005 " pdb=" OG1 THR A1009 " model vdw 1.971 3.040 ... (remaining 254055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 320 or resid 335 through 366 or resid 376 throu \ gh 527 or resid 544 through 1147)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 68.190 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.658 33453 Z= 0.304 Angle : 1.060 29.211 45523 Z= 0.586 Chirality : 0.055 0.407 5027 Planarity : 0.008 0.130 5898 Dihedral : 18.406 89.590 12036 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.88 % Favored : 86.92 % Rotamer: Outliers : 0.67 % Allowed : 29.50 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.12), residues: 4053 helix: -0.09 (0.14), residues: 1325 sheet: -1.47 (0.25), residues: 372 loop : -3.19 (0.11), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 349 HIS 0.015 0.002 HIS D 535 PHE 0.063 0.003 PHE A 275 TYR 0.049 0.002 TYR A 279 ARG 0.011 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.17479 ( 1236) hydrogen bonds : angle 7.57972 ( 3588) SS BOND : bond 0.00648 ( 41) SS BOND : angle 2.50166 ( 82) covalent geometry : bond 0.00730 (33412) covalent geometry : angle 1.05532 (45441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 485 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5841 (p) cc_final: 0.5351 (t) REVERT: B 200 TYR cc_start: 0.2415 (OUTLIER) cc_final: 0.2002 (m-80) REVERT: B 237 ARG cc_start: 0.4922 (mmm160) cc_final: 0.4658 (mmp-170) REVERT: C 237 ARG cc_start: 0.4916 (ptm160) cc_final: 0.4619 (ppt170) REVERT: C 355 ARG cc_start: 0.4983 (OUTLIER) cc_final: 0.4368 (ttm170) REVERT: C 1077 THR cc_start: 0.5046 (t) cc_final: 0.4473 (m) REVERT: D 48 TRP cc_start: 0.1286 (t-100) cc_final: 0.0759 (t-100) REVERT: D 152 MET cc_start: -0.1122 (mmt) cc_final: -0.3592 (ptm) REVERT: D 376 MET cc_start: 0.0469 (tpt) cc_final: 0.0107 (ptm) REVERT: D 400 PHE cc_start: 0.2778 (t80) cc_final: 0.2102 (m-10) REVERT: E 62 MET cc_start: 0.2118 (tmm) cc_final: 0.1592 (tmm) REVERT: E 123 MET cc_start: 0.1290 (tmm) cc_final: 0.0388 (tmm) REVERT: E 190 MET cc_start: 0.3774 (tmm) cc_final: 0.3454 (ptt) REVERT: E 474 MET cc_start: 0.0114 (tmm) cc_final: -0.1133 (mmt) REVERT: E 480 MET cc_start: 0.1229 (mmp) cc_final: 0.0387 (tpp) REVERT: E 557 MET cc_start: -0.1441 (OUTLIER) cc_final: -0.1916 (mtm) outliers start: 24 outliers final: 5 residues processed: 504 average time/residue: 0.4256 time to fit residues: 354.1336 Evaluate side-chains 300 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 292 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 321 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 195 optimal weight: 0.2980 chunk 239 optimal weight: 0.9980 chunk 372 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 690 GLN B 957 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1106 GLN D 33 ASN D 49 ASN D 117 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 265 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS E 49 ASN E 58 ASN ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN E 397 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.244594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.188733 restraints weight = 66690.563| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 4.64 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 33453 Z= 0.225 Angle : 0.900 15.732 45523 Z= 0.474 Chirality : 0.053 0.348 5027 Planarity : 0.007 0.103 5898 Dihedral : 7.346 59.962 4435 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.04 % Favored : 89.81 % Rotamer: Outliers : 5.94 % Allowed : 25.03 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 4053 helix: -0.09 (0.14), residues: 1346 sheet: -1.04 (0.25), residues: 387 loop : -3.01 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 610 HIS 0.010 0.002 HIS E 373 PHE 0.038 0.002 PHE A 562 TYR 0.029 0.002 TYR A 279 ARG 0.012 0.001 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.06662 ( 1236) hydrogen bonds : angle 6.61705 ( 3588) SS BOND : bond 0.00812 ( 41) SS BOND : angle 1.98846 ( 82) covalent geometry : bond 0.00459 (33412) covalent geometry : angle 0.89653 (45441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 330 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.4635 (mtm-85) cc_final: 0.4408 (mtm-85) REVERT: A 229 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.3138 (mp) REVERT: A 492 LEU cc_start: -0.1000 (OUTLIER) cc_final: -0.1314 (mt) REVERT: A 658 ASN cc_start: 0.7125 (m-40) cc_final: 0.6792 (m110) REVERT: A 996 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6873 (tt) REVERT: A 998 THR cc_start: 0.8284 (t) cc_final: 0.8078 (p) REVERT: B 200 TYR cc_start: 0.2649 (OUTLIER) cc_final: 0.2057 (m-80) REVERT: B 237 ARG cc_start: 0.5738 (mmm160) cc_final: 0.5381 (mmp-170) REVERT: B 472 ILE cc_start: -0.1754 (OUTLIER) cc_final: -0.2536 (tt) REVERT: B 568 ASP cc_start: 0.7082 (t0) cc_final: 0.6857 (t0) REVERT: B 582 LEU cc_start: 0.7430 (mt) cc_final: 0.7143 (pt) REVERT: B 898 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.5549 (m-80) REVERT: B 1000 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7818 (ptm-80) REVERT: C 54 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6181 (tp) REVERT: C 170 TYR cc_start: 0.5779 (t80) cc_final: 0.5208 (t80) REVERT: C 355 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.4337 (tpp-160) REVERT: C 436 TRP cc_start: 0.3383 (OUTLIER) cc_final: 0.2963 (p90) REVERT: C 492 LEU cc_start: 0.3504 (OUTLIER) cc_final: 0.3205 (pp) REVERT: C 780 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6887 (pt0) REVERT: D 101 GLN cc_start: 0.2185 (tm-30) cc_final: 0.1760 (mm-40) REVERT: D 131 LYS cc_start: -0.0465 (OUTLIER) cc_final: -0.0678 (pttt) REVERT: D 367 ASP cc_start: 0.2793 (OUTLIER) cc_final: 0.2574 (m-30) REVERT: D 400 PHE cc_start: 0.3841 (t80) cc_final: 0.2567 (m-10) REVERT: D 408 MET cc_start: -0.0955 (ptp) cc_final: -0.1637 (mtm) REVERT: E 123 MET cc_start: -0.0473 (tmm) cc_final: -0.1097 (tmm) REVERT: E 176 LEU cc_start: 0.1478 (OUTLIER) cc_final: 0.0979 (mm) REVERT: E 190 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.2593 (ptt) REVERT: E 285 PHE cc_start: -0.0651 (OUTLIER) cc_final: -0.1764 (p90) REVERT: E 297 MET cc_start: -0.0317 (ttp) cc_final: -0.0740 (ptm) REVERT: E 310 GLU cc_start: 0.1328 (OUTLIER) cc_final: 0.0570 (tp30) REVERT: E 480 MET cc_start: 0.0850 (mmp) cc_final: 0.0344 (tpt) outliers start: 214 outliers final: 90 residues processed: 516 average time/residue: 0.4231 time to fit residues: 364.0852 Evaluate side-chains 370 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 262 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 281 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 228 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 397 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B1002 GLN C 965 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.243268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.207285 restraints weight = 63787.536| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 3.44 r_work: 0.4072 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 33453 Z= 0.212 Angle : 0.842 16.204 45523 Z= 0.445 Chirality : 0.050 0.340 5027 Planarity : 0.006 0.079 5898 Dihedral : 6.926 57.814 4429 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.66 % Favored : 89.24 % Rotamer: Outliers : 6.02 % Allowed : 25.28 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.13), residues: 4053 helix: 0.08 (0.14), residues: 1353 sheet: -0.58 (0.25), residues: 380 loop : -2.99 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 349 HIS 0.008 0.001 HIS E 373 PHE 0.028 0.002 PHE B 43 TYR 0.028 0.002 TYR A 279 ARG 0.016 0.001 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.07147 ( 1236) hydrogen bonds : angle 6.38320 ( 3588) SS BOND : bond 0.01444 ( 41) SS BOND : angle 2.08344 ( 82) covalent geometry : bond 0.00444 (33412) covalent geometry : angle 0.83765 (45441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 270 time to evaluate : 3.854 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 37 TYR cc_start: 0.1307 (OUTLIER) cc_final: -0.0131 (m-80) REVERT: A 194 PHE cc_start: 0.6141 (m-10) cc_final: 0.5812 (m-10) REVERT: A 241 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5921 (tt) REVERT: A 492 LEU cc_start: -0.0820 (OUTLIER) cc_final: -0.1116 (mt) REVERT: A 855 PHE cc_start: 0.5600 (m-10) cc_final: 0.5350 (m-10) REVERT: A 962 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8596 (pt) REVERT: A 983 ARG cc_start: 0.2708 (OUTLIER) cc_final: 0.2347 (ptt-90) REVERT: A 996 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7630 (tt) REVERT: B 43 PHE cc_start: 0.3253 (m-80) cc_final: 0.2893 (m-10) REVERT: B 210 ILE cc_start: 0.6102 (OUTLIER) cc_final: 0.5569 (mm) REVERT: B 237 ARG cc_start: 0.5383 (mmm160) cc_final: 0.5024 (mmp-170) REVERT: B 904 TYR cc_start: 0.8111 (m-10) cc_final: 0.7888 (m-10) REVERT: B 935 GLN cc_start: 0.5407 (OUTLIER) cc_final: 0.4655 (tp40) REVERT: B 962 LEU cc_start: 0.1871 (OUTLIER) cc_final: 0.1614 (tt) REVERT: B 994 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7939 (p0) REVERT: C 65 PHE cc_start: 0.5543 (m-80) cc_final: 0.5323 (m-80) REVERT: C 115 GLN cc_start: 0.2033 (OUTLIER) cc_final: 0.1392 (tp40) REVERT: C 170 TYR cc_start: 0.6002 (t80) cc_final: 0.5681 (t80) REVERT: C 355 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4126 (tpp-160) REVERT: D 174 LYS cc_start: 0.0776 (mmtt) cc_final: 0.0119 (ptmm) REVERT: D 297 MET cc_start: 0.1786 (mmm) cc_final: 0.1264 (mmm) REVERT: D 332 MET cc_start: 0.2001 (tmm) cc_final: 0.1528 (tmm) REVERT: D 342 VAL cc_start: -0.0739 (OUTLIER) cc_final: -0.0962 (p) REVERT: D 376 MET cc_start: 0.1421 (tpp) cc_final: -0.0158 (ttm) REVERT: D 400 PHE cc_start: 0.3504 (t80) cc_final: 0.2340 (m-10) REVERT: D 408 MET cc_start: -0.0559 (ptp) cc_final: -0.2316 (mtt) REVERT: D 564 LYS cc_start: 0.2302 (mmmt) cc_final: 0.1920 (ttpp) REVERT: D 579 MET cc_start: -0.1149 (mtm) cc_final: -0.2802 (tmm) REVERT: E 123 MET cc_start: 0.0461 (tmm) cc_final: -0.0240 (tmm) REVERT: E 176 LEU cc_start: 0.1263 (OUTLIER) cc_final: 0.0644 (mm) REVERT: E 190 MET cc_start: 0.3595 (OUTLIER) cc_final: 0.2947 (ptt) REVERT: E 285 PHE cc_start: 0.0377 (OUTLIER) cc_final: -0.1173 (p90) REVERT: E 297 MET cc_start: 0.0392 (ttp) cc_final: -0.0366 (ptm) REVERT: E 357 ARG cc_start: 0.3939 (mtm110) cc_final: 0.1077 (mtt180) REVERT: E 360 MET cc_start: 0.4016 (pmm) cc_final: 0.3796 (pmm) REVERT: E 480 MET cc_start: 0.1674 (mmp) cc_final: 0.0637 (tpt) REVERT: E 498 CYS cc_start: 0.5359 (OUTLIER) cc_final: 0.5155 (p) REVERT: E 536 GLU cc_start: -0.0246 (OUTLIER) cc_final: -0.1883 (mp0) outliers start: 217 outliers final: 97 residues processed: 461 average time/residue: 0.4209 time to fit residues: 322.0337 Evaluate side-chains 347 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 232 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 325 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 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 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 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 267 VAL 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 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 698 SER 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 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 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 64 TRP 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 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 399 SER Chi-restraints excluded: chain C residue 436 TRP 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 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 ILE 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 367 ASP Chi-restraints excluded: chain D residue 523 PHE 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 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 498 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 118 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 369 optimal weight: 2.9990 chunk 305 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 368 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 341 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 540 ASN A 955 ASN B 66 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 804 GLN C 926 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 378 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 380 GLN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.238952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.210479 restraints weight = 64061.204| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 3.13 r_work: 0.4038 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 33453 Z= 0.257 Angle : 0.909 16.648 45523 Z= 0.478 Chirality : 0.054 0.373 5027 Planarity : 0.007 0.085 5898 Dihedral : 7.144 49.621 4427 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.88 % Favored : 89.00 % Rotamer: Outliers : 7.60 % Allowed : 24.45 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 4053 helix: -0.07 (0.14), residues: 1354 sheet: -0.87 (0.26), residues: 373 loop : -2.99 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 594 HIS 0.008 0.002 HIS E 265 PHE 0.038 0.003 PHE B 106 TYR 0.032 0.002 TYR A 279 ARG 0.019 0.001 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.08440 ( 1236) hydrogen bonds : angle 6.71869 ( 3588) SS BOND : bond 0.00630 ( 41) SS BOND : angle 2.08232 ( 82) covalent geometry : bond 0.00569 (33412) covalent geometry : angle 0.90543 (45441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 237 time to evaluate : 5.161 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 37 TYR cc_start: 0.1911 (OUTLIER) cc_final: 0.0757 (m-80) REVERT: A 353 TRP cc_start: 0.4804 (p-90) cc_final: 0.4386 (p-90) REVERT: A 492 LEU cc_start: -0.0798 (OUTLIER) cc_final: -0.1166 (mt) REVERT: A 996 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 1041 ASP cc_start: 0.7927 (t0) cc_final: 0.7720 (t0) REVERT: B 32 PHE cc_start: 0.7753 (m-80) cc_final: 0.7507 (m-80) REVERT: B 106 PHE cc_start: 0.2011 (OUTLIER) cc_final: 0.1642 (m-80) REVERT: B 117 LEU cc_start: 0.4912 (OUTLIER) cc_final: 0.4549 (mt) REVERT: B 210 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5589 (mm) REVERT: B 237 ARG cc_start: 0.5243 (mmm160) cc_final: 0.4565 (mmp-170) REVERT: B 402 ILE cc_start: 0.2820 (OUTLIER) cc_final: 0.2535 (pt) REVERT: B 935 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6334 (tp-100) REVERT: B 1000 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8500 (ptm-80) REVERT: B 1004 LEU cc_start: 0.6643 (tp) cc_final: 0.5633 (tp) REVERT: B 1005 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6052 (tm-30) REVERT: B 1105 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8980 (p) REVERT: C 115 GLN cc_start: 0.3217 (OUTLIER) cc_final: 0.2908 (tm-30) REVERT: C 170 TYR cc_start: 0.6556 (t80) cc_final: 0.6055 (t80) REVERT: C 191 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: C 355 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.4253 (tpp-160) REVERT: C 740 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8165 (ttt) REVERT: C 950 ASP cc_start: 0.8238 (m-30) cc_final: 0.8018 (m-30) REVERT: C 980 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7777 (mp) REVERT: D 90 ASP cc_start: 0.1595 (OUTLIER) cc_final: 0.1296 (p0) REVERT: D 394 ASN cc_start: 0.4903 (OUTLIER) cc_final: 0.2883 (m-40) REVERT: D 400 PHE cc_start: 0.4069 (t80) cc_final: 0.2697 (m-10) REVERT: D 408 MET cc_start: -0.0442 (ptp) cc_final: -0.2208 (mtt) REVERT: D 459 TRP cc_start: 0.0545 (OUTLIER) cc_final: 0.0177 (m-10) REVERT: D 543 ASP cc_start: 0.3304 (OUTLIER) cc_final: 0.3007 (m-30) REVERT: D 564 LYS cc_start: 0.2149 (mmmt) cc_final: 0.1878 (ttpp) REVERT: D 579 MET cc_start: 0.1411 (OUTLIER) cc_final: -0.0216 (pmm) REVERT: E 61 LYS cc_start: 0.1696 (OUTLIER) cc_final: 0.1237 (tptp) REVERT: E 123 MET cc_start: -0.0177 (tmm) cc_final: -0.0516 (tmm) REVERT: E 152 MET cc_start: 0.4545 (tpp) cc_final: 0.4104 (mpp) REVERT: E 176 LEU cc_start: 0.1286 (OUTLIER) cc_final: 0.0295 (mp) REVERT: E 190 MET cc_start: 0.3689 (OUTLIER) cc_final: 0.2981 (ptt) REVERT: E 285 PHE cc_start: 0.1044 (OUTLIER) cc_final: -0.0399 (p90) REVERT: E 297 MET cc_start: 0.0456 (ttp) cc_final: -0.0309 (ptm) REVERT: E 446 ILE cc_start: 0.2890 (OUTLIER) cc_final: 0.2463 (mp) REVERT: E 480 MET cc_start: 0.1791 (mmp) cc_final: 0.0545 (tpt) REVERT: E 498 CYS cc_start: 0.5616 (OUTLIER) cc_final: 0.5190 (p) REVERT: E 536 GLU cc_start: -0.0003 (OUTLIER) cc_final: -0.1885 (mp0) outliers start: 274 outliers final: 146 residues processed: 489 average time/residue: 0.4937 time to fit residues: 404.7716 Evaluate side-chains 381 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 208 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR 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 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 64 TRP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE 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 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 494 SER 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 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 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP 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 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 88 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 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 385 THR Chi-restraints excluded: chain C residue 391 CYS 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 472 ILE 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 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 864 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 124 SER 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 313 LYS Chi-restraints excluded: chain D residue 343 VAL 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 459 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 579 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 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 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 384 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 361 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 376 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 174 optimal weight: 0.6980 chunk 346 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN D 63 ASN D 221 GLN D 378 HIS ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.241277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.206375 restraints weight = 64774.172| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.52 r_work: 0.4050 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33453 Z= 0.181 Angle : 0.799 16.222 45523 Z= 0.418 Chirality : 0.049 0.341 5027 Planarity : 0.006 0.077 5898 Dihedral : 6.738 51.079 4427 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.57 % Favored : 90.30 % Rotamer: Outliers : 5.33 % Allowed : 25.87 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.13), residues: 4053 helix: 0.18 (0.14), residues: 1341 sheet: -0.73 (0.27), residues: 357 loop : -2.88 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 594 HIS 0.008 0.001 HIS C1083 PHE 0.029 0.002 PHE B 106 TYR 0.038 0.002 TYR A 279 ARG 0.011 0.001 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.06671 ( 1236) hydrogen bonds : angle 6.33215 ( 3588) SS BOND : bond 0.00487 ( 41) SS BOND : angle 1.63837 ( 82) covalent geometry : bond 0.00370 (33412) covalent geometry : angle 0.79622 (45441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 220 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6754 (m90) cc_final: 0.6217 (m90) REVERT: A 492 LEU cc_start: -0.0847 (OUTLIER) cc_final: -0.1105 (mt) REVERT: A 855 PHE cc_start: 0.5824 (m-10) cc_final: 0.5511 (m-10) REVERT: A 996 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7732 (tt) REVERT: B 206 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6256 (tptt) REVERT: B 237 ARG cc_start: 0.5480 (mmm160) cc_final: 0.4952 (mmp-170) REVERT: B 402 ILE cc_start: 0.2608 (OUTLIER) cc_final: 0.2318 (pt) REVERT: B 697 MET cc_start: 0.8140 (mtm) cc_final: 0.7931 (mtm) REVERT: B 935 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6212 (tp40) REVERT: B 1000 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8436 (ptm-80) REVERT: B 1002 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8078 (tm-30) REVERT: C 65 PHE cc_start: 0.6164 (m-80) cc_final: 0.5648 (m-80) REVERT: C 115 GLN cc_start: 0.3610 (OUTLIER) cc_final: 0.3299 (mm-40) REVERT: C 170 TYR cc_start: 0.6445 (t80) cc_final: 0.5920 (t80) REVERT: C 191 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: C 237 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6122 (ptm160) REVERT: C 355 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.4130 (tpp-160) REVERT: C 950 ASP cc_start: 0.8188 (m-30) cc_final: 0.7986 (m-30) REVERT: C 980 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7659 (mp) REVERT: D 90 ASP cc_start: 0.1584 (OUTLIER) cc_final: 0.1336 (p0) REVERT: D 270 MET cc_start: 0.2535 (ttt) cc_final: 0.2308 (ttm) REVERT: D 297 MET cc_start: 0.2361 (mmm) cc_final: 0.1786 (mmm) REVERT: D 376 MET cc_start: 0.1469 (tpp) cc_final: 0.0593 (ttm) REVERT: D 379 ILE cc_start: -0.1092 (mm) cc_final: -0.1385 (pt) REVERT: D 400 PHE cc_start: 0.4058 (t80) cc_final: 0.2833 (m-10) REVERT: D 408 MET cc_start: -0.0897 (ptp) cc_final: -0.2448 (mtt) REVERT: D 459 TRP cc_start: 0.0536 (OUTLIER) cc_final: 0.0127 (m-10) REVERT: D 564 LYS cc_start: 0.2295 (mmmt) cc_final: 0.1923 (ttpp) REVERT: D 579 MET cc_start: 0.1284 (mtm) cc_final: -0.0068 (pmm) REVERT: E 61 LYS cc_start: 0.1646 (OUTLIER) cc_final: 0.1234 (tptp) REVERT: E 190 MET cc_start: 0.3564 (OUTLIER) cc_final: 0.2809 (ptt) REVERT: E 285 PHE cc_start: 0.0654 (OUTLIER) cc_final: -0.0737 (p90) REVERT: E 297 MET cc_start: 0.0575 (ttp) cc_final: -0.0237 (ptm) REVERT: E 310 GLU cc_start: 0.0754 (OUTLIER) cc_final: 0.0059 (tp30) REVERT: E 446 ILE cc_start: 0.2844 (OUTLIER) cc_final: 0.2394 (mp) REVERT: E 480 MET cc_start: 0.1762 (mmp) cc_final: 0.0512 (tpt) REVERT: E 498 CYS cc_start: 0.5390 (OUTLIER) cc_final: 0.5037 (p) REVERT: E 536 GLU cc_start: 0.0049 (OUTLIER) cc_final: -0.1795 (mp0) REVERT: E 600 ARG cc_start: 0.2881 (OUTLIER) cc_final: 0.2486 (tpp-160) outliers start: 192 outliers final: 106 residues processed: 393 average time/residue: 0.4831 time to fit residues: 315.4243 Evaluate side-chains 329 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 202 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 858 LEU 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 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 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1133 VAL 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 206 LYS Chi-restraints excluded: chain B residue 293 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 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU 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 994 ASP Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1043 CYS 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 215 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS 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 858 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER 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 230 PHE Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 498 CYS 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 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 12 optimal weight: 0.7980 chunk 264 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 99 optimal weight: 0.1980 chunk 285 optimal weight: 0.9990 chunk 352 optimal weight: 8.9990 chunk 226 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 354 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 935 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 957 GLN C1010 GLN D 117 ASN D 378 HIS D 493 HIS D 607 ASN E 417 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.241351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.205539 restraints weight = 66180.951| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 3.52 r_work: 0.4087 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33453 Z= 0.167 Angle : 0.769 16.218 45523 Z= 0.400 Chirality : 0.049 0.327 5027 Planarity : 0.006 0.084 5898 Dihedral : 6.456 53.919 4427 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.47 % Favored : 90.45 % Rotamer: Outliers : 4.86 % Allowed : 26.34 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 4053 helix: 0.38 (0.14), residues: 1324 sheet: -0.44 (0.27), residues: 347 loop : -2.83 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 594 HIS 0.005 0.001 HIS E 373 PHE 0.038 0.002 PHE A 55 TYR 0.040 0.001 TYR A 279 ARG 0.024 0.001 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.06095 ( 1236) hydrogen bonds : angle 6.10713 ( 3588) SS BOND : bond 0.00377 ( 41) SS BOND : angle 1.52324 ( 82) covalent geometry : bond 0.00334 (33412) covalent geometry : angle 0.76746 (45441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 226 time to evaluate : 4.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6942 (mm) cc_final: 0.6630 (mp) REVERT: A 207 HIS cc_start: 0.6656 (m90) cc_final: 0.5990 (m90) REVERT: A 235 ILE cc_start: 0.4681 (OUTLIER) cc_final: 0.3532 (mt) REVERT: A 533 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7049 (tt) REVERT: A 855 PHE cc_start: 0.6056 (m-10) cc_final: 0.5709 (m-10) REVERT: A 996 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7612 (tt) REVERT: A 1000 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7168 (ptm-80) REVERT: A 1138 TYR cc_start: 0.7710 (t80) cc_final: 0.7331 (t80) REVERT: B 206 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6191 (tptt) REVERT: B 210 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5365 (mm) REVERT: B 237 ARG cc_start: 0.5403 (mmm160) cc_final: 0.4780 (mmp-170) REVERT: B 825 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8215 (tttp) REVERT: B 935 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6000 (tp40) REVERT: B 1000 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8283 (ptm-80) REVERT: C 115 GLN cc_start: 0.3694 (OUTLIER) cc_final: 0.3206 (tm-30) REVERT: C 170 TYR cc_start: 0.6388 (t80) cc_final: 0.5857 (t80) REVERT: C 191 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: C 355 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.3531 (ttm170) REVERT: C 965 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: C 980 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7552 (mp) REVERT: C 983 ARG cc_start: 0.4103 (mmm160) cc_final: 0.3882 (mmm160) REVERT: D 90 ASP cc_start: 0.1862 (OUTLIER) cc_final: 0.1606 (p0) REVERT: D 199 TYR cc_start: 0.1529 (OUTLIER) cc_final: -0.0252 (t80) REVERT: D 270 MET cc_start: 0.2871 (ttt) cc_final: 0.2592 (ttm) REVERT: D 366 MET cc_start: 0.1941 (pmm) cc_final: -0.1552 (mmm) REVERT: D 376 MET cc_start: 0.1322 (tpp) cc_final: 0.0962 (mtp) REVERT: D 379 ILE cc_start: -0.1074 (mm) cc_final: -0.1546 (pt) REVERT: D 400 PHE cc_start: 0.3700 (t80) cc_final: 0.2197 (m-80) REVERT: D 408 MET cc_start: -0.1063 (ptp) cc_final: -0.1746 (mtm) REVERT: D 459 TRP cc_start: 0.0556 (OUTLIER) cc_final: 0.0112 (m-10) REVERT: D 474 MET cc_start: 0.1645 (tpt) cc_final: -0.0879 (ttt) REVERT: D 564 LYS cc_start: 0.2555 (mmmt) cc_final: 0.2185 (ttpp) REVERT: D 579 MET cc_start: 0.1723 (mtm) cc_final: 0.0322 (pmm) REVERT: E 61 LYS cc_start: 0.1891 (OUTLIER) cc_final: 0.1454 (tptp) REVERT: E 89 GLN cc_start: 0.3620 (tp40) cc_final: 0.1912 (mt0) REVERT: E 176 LEU cc_start: 0.1137 (OUTLIER) cc_final: 0.0421 (mp) REVERT: E 190 MET cc_start: 0.3536 (tmm) cc_final: 0.2917 (ptt) REVERT: E 285 PHE cc_start: 0.0548 (OUTLIER) cc_final: -0.0816 (p90) REVERT: E 297 MET cc_start: 0.0439 (ttp) cc_final: -0.0418 (ptm) REVERT: E 310 GLU cc_start: 0.0713 (OUTLIER) cc_final: 0.0006 (tp30) REVERT: E 446 ILE cc_start: 0.2735 (OUTLIER) cc_final: 0.2229 (mp) REVERT: E 480 MET cc_start: 0.1987 (mmp) cc_final: 0.0622 (tpt) REVERT: E 514 ARG cc_start: 0.2269 (mmp-170) cc_final: -0.0331 (mtp85) REVERT: E 536 GLU cc_start: 0.0050 (OUTLIER) cc_final: -0.1786 (mp0) REVERT: E 600 ARG cc_start: 0.2840 (OUTLIER) cc_final: 0.2476 (tpp-160) outliers start: 175 outliers final: 107 residues processed: 380 average time/residue: 0.4959 time to fit residues: 316.1394 Evaluate side-chains 341 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 211 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 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 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP 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 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 215 ASP 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 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 585 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS 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 762 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 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 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 349 TRP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 529 LEU 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 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 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 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 588 PHE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 392 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 340 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 178 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1119 ASN B1002 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 957 GLN D 378 HIS D 397 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.240474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.203212 restraints weight = 64514.087| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 3.57 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33453 Z= 0.182 Angle : 0.782 15.722 45523 Z= 0.406 Chirality : 0.049 0.329 5027 Planarity : 0.006 0.083 5898 Dihedral : 6.334 53.409 4424 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.97 % Favored : 90.01 % Rotamer: Outliers : 5.16 % Allowed : 25.98 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 4053 helix: 0.45 (0.14), residues: 1327 sheet: -0.47 (0.27), residues: 351 loop : -2.87 (0.11), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 594 HIS 0.005 0.001 HIS E 373 PHE 0.035 0.002 PHE B 106 TYR 0.040 0.002 TYR A 279 ARG 0.009 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.06582 ( 1236) hydrogen bonds : angle 6.08811 ( 3588) SS BOND : bond 0.00382 ( 41) SS BOND : angle 1.60250 ( 82) covalent geometry : bond 0.00381 (33412) covalent geometry : angle 0.77961 (45441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 213 time to evaluate : 3.688 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 235 ILE cc_start: 0.4163 (OUTLIER) cc_final: 0.3139 (mt) REVERT: A 533 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6908 (tt) REVERT: A 996 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 1138 TYR cc_start: 0.7139 (t80) cc_final: 0.6802 (t80) REVERT: B 210 ILE cc_start: 0.4767 (OUTLIER) cc_final: 0.4276 (mm) REVERT: B 393 THR cc_start: 0.5123 (OUTLIER) cc_final: 0.4823 (p) REVERT: B 1000 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8153 (ptm-80) REVERT: C 115 GLN cc_start: 0.3688 (OUTLIER) cc_final: 0.3188 (tm-30) REVERT: C 191 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5985 (mm-30) REVERT: C 237 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5455 (ptm160) REVERT: C 355 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.2921 (ttm170) REVERT: C 947 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7090 (mmmm) REVERT: C 965 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: D 90 ASP cc_start: 0.2723 (OUTLIER) cc_final: 0.2473 (p0) REVERT: D 297 MET cc_start: 0.2467 (mmm) cc_final: 0.1965 (mmm) REVERT: D 366 MET cc_start: 0.2333 (pmm) cc_final: -0.1322 (mmm) REVERT: D 379 ILE cc_start: -0.0619 (mm) cc_final: -0.1033 (pt) REVERT: D 400 PHE cc_start: 0.2730 (t80) cc_final: 0.1701 (m-80) REVERT: D 408 MET cc_start: -0.2087 (ptp) cc_final: -0.2734 (mtm) REVERT: D 459 TRP cc_start: 0.0334 (OUTLIER) cc_final: -0.0268 (m-10) REVERT: D 474 MET cc_start: 0.1293 (tpt) cc_final: -0.1042 (ttt) REVERT: D 579 MET cc_start: 0.0894 (mtm) cc_final: -0.0081 (pmm) REVERT: E 61 LYS cc_start: 0.3095 (OUTLIER) cc_final: 0.2443 (tptp) REVERT: E 89 GLN cc_start: 0.3917 (tp40) cc_final: 0.2180 (mt0) REVERT: E 152 MET cc_start: 0.5133 (mpp) cc_final: 0.4647 (tpp) REVERT: E 190 MET cc_start: 0.4047 (OUTLIER) cc_final: 0.3427 (ptt) REVERT: E 285 PHE cc_start: 0.0649 (OUTLIER) cc_final: -0.0480 (p90) REVERT: E 297 MET cc_start: 0.1751 (ttp) cc_final: 0.0569 (ptm) REVERT: E 446 ILE cc_start: 0.2657 (OUTLIER) cc_final: 0.1946 (mp) REVERT: E 480 MET cc_start: 0.2708 (mmp) cc_final: 0.1165 (tpt) REVERT: E 536 GLU cc_start: 0.0099 (OUTLIER) cc_final: -0.1889 (mp0) outliers start: 186 outliers final: 131 residues processed: 380 average time/residue: 0.4172 time to fit residues: 265.3139 Evaluate side-chains 354 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 204 time to evaluate : 3.643 ------------------------------------------------------------------------------- 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 165 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASN 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 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 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 1081 ILE 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 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 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR 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 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 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 215 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS 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 762 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER 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 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 436 ILE Chi-restraints excluded: chain D residue 459 TRP Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR 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 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 588 PHE Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 266 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 261 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 407 optimal weight: 1.9990 chunk 339 optimal weight: 0.7980 chunk 344 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 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** D 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.241660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.204668 restraints weight = 64778.293| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 3.50 r_work: 0.4050 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 33453 Z= 0.165 Angle : 0.760 15.855 45523 Z= 0.396 Chirality : 0.048 0.331 5027 Planarity : 0.006 0.071 5898 Dihedral : 6.184 56.998 4424 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.10 % Favored : 90.85 % Rotamer: Outliers : 4.39 % Allowed : 26.95 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 4053 helix: 0.52 (0.14), residues: 1329 sheet: -0.18 (0.27), residues: 348 loop : -2.85 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 594 HIS 0.006 0.001 HIS B 207 PHE 0.042 0.001 PHE B 106 TYR 0.040 0.001 TYR A 279 ARG 0.010 0.001 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.05925 ( 1236) hydrogen bonds : angle 5.92677 ( 3588) SS BOND : bond 0.00348 ( 41) SS BOND : angle 1.43469 ( 82) covalent geometry : bond 0.00341 (33412) covalent geometry : angle 0.75849 (45441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 225 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6629 (mmt180) cc_final: 0.6338 (mmp-170) REVERT: A 533 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7131 (tt) REVERT: A 855 PHE cc_start: 0.6205 (m-10) cc_final: 0.5905 (m-10) REVERT: A 980 ILE cc_start: 0.3917 (mm) cc_final: 0.3695 (mm) REVERT: A 996 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 1138 TYR cc_start: 0.7667 (t80) cc_final: 0.7301 (t80) REVERT: B 106 PHE cc_start: 0.1402 (OUTLIER) cc_final: 0.0851 (m-80) REVERT: B 210 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5256 (mm) REVERT: B 237 ARG cc_start: 0.4726 (mmm-85) cc_final: 0.3668 (mmp-170) REVERT: B 393 THR cc_start: 0.5533 (OUTLIER) cc_final: 0.5204 (p) REVERT: C 191 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6645 (mm-30) REVERT: C 215 ASP cc_start: 0.3259 (OUTLIER) cc_final: 0.2989 (t0) REVERT: C 947 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6482 (mmmm) REVERT: C 965 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: C 983 ARG cc_start: 0.4181 (mmm160) cc_final: 0.3953 (mmm160) REVERT: C 1029 MET cc_start: 0.9155 (tpp) cc_final: 0.8933 (ttm) REVERT: D 199 TYR cc_start: 0.1682 (OUTLIER) cc_final: -0.0157 (t80) REVERT: D 270 MET cc_start: 0.2142 (ttm) cc_final: 0.1048 (ttm) REVERT: D 297 MET cc_start: 0.2477 (mmm) cc_final: 0.1935 (mmm) REVERT: D 366 MET cc_start: 0.1350 (pmm) cc_final: -0.1606 (mmm) REVERT: D 379 ILE cc_start: -0.0928 (mm) cc_final: -0.1475 (pt) REVERT: D 400 PHE cc_start: 0.3776 (t80) cc_final: 0.2358 (m-80) REVERT: D 408 MET cc_start: -0.1058 (ptp) cc_final: -0.2231 (mtt) REVERT: D 465 LYS cc_start: 0.0337 (mttt) cc_final: -0.0049 (mttt) REVERT: D 474 MET cc_start: 0.1463 (tpt) cc_final: -0.0847 (ttt) REVERT: D 496 THR cc_start: 0.4587 (m) cc_final: 0.4049 (p) REVERT: D 579 MET cc_start: 0.1614 (mtm) cc_final: 0.0824 (pmm) REVERT: E 61 LYS cc_start: 0.2172 (OUTLIER) cc_final: 0.1715 (tptp) REVERT: E 89 GLN cc_start: 0.3572 (tp40) cc_final: 0.1560 (mt0) REVERT: E 152 MET cc_start: 0.4781 (mpp) cc_final: 0.4486 (tpp) REVERT: E 176 LEU cc_start: 0.1226 (OUTLIER) cc_final: 0.0462 (mp) REVERT: E 285 PHE cc_start: 0.0552 (OUTLIER) cc_final: -0.0727 (p90) REVERT: E 297 MET cc_start: 0.0314 (ttp) cc_final: -0.0481 (ptm) REVERT: E 446 ILE cc_start: 0.3472 (OUTLIER) cc_final: 0.3060 (mp) REVERT: E 480 MET cc_start: 0.2057 (mmp) cc_final: 0.0620 (tpt) REVERT: E 514 ARG cc_start: 0.2111 (mmp-170) cc_final: 0.0087 (tmt170) outliers start: 158 outliers final: 111 residues processed: 365 average time/residue: 0.4269 time to fit residues: 260.0423 Evaluate side-chains 337 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 212 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 229 LEU 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 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain 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 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS 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 762 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 127 TYR 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 343 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 403 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 chunk 164 optimal weight: 0.6980 chunk 323 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** 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** B 965 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.238724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.203806 restraints weight = 62550.062| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.37 r_work: 0.3999 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.8071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 33453 Z= 0.205 Angle : 0.815 15.647 45523 Z= 0.426 Chirality : 0.050 0.338 5027 Planarity : 0.006 0.079 5898 Dihedral : 6.302 59.580 4420 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.73 % Favored : 89.22 % Rotamer: Outliers : 4.39 % Allowed : 27.20 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 4053 helix: 0.42 (0.14), residues: 1326 sheet: -0.32 (0.27), residues: 333 loop : -2.87 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 594 HIS 0.008 0.001 HIS B 207 PHE 0.068 0.002 PHE A 55 TYR 0.040 0.002 TYR A 279 ARG 0.012 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.07319 ( 1236) hydrogen bonds : angle 6.11504 ( 3588) SS BOND : bond 0.00425 ( 41) SS BOND : angle 1.68919 ( 82) covalent geometry : bond 0.00444 (33412) covalent geometry : angle 0.81235 (45441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 205 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 980 ILE cc_start: 0.4061 (mm) cc_final: 0.3672 (mm) REVERT: A 996 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 1138 TYR cc_start: 0.7775 (t80) cc_final: 0.7416 (t80) REVERT: B 106 PHE cc_start: 0.2061 (OUTLIER) cc_final: 0.1416 (m-80) REVERT: B 210 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5584 (mm) REVERT: B 966 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6142 (mt) REVERT: B 1000 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8241 (ptm-80) REVERT: C 191 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6723 (mm-30) REVERT: C 215 ASP cc_start: 0.3723 (OUTLIER) cc_final: 0.3411 (t0) REVERT: C 338 PHE cc_start: 0.4583 (t80) cc_final: 0.4308 (t80) REVERT: C 947 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7174 (mmmm) REVERT: C 965 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: D 199 TYR cc_start: 0.1438 (OUTLIER) cc_final: -0.0322 (t80) REVERT: D 297 MET cc_start: 0.2542 (mmm) cc_final: 0.2042 (mmm) REVERT: D 366 MET cc_start: 0.0207 (pmm) cc_final: -0.0374 (ppp) REVERT: D 400 PHE cc_start: 0.3642 (t80) cc_final: 0.2668 (m-10) REVERT: D 408 MET cc_start: -0.0671 (ptp) cc_final: -0.1751 (mtt) REVERT: D 474 MET cc_start: 0.1849 (tpt) cc_final: -0.0488 (ttt) REVERT: D 579 MET cc_start: 0.1653 (mtm) cc_final: 0.0805 (pmm) REVERT: E 61 LYS cc_start: 0.1976 (OUTLIER) cc_final: 0.1554 (tptp) REVERT: E 89 GLN cc_start: 0.3646 (tp40) cc_final: 0.1342 (pt0) REVERT: E 176 LEU cc_start: 0.1246 (OUTLIER) cc_final: 0.0433 (mp) REVERT: E 211 TRP cc_start: 0.3537 (t-100) cc_final: 0.3316 (t-100) REVERT: E 285 PHE cc_start: 0.1343 (OUTLIER) cc_final: -0.0031 (p90) REVERT: E 297 MET cc_start: 0.1093 (ttp) cc_final: 0.0168 (ptm) REVERT: E 446 ILE cc_start: 0.3460 (OUTLIER) cc_final: 0.2991 (mp) REVERT: E 480 MET cc_start: 0.1811 (mmp) cc_final: 0.0450 (ptt) REVERT: E 510 TYR cc_start: 0.2815 (m-80) cc_final: 0.1099 (m-80) outliers start: 158 outliers final: 124 residues processed: 349 average time/residue: 0.4295 time to fit residues: 252.2682 Evaluate side-chains 338 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 200 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 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 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE 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 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR 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 994 ASP 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 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 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 215 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 488 VAL 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 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 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 516 TYR Chi-restraints excluded: chain E residue 532 ILE 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 391 optimal weight: 0.0060 chunk 17 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 385 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 331 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 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 = 0.4838 r_free = 0.4838 target = 0.238799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.202590 restraints weight = 63426.139| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 3.46 r_work: 0.4027 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 33453 Z= 0.201 Angle : 0.884 59.200 45523 Z= 0.475 Chirality : 0.049 0.355 5027 Planarity : 0.006 0.079 5898 Dihedral : 6.299 59.718 4420 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.68 % Favored : 89.29 % Rotamer: Outliers : 4.05 % Allowed : 27.75 % Favored : 68.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 4053 helix: 0.40 (0.14), residues: 1326 sheet: -0.31 (0.27), residues: 333 loop : -2.86 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 594 HIS 0.005 0.001 HIS B 207 PHE 0.060 0.002 PHE A 55 TYR 0.040 0.002 TYR A 279 ARG 0.013 0.001 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.07229 ( 1236) hydrogen bonds : angle 6.10867 ( 3588) SS BOND : bond 0.00425 ( 41) SS BOND : angle 1.66084 ( 82) covalent geometry : bond 0.00428 (33412) covalent geometry : angle 0.88149 (45441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 201 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 980 ILE cc_start: 0.3798 (mm) cc_final: 0.3566 (mm) REVERT: A 996 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7720 (tt) REVERT: A 1138 TYR cc_start: 0.7595 (t80) cc_final: 0.7259 (t80) REVERT: B 106 PHE cc_start: 0.1929 (OUTLIER) cc_final: 0.1289 (m-80) REVERT: B 210 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5341 (mm) REVERT: B 1000 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8118 (ptm-80) REVERT: C 191 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: C 215 ASP cc_start: 0.3609 (OUTLIER) cc_final: 0.3303 (t0) REVERT: C 947 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6921 (mmmm) REVERT: C 965 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: D 199 TYR cc_start: 0.1841 (OUTLIER) cc_final: -0.0135 (t80) REVERT: D 297 MET cc_start: 0.2653 (mmm) cc_final: 0.2132 (mmm) REVERT: D 366 MET cc_start: 0.0198 (pmm) cc_final: -0.1511 (mmm) REVERT: D 400 PHE cc_start: 0.3627 (t80) cc_final: 0.2644 (m-10) REVERT: D 408 MET cc_start: -0.0586 (ptp) cc_final: -0.1656 (mtt) REVERT: D 474 MET cc_start: 0.1683 (tpt) cc_final: -0.0589 (ttt) REVERT: D 579 MET cc_start: 0.1837 (mtm) cc_final: 0.0916 (pmm) REVERT: E 61 LYS cc_start: 0.2217 (OUTLIER) cc_final: 0.1698 (tptp) REVERT: E 89 GLN cc_start: 0.3628 (tp40) cc_final: 0.1278 (pt0) REVERT: E 176 LEU cc_start: 0.1215 (OUTLIER) cc_final: 0.0414 (mp) REVERT: E 211 TRP cc_start: 0.3403 (t-100) cc_final: 0.3193 (t-100) REVERT: E 285 PHE cc_start: 0.1409 (OUTLIER) cc_final: 0.0005 (p90) REVERT: E 297 MET cc_start: 0.1010 (ttp) cc_final: 0.0131 (ptm) REVERT: E 446 ILE cc_start: 0.3504 (OUTLIER) cc_final: 0.3088 (mp) REVERT: E 480 MET cc_start: 0.1916 (mmp) cc_final: 0.0500 (ptt) REVERT: E 510 TYR cc_start: 0.2791 (m-80) cc_final: 0.1139 (m-80) outliers start: 146 outliers final: 125 residues processed: 336 average time/residue: 0.4134 time to fit residues: 234.0426 Evaluate side-chains 336 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 198 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 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 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE 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 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 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP 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 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 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 215 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 127 TYR 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 282 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 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 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 356 optimal weight: 7.9990 chunk 396 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 272 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 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 = 0.4840 r_free = 0.4840 target = 0.238799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.203754 restraints weight = 62626.955| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.32 r_work: 0.4004 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.8083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 33453 Z= 0.206 Angle : 0.885 59.200 45523 Z= 0.476 Chirality : 0.049 0.355 5027 Planarity : 0.006 0.079 5898 Dihedral : 6.299 59.718 4420 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.68 % Favored : 89.29 % Rotamer: Outliers : 3.83 % Allowed : 27.87 % Favored : 68.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 4053 helix: 0.40 (0.14), residues: 1326 sheet: -0.31 (0.27), residues: 333 loop : -2.86 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 594 HIS 0.005 0.001 HIS B 207 PHE 0.060 0.002 PHE A 55 TYR 0.040 0.002 TYR A 279 ARG 0.013 0.001 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.07229 ( 1236) hydrogen bonds : angle 6.10867 ( 3588) SS BOND : bond 0.02728 ( 41) SS BOND : angle 2.03064 ( 82) covalent geometry : bond 0.00428 (33412) covalent geometry : angle 0.88149 (45441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17917.49 seconds wall clock time: 313 minutes 29.62 seconds (18809.62 seconds total)