Starting phenix.real_space_refine on Mon Feb 19 08:40:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb1_31512/02_2024/7fb1_31512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb1_31512/02_2024/7fb1_31512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb1_31512/02_2024/7fb1_31512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb1_31512/02_2024/7fb1_31512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb1_31512/02_2024/7fb1_31512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb1_31512/02_2024/7fb1_31512.pdb" } resolution = 3.7 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= 0.001 sd= 0.070 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 112 5.16 5 C 15437 2.51 5 N 4020 2.21 5 O 4599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24168 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8039 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 50, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8091 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 52, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8038 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 52, 'TRANS': 976} Chain breaks: 8 Time building chain proxies: 12.57, per 1000 atoms: 0.52 Number of scatterers: 24168 At special positions: 0 Unit cell: (138.72, 136, 195.84, 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 112 16.00 O 4599 8.00 N 4020 7.00 C 15437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 9.65 Conformation dependent library (CDL) restraints added in 4.5 seconds 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 48 sheets defined 24.2% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.219A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.721A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.710A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.623A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 7.122A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.963A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.933A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.630A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.140A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.566A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.696A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.924A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.530A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.680A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.697A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.626A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.780A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.897A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.533A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.823A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 857 removed outlier: 4.037A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 857 " --> pdb=" O LYS C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.518A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.656A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.056A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.081A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 197 removed outlier: 3.569A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.600A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.596A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 554 removed outlier: 4.011A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.854A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 719 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 718 through 719 current: chain 'A' and resid 1059 through 1069 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.701A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.665A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.775A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.762A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.144A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.065A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 6.398A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 356 through 357 removed outlier: 4.826A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.705A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.503A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 643 through 645 removed outlier: 3.619A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.796A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 720 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 720 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.758A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 1087 through 1090 removed outlier: 4.036A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.996A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.803A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.545A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 188 through 197 removed outlier: 3.840A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.570A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.821A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.579A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.511A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 642 through 645 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.748A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 722 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 712 through 722 current: chain 'C' and resid 1059 through 1075 No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.086A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF3, first strand: chain 'C' and resid 1095 through 1096 778 hydrogen bonds defined for protein. 2088 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: 10.31 Time building geometry restraints manager: 10.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7829 1.35 - 1.47: 6317 1.47 - 1.60: 10427 1.60 - 1.73: 0 1.73 - 1.85: 140 Bond restraints: 24713 Sorted by residual: bond pdb=" C ALA A 609 " pdb=" N VAL A 610 " ideal model delta sigma weight residual 1.334 1.299 0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" CA LEU B1034 " pdb=" C LEU B1034 " ideal model delta sigma weight residual 1.522 1.476 0.045 1.72e-02 3.38e+03 6.94e+00 bond pdb=" N SER C 940 " pdb=" CA SER C 940 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.16e-02 7.43e+03 6.23e+00 bond pdb=" C THR A 599 " pdb=" N PRO A 600 " ideal model delta sigma weight residual 1.332 1.311 0.022 8.90e-03 1.26e+04 5.89e+00 bond pdb=" CA TYR A 917 " pdb=" C TYR A 917 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.72e-02 3.38e+03 5.85e+00 ... (remaining 24708 not shown) Histogram of bond angle deviations from ideal: 97.84 - 106.06: 586 106.06 - 114.28: 14468 114.28 - 122.50: 15083 122.50 - 130.72: 3428 130.72 - 138.94: 57 Bond angle restraints: 33622 Sorted by residual: angle pdb=" C VAL B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 120.67 138.94 -18.27 1.34e+00 5.57e-01 1.86e+02 angle pdb=" N PHE B 79 " pdb=" CA PHE B 79 " pdb=" C PHE B 79 " ideal model delta sigma weight residual 112.72 105.49 7.23 1.36e+00 5.41e-01 2.83e+01 angle pdb=" N VAL B 483 " pdb=" CA VAL B 483 " pdb=" C VAL B 483 " ideal model delta sigma weight residual 113.71 109.24 4.47 9.50e-01 1.11e+00 2.21e+01 angle pdb=" C LEU B 335 " pdb=" N CYS B 336 " pdb=" CA CYS B 336 " ideal model delta sigma weight residual 120.94 112.71 8.23 1.90e+00 2.77e-01 1.88e+01 angle pdb=" C ARG B 328 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 121.80 132.26 -10.46 2.44e+00 1.68e-01 1.84e+01 ... (remaining 33617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13267 17.92 - 35.84: 1243 35.84 - 53.76: 173 53.76 - 71.68: 35 71.68 - 89.61: 34 Dihedral angle restraints: 14752 sinusoidal: 5745 harmonic: 9007 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -174.09 88.09 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -5.53 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CA PHE B 329 " pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta harmonic sigma weight residual 180.00 136.75 43.25 0 5.00e+00 4.00e-02 7.48e+01 ... (remaining 14749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2657 0.043 - 0.086: 874 0.086 - 0.129: 273 0.129 - 0.172: 26 0.172 - 0.215: 1 Chirality restraints: 3831 Sorted by residual: chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL B 213 " pdb=" CA VAL B 213 " pdb=" CG1 VAL B 213 " pdb=" CG2 VAL B 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CB ILE C 896 " pdb=" CA ILE C 896 " pdb=" CG1 ILE C 896 " pdb=" CG2 ILE C 896 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 3828 not shown) Planarity restraints: 4365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO B 330 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 425 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO A 426 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 330 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.029 5.00e-02 4.00e+02 ... (remaining 4362 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 815 2.65 - 3.21: 26029 3.21 - 3.78: 38419 3.78 - 4.34: 50900 4.34 - 4.90: 80155 Nonbonded interactions: 196318 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.091 2.440 nonbonded pdb=" O THR A 108 " pdb=" OG1 THR A 236 " model vdw 2.103 2.440 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.120 2.440 nonbonded pdb=" ND2 ASN B 81 " pdb=" O THR B 240 " model vdw 2.129 2.520 nonbonded pdb=" O THR C 109 " pdb=" NH2 ARG C 237 " model vdw 2.137 2.520 ... (remaining 196313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 141 or resid 156 through 244 or resid 260 throu \ gh 827 or resid 851 through 1146)) selection = (chain 'B' and (resid 26 through 68 or resid 78 through 141 or resid 156 through \ 244 or resid 260 through 620 or resid 641 through 827 or resid 851 through 1146 \ )) selection = (chain 'C' and (resid 26 through 68 or resid 78 through 244 or resid 260 through \ 1146)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.950 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 66.720 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.093 24713 Z= 0.444 Angle : 0.830 18.266 33622 Z= 0.478 Chirality : 0.046 0.215 3831 Planarity : 0.004 0.061 4365 Dihedral : 14.192 89.606 8835 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 0.07 % Allowed : 9.51 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.12), residues: 3045 helix: -1.59 (0.18), residues: 657 sheet: -3.49 (0.18), residues: 538 loop : -3.85 (0.11), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 886 HIS 0.006 0.001 HIS C 207 PHE 0.024 0.002 PHE B 329 TYR 0.021 0.002 TYR A 170 ARG 0.005 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 2.688 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: symmetry clash REVERT: A 165 ASN cc_start: 0.6809 (OUTLIER) cc_final: 0.5638 (p0) REVERT: A 177 MET cc_start: 0.8241 (mmt) cc_final: 0.7959 (ptp) REVERT: A 191 GLU cc_start: 0.6814 (pm20) cc_final: 0.6374 (pm20) REVERT: A 353 TRP cc_start: 0.8499 (p-90) cc_final: 0.8215 (p-90) REVERT: A 369 TYR cc_start: 0.7583 (m-10) cc_final: 0.7335 (m-10) REVERT: A 426 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8392 (Cg_endo) REVERT: A 456 PHE cc_start: 0.8795 (m-80) cc_final: 0.8368 (m-80) REVERT: A 731 MET cc_start: 0.9204 (ptm) cc_final: 0.8911 (ptp) REVERT: A 855 PHE cc_start: 0.8240 (m-10) cc_final: 0.7949 (m-80) REVERT: A 869 MET cc_start: 0.9045 (mtt) cc_final: 0.8711 (mtt) REVERT: A 1050 MET cc_start: 0.9187 (ptp) cc_final: 0.8846 (ptm) REVERT: A 1138 TYR cc_start: 0.8328 (t80) cc_final: 0.7579 (t80) REVERT: B 858 LEU cc_start: 0.9750 (mp) cc_final: 0.9525 (mp) REVERT: B 954 GLN cc_start: 0.9167 (mt0) cc_final: 0.8869 (mt0) REVERT: B 995 ARG cc_start: 0.9219 (mtt180) cc_final: 0.8892 (mmm-85) REVERT: B 1029 MET cc_start: 0.9682 (tpp) cc_final: 0.9461 (tpp) REVERT: C 52 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8341 (pp30) REVERT: C 489 TYR cc_start: 0.8547 (m-10) cc_final: 0.8115 (m-80) REVERT: C 740 MET cc_start: 0.9240 (tpp) cc_final: 0.9032 (tpp) REVERT: C 759 PHE cc_start: 0.8630 (m-80) cc_final: 0.8092 (m-80) REVERT: C 780 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7945 (mt-10) REVERT: C 869 MET cc_start: 0.9219 (mtt) cc_final: 0.8996 (mtm) REVERT: C 1002 GLN cc_start: 0.9203 (tp40) cc_final: 0.8745 (tm-30) REVERT: C 1005 GLN cc_start: 0.9493 (tp-100) cc_final: 0.9123 (tp40) REVERT: C 1017 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8583 (tp30) REVERT: C 1029 MET cc_start: 0.9600 (tpp) cc_final: 0.8873 (tpp) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.3560 time to fit residues: 81.3823 Evaluate side-chains 93 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.0370 chunk 124 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 30.0000 chunk 179 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 164 ASN A 314 GLN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 536 ASN A 564 GLN A 657 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 928 ASN A 953 ASN A 969 ASN A 978 ASN A1036 GLN A1083 HIS B 115 GLN B 218 GLN B 317 ASN B 388 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 657 ASN B 751 ASN B 755 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 949 GLN B 953 ASN B 954 GLN B1010 GLN B1071 GLN B1088 HIS C 61 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 317 ASN C 321 GLN C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 536 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN C 901 GLN C 925 ASN C 935 GLN C 954 GLN C 955 ASN C1005 GLN C1036 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24713 Z= 0.202 Angle : 0.635 10.766 33622 Z= 0.331 Chirality : 0.045 0.219 3831 Planarity : 0.004 0.065 4365 Dihedral : 5.744 42.551 3306 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.55 % Allowed : 12.47 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.14), residues: 3045 helix: 0.45 (0.20), residues: 646 sheet: -2.75 (0.19), residues: 560 loop : -3.29 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.007 0.001 HIS A1048 PHE 0.026 0.001 PHE B 329 TYR 0.020 0.001 TYR C 266 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 119 time to evaluate : 2.757 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 53 ASP cc_start: 0.8986 (m-30) cc_final: 0.8665 (m-30) REVERT: A 177 MET cc_start: 0.8158 (mmt) cc_final: 0.7931 (ptp) REVERT: A 191 GLU cc_start: 0.6704 (pm20) cc_final: 0.5954 (pm20) REVERT: A 353 TRP cc_start: 0.8433 (p-90) cc_final: 0.8076 (p-90) REVERT: A 369 TYR cc_start: 0.7583 (m-10) cc_final: 0.7301 (m-10) REVERT: A 426 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: A 456 PHE cc_start: 0.8748 (m-80) cc_final: 0.8308 (m-80) REVERT: A 731 MET cc_start: 0.9170 (ptm) cc_final: 0.8825 (ptp) REVERT: A 869 MET cc_start: 0.9010 (mtt) cc_final: 0.8773 (mtt) REVERT: A 873 TYR cc_start: 0.9550 (OUTLIER) cc_final: 0.9296 (m-10) REVERT: A 1050 MET cc_start: 0.9076 (ptp) cc_final: 0.8622 (ptm) REVERT: A 1138 TYR cc_start: 0.8306 (t80) cc_final: 0.7518 (t80) REVERT: B 118 LEU cc_start: 0.9412 (tt) cc_final: 0.8946 (mt) REVERT: B 737 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7458 (p0) REVERT: B 858 LEU cc_start: 0.9726 (mp) cc_final: 0.9455 (mp) REVERT: B 954 GLN cc_start: 0.9115 (mt0) cc_final: 0.8751 (mt0) REVERT: B 995 ARG cc_start: 0.9167 (mtt180) cc_final: 0.8957 (mmm-85) REVERT: B 1017 GLU cc_start: 0.8857 (tp30) cc_final: 0.8392 (tp30) REVERT: B 1029 MET cc_start: 0.9637 (tpp) cc_final: 0.9263 (tpt) REVERT: C 378 LYS cc_start: 0.9460 (mmtt) cc_final: 0.9174 (pttp) REVERT: C 489 TYR cc_start: 0.8478 (m-10) cc_final: 0.8021 (m-80) REVERT: C 671 CYS cc_start: 0.4683 (OUTLIER) cc_final: 0.4196 (p) REVERT: C 762 GLN cc_start: 0.9201 (tp40) cc_final: 0.8978 (tp40) REVERT: C 775 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8727 (t70) REVERT: C 780 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 1002 GLN cc_start: 0.9160 (tp40) cc_final: 0.8599 (tm-30) REVERT: C 1005 GLN cc_start: 0.9331 (tp40) cc_final: 0.9046 (tp40) REVERT: C 1029 MET cc_start: 0.9431 (tpp) cc_final: 0.9197 (tpp) outliers start: 42 outliers final: 16 residues processed: 155 average time/residue: 0.3312 time to fit residues: 84.9892 Evaluate side-chains 116 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 8.9990 chunk 86 optimal weight: 0.0970 chunk 232 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1036 GLN B 218 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN C1011 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24713 Z= 0.384 Angle : 0.682 11.647 33622 Z= 0.354 Chirality : 0.045 0.217 3831 Planarity : 0.004 0.064 4365 Dihedral : 5.694 40.702 3306 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 2.55 % Allowed : 14.69 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.14), residues: 3045 helix: 0.81 (0.20), residues: 646 sheet: -2.49 (0.20), residues: 566 loop : -3.18 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 886 HIS 0.009 0.001 HIS C 66 PHE 0.024 0.002 PHE B 329 TYR 0.015 0.001 TYR B 160 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 101 time to evaluate : 3.017 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 53 ASP cc_start: 0.8906 (m-30) cc_final: 0.8517 (m-30) REVERT: A 191 GLU cc_start: 0.6515 (pm20) cc_final: 0.5715 (pm20) REVERT: A 223 LEU cc_start: 0.8530 (mt) cc_final: 0.8299 (mt) REVERT: A 353 TRP cc_start: 0.8498 (p-90) cc_final: 0.8195 (p-90) REVERT: A 369 TYR cc_start: 0.7633 (m-10) cc_final: 0.7339 (m-10) REVERT: A 456 PHE cc_start: 0.8730 (m-80) cc_final: 0.8393 (m-80) REVERT: A 505 TYR cc_start: 0.9246 (m-80) cc_final: 0.9013 (m-80) REVERT: A 725 GLU cc_start: 0.8409 (tt0) cc_final: 0.8168 (tt0) REVERT: A 731 MET cc_start: 0.9176 (ptm) cc_final: 0.8844 (ptp) REVERT: A 855 PHE cc_start: 0.7615 (m-80) cc_final: 0.7181 (m-80) REVERT: A 869 MET cc_start: 0.8998 (mtt) cc_final: 0.8682 (mtt) REVERT: A 873 TYR cc_start: 0.9545 (OUTLIER) cc_final: 0.9315 (m-10) REVERT: A 1050 MET cc_start: 0.9146 (ptp) cc_final: 0.8799 (ptm) REVERT: A 1138 TYR cc_start: 0.8433 (t80) cc_final: 0.7598 (t80) REVERT: B 118 LEU cc_start: 0.9461 (tt) cc_final: 0.8951 (mt) REVERT: B 224 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: B 737 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7439 (p0) REVERT: B 756 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: B 858 LEU cc_start: 0.9763 (mp) cc_final: 0.9503 (mp) REVERT: B 954 GLN cc_start: 0.9140 (mt0) cc_final: 0.8774 (mt0) REVERT: B 995 ARG cc_start: 0.9208 (mtt180) cc_final: 0.8903 (mmm-85) REVERT: B 1029 MET cc_start: 0.9683 (tpp) cc_final: 0.9439 (tpp) REVERT: C 52 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8466 (pp30) REVERT: C 334 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.7892 (t0) REVERT: C 671 CYS cc_start: 0.4830 (OUTLIER) cc_final: 0.4453 (p) REVERT: C 759 PHE cc_start: 0.8632 (m-80) cc_final: 0.8102 (m-80) REVERT: C 762 GLN cc_start: 0.9268 (tp40) cc_final: 0.8944 (tp40) REVERT: C 777 ASN cc_start: 0.9246 (t0) cc_final: 0.8945 (t0) REVERT: C 780 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 1002 GLN cc_start: 0.9254 (tp40) cc_final: 0.8796 (tp-100) REVERT: C 1005 GLN cc_start: 0.9412 (tp40) cc_final: 0.9095 (tp40) outliers start: 69 outliers final: 45 residues processed: 165 average time/residue: 0.3448 time to fit residues: 94.1263 Evaluate side-chains 144 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 93 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 133 optimal weight: 30.0000 chunk 187 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 265 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 388 ASN A 690 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B1036 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24713 Z= 0.160 Angle : 0.577 11.102 33622 Z= 0.299 Chirality : 0.044 0.215 3831 Planarity : 0.004 0.066 4365 Dihedral : 5.175 40.857 3306 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.85 % Allowed : 15.91 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.15), residues: 3045 helix: 1.31 (0.21), residues: 670 sheet: -2.06 (0.21), residues: 567 loop : -2.87 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.008 0.001 HIS C 66 PHE 0.022 0.001 PHE B 329 TYR 0.018 0.001 TYR B 451 ARG 0.009 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 115 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7512 (m-10) cc_final: 0.7295 (m-10) REVERT: A 456 PHE cc_start: 0.9014 (m-80) cc_final: 0.8704 (m-80) REVERT: A 505 TYR cc_start: 0.9151 (m-80) cc_final: 0.8927 (m-80) REVERT: A 516 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: A 518 LEU cc_start: 0.8969 (tp) cc_final: 0.8741 (tt) REVERT: A 725 GLU cc_start: 0.8355 (tt0) cc_final: 0.8076 (tt0) REVERT: A 731 MET cc_start: 0.9131 (ptm) cc_final: 0.8820 (ptp) REVERT: A 855 PHE cc_start: 0.7744 (m-80) cc_final: 0.7305 (m-80) REVERT: A 869 MET cc_start: 0.8976 (mtt) cc_final: 0.8541 (mtp) REVERT: A 873 TYR cc_start: 0.9451 (OUTLIER) cc_final: 0.9247 (m-80) REVERT: A 1138 TYR cc_start: 0.8420 (t80) cc_final: 0.7556 (t80) REVERT: B 177 MET cc_start: 0.0507 (ttp) cc_final: 0.0264 (ttp) REVERT: B 726 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9156 (mt) REVERT: B 737 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7252 (p0) REVERT: B 762 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8652 (tm-30) REVERT: B 858 LEU cc_start: 0.9704 (mp) cc_final: 0.9407 (mp) REVERT: B 954 GLN cc_start: 0.9072 (mt0) cc_final: 0.8716 (mt0) REVERT: B 995 ARG cc_start: 0.9198 (mtt180) cc_final: 0.8854 (mmm-85) REVERT: B 1017 GLU cc_start: 0.8826 (tp30) cc_final: 0.8333 (tp30) REVERT: B 1029 MET cc_start: 0.9613 (tpp) cc_final: 0.9257 (tpt) REVERT: B 1041 ASP cc_start: 0.8063 (t70) cc_final: 0.7727 (t70) REVERT: C 334 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.7808 (t0) REVERT: C 729 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9206 (p) REVERT: C 777 ASN cc_start: 0.9070 (t0) cc_final: 0.8648 (t0) REVERT: C 780 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8141 (mp0) REVERT: C 900 MET cc_start: 0.8935 (mmt) cc_final: 0.8727 (mmm) REVERT: C 1002 GLN cc_start: 0.9109 (tp40) cc_final: 0.8428 (tm-30) outliers start: 77 outliers final: 46 residues processed: 186 average time/residue: 0.3335 time to fit residues: 103.5080 Evaluate side-chains 146 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 94 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24713 Z= 0.346 Angle : 0.636 11.976 33622 Z= 0.327 Chirality : 0.044 0.340 3831 Planarity : 0.004 0.066 4365 Dihedral : 5.243 39.274 3306 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 3.55 % Allowed : 16.51 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.15), residues: 3045 helix: 1.29 (0.21), residues: 668 sheet: -2.01 (0.21), residues: 549 loop : -2.86 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.005 0.001 HIS C 66 PHE 0.020 0.001 PHE B 329 TYR 0.013 0.001 TYR B 160 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 92 time to evaluate : 2.994 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 369 TYR cc_start: 0.7447 (m-10) cc_final: 0.7151 (m-10) REVERT: A 456 PHE cc_start: 0.9080 (m-80) cc_final: 0.8718 (m-80) REVERT: A 505 TYR cc_start: 0.9216 (m-80) cc_final: 0.9002 (m-80) REVERT: A 725 GLU cc_start: 0.8431 (tt0) cc_final: 0.8212 (tt0) REVERT: A 731 MET cc_start: 0.9189 (ptm) cc_final: 0.8822 (ptp) REVERT: A 855 PHE cc_start: 0.7830 (m-80) cc_final: 0.7424 (m-80) REVERT: A 869 MET cc_start: 0.9092 (mtt) cc_final: 0.8703 (mtp) REVERT: A 1138 TYR cc_start: 0.8446 (t80) cc_final: 0.7594 (t80) REVERT: B 118 LEU cc_start: 0.9419 (tt) cc_final: 0.8888 (mt) REVERT: B 737 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7247 (p0) REVERT: B 858 LEU cc_start: 0.9767 (mp) cc_final: 0.9486 (mp) REVERT: B 869 MET cc_start: 0.9215 (mtt) cc_final: 0.8662 (mpp) REVERT: B 954 GLN cc_start: 0.9128 (mt0) cc_final: 0.8762 (mt0) REVERT: B 995 ARG cc_start: 0.9218 (mtt180) cc_final: 0.8897 (mmm-85) REVERT: C 334 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.7818 (t0) REVERT: C 729 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9244 (p) REVERT: C 775 ASP cc_start: 0.8921 (t70) cc_final: 0.8721 (t70) REVERT: C 780 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8061 (mt-10) REVERT: C 1002 GLN cc_start: 0.9216 (tp40) cc_final: 0.8708 (tp-100) REVERT: C 1029 MET cc_start: 0.9498 (tpp) cc_final: 0.8862 (tpp) outliers start: 96 outliers final: 75 residues processed: 181 average time/residue: 0.3234 time to fit residues: 99.2317 Evaluate side-chains 167 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 89 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 246 optimal weight: 30.0000 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1036 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24713 Z= 0.181 Angle : 0.566 11.003 33622 Z= 0.290 Chirality : 0.043 0.208 3831 Planarity : 0.004 0.066 4365 Dihedral : 5.016 39.412 3306 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.18 % Allowed : 17.54 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 3045 helix: 1.56 (0.21), residues: 665 sheet: -1.79 (0.21), residues: 588 loop : -2.71 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 353 HIS 0.006 0.001 HIS C 66 PHE 0.018 0.001 PHE B 329 TYR 0.014 0.001 TYR B 160 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 105 time to evaluate : 2.853 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 456 PHE cc_start: 0.9076 (m-80) cc_final: 0.8714 (m-80) REVERT: A 505 TYR cc_start: 0.9192 (m-80) cc_final: 0.8987 (m-80) REVERT: A 725 GLU cc_start: 0.8315 (tt0) cc_final: 0.8042 (tt0) REVERT: A 731 MET cc_start: 0.9176 (ptm) cc_final: 0.8852 (ptp) REVERT: A 773 GLU cc_start: 0.8427 (tp30) cc_final: 0.8080 (tp30) REVERT: A 869 MET cc_start: 0.9084 (mtt) cc_final: 0.8667 (mtp) REVERT: A 1050 MET cc_start: 0.9088 (ptp) cc_final: 0.8820 (ptm) REVERT: A 1138 TYR cc_start: 0.8437 (t80) cc_final: 0.7567 (t80) REVERT: B 118 LEU cc_start: 0.9457 (tt) cc_final: 0.8989 (mt) REVERT: B 177 MET cc_start: -0.0926 (ttp) cc_final: -0.1361 (ttp) REVERT: B 740 MET cc_start: 0.8975 (tpp) cc_final: 0.8650 (tpp) REVERT: B 858 LEU cc_start: 0.9727 (mp) cc_final: 0.9451 (mp) REVERT: B 954 GLN cc_start: 0.9135 (mt0) cc_final: 0.8733 (mt0) REVERT: B 995 ARG cc_start: 0.9207 (mtt180) cc_final: 0.8851 (mmm-85) REVERT: B 1041 ASP cc_start: 0.8070 (t70) cc_final: 0.7738 (t70) REVERT: C 334 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.7808 (t0) REVERT: C 400 PHE cc_start: 0.9242 (p90) cc_final: 0.8814 (p90) REVERT: C 489 TYR cc_start: 0.8417 (m-10) cc_final: 0.7940 (m-80) REVERT: C 1002 GLN cc_start: 0.9170 (tp40) cc_final: 0.8632 (tp-100) outliers start: 86 outliers final: 65 residues processed: 184 average time/residue: 0.3196 time to fit residues: 99.6894 Evaluate side-chains 161 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 95 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 786 LYS 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 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 216 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 165 optimal weight: 0.0870 chunk 295 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 136 optimal weight: 30.0000 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24713 Z= 0.162 Angle : 0.554 10.926 33622 Z= 0.284 Chirality : 0.043 0.209 3831 Planarity : 0.004 0.067 4365 Dihedral : 4.824 38.309 3306 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.81 % Allowed : 17.91 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.15), residues: 3045 helix: 1.62 (0.21), residues: 665 sheet: -1.64 (0.21), residues: 588 loop : -2.59 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 353 HIS 0.005 0.001 HIS C 66 PHE 0.017 0.001 PHE B 329 TYR 0.024 0.001 TYR A 365 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 103 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9071 (mp0) cc_final: 0.8837 (mp0) REVERT: A 202 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8291 (mmmt) REVERT: A 223 LEU cc_start: 0.8035 (mt) cc_final: 0.7833 (mt) REVERT: A 456 PHE cc_start: 0.9081 (m-80) cc_final: 0.8721 (m-80) REVERT: A 725 GLU cc_start: 0.8311 (tt0) cc_final: 0.8033 (tt0) REVERT: A 737 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8062 (p0) REVERT: A 773 GLU cc_start: 0.8516 (tp30) cc_final: 0.7918 (tp30) REVERT: A 777 ASN cc_start: 0.8728 (m-40) cc_final: 0.8382 (m110) REVERT: A 855 PHE cc_start: 0.7859 (m-80) cc_final: 0.7621 (m-80) REVERT: A 869 MET cc_start: 0.8957 (mtt) cc_final: 0.8569 (mtp) REVERT: A 1050 MET cc_start: 0.9037 (ptp) cc_final: 0.8736 (ptm) REVERT: A 1138 TYR cc_start: 0.8450 (t80) cc_final: 0.7578 (t80) REVERT: B 118 LEU cc_start: 0.9449 (tt) cc_final: 0.8978 (mp) REVERT: B 177 MET cc_start: -0.0898 (ttp) cc_final: -0.1350 (ttp) REVERT: B 737 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6871 (p0) REVERT: B 740 MET cc_start: 0.8970 (tpp) cc_final: 0.8377 (tpp) REVERT: B 858 LEU cc_start: 0.9724 (mp) cc_final: 0.9459 (mp) REVERT: B 869 MET cc_start: 0.9140 (mtt) cc_final: 0.8667 (mpp) REVERT: B 954 GLN cc_start: 0.9102 (mt0) cc_final: 0.8694 (mt0) REVERT: B 995 ARG cc_start: 0.9205 (mtt180) cc_final: 0.8844 (mmm-85) REVERT: B 1041 ASP cc_start: 0.8031 (t70) cc_final: 0.7693 (t70) REVERT: C 298 GLU cc_start: 0.9481 (mm-30) cc_final: 0.8995 (mp0) REVERT: C 334 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.7785 (t0) REVERT: C 400 PHE cc_start: 0.9307 (p90) cc_final: 0.8944 (p90) REVERT: C 489 TYR cc_start: 0.8417 (m-10) cc_final: 0.7926 (m-80) REVERT: C 1002 GLN cc_start: 0.9160 (tp40) cc_final: 0.8612 (tp-100) outliers start: 76 outliers final: 63 residues processed: 177 average time/residue: 0.3171 time to fit residues: 94.7212 Evaluate side-chains 161 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 95 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LYS 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 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 232 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24713 Z= 0.161 Angle : 0.541 10.994 33622 Z= 0.278 Chirality : 0.042 0.208 3831 Planarity : 0.004 0.069 4365 Dihedral : 4.680 37.668 3306 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.03 % Allowed : 17.91 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 3045 helix: 1.72 (0.21), residues: 664 sheet: -1.59 (0.21), residues: 598 loop : -2.46 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 353 HIS 0.005 0.001 HIS C 66 PHE 0.019 0.001 PHE A 562 TYR 0.017 0.001 TYR A 365 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 106 time to evaluate : 2.809 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 132 GLU cc_start: 0.9024 (mp0) cc_final: 0.8817 (mp0) REVERT: A 202 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8303 (mmmt) REVERT: A 456 PHE cc_start: 0.9085 (m-80) cc_final: 0.8727 (m-80) REVERT: A 725 GLU cc_start: 0.8315 (tt0) cc_final: 0.8036 (tt0) REVERT: A 773 GLU cc_start: 0.8606 (tp30) cc_final: 0.7992 (tp30) REVERT: A 777 ASN cc_start: 0.8686 (m-40) cc_final: 0.8354 (m110) REVERT: A 869 MET cc_start: 0.8947 (mtt) cc_final: 0.8560 (mtp) REVERT: A 1050 MET cc_start: 0.9036 (ptp) cc_final: 0.8731 (ptm) REVERT: A 1138 TYR cc_start: 0.8448 (t80) cc_final: 0.7571 (t80) REVERT: B 177 MET cc_start: -0.0987 (ttp) cc_final: -0.1405 (ttp) REVERT: B 737 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6826 (p0) REVERT: B 740 MET cc_start: 0.8926 (tpp) cc_final: 0.8351 (tpp) REVERT: B 858 LEU cc_start: 0.9722 (mp) cc_final: 0.9458 (mp) REVERT: B 954 GLN cc_start: 0.9096 (mt0) cc_final: 0.8691 (mt0) REVERT: B 995 ARG cc_start: 0.9225 (mtt180) cc_final: 0.8857 (mmm-85) REVERT: B 1041 ASP cc_start: 0.8025 (t70) cc_final: 0.7675 (t70) REVERT: C 334 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8067 (t0) REVERT: C 400 PHE cc_start: 0.9268 (p90) cc_final: 0.8863 (p90) REVERT: C 489 TYR cc_start: 0.8135 (m-10) cc_final: 0.7712 (m-80) REVERT: C 900 MET cc_start: 0.9202 (mmt) cc_final: 0.8943 (mmm) REVERT: C 1002 GLN cc_start: 0.9118 (tp40) cc_final: 0.8579 (tp-100) REVERT: C 1029 MET cc_start: 0.9479 (tpp) cc_final: 0.8783 (tpp) outliers start: 82 outliers final: 62 residues processed: 183 average time/residue: 0.3233 time to fit residues: 99.9058 Evaluate side-chains 156 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 92 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LYS 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 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24713 Z= 0.212 Angle : 0.565 12.616 33622 Z= 0.291 Chirality : 0.043 0.208 3831 Planarity : 0.004 0.067 4365 Dihedral : 4.689 37.008 3306 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.81 % Allowed : 18.43 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 3045 helix: 1.77 (0.21), residues: 657 sheet: -1.60 (0.21), residues: 578 loop : -2.40 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 353 HIS 0.005 0.001 HIS C 66 PHE 0.014 0.001 PHE B 329 TYR 0.012 0.001 TYR A 365 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 92 time to evaluate : 2.959 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 132 GLU cc_start: 0.9028 (mp0) cc_final: 0.8827 (mp0) REVERT: A 456 PHE cc_start: 0.9091 (m-80) cc_final: 0.8735 (m-80) REVERT: A 725 GLU cc_start: 0.8278 (tt0) cc_final: 0.7995 (tt0) REVERT: A 773 GLU cc_start: 0.8633 (tp30) cc_final: 0.8022 (tp30) REVERT: A 777 ASN cc_start: 0.8750 (m-40) cc_final: 0.8408 (m110) REVERT: A 869 MET cc_start: 0.8966 (mtt) cc_final: 0.8620 (mtp) REVERT: A 1050 MET cc_start: 0.9078 (ptp) cc_final: 0.8763 (ptm) REVERT: A 1138 TYR cc_start: 0.8463 (t80) cc_final: 0.7594 (t80) REVERT: B 177 MET cc_start: -0.1037 (ttp) cc_final: -0.1436 (ttp) REVERT: B 737 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6817 (p0) REVERT: B 740 MET cc_start: 0.8951 (tpp) cc_final: 0.8397 (tpp) REVERT: B 858 LEU cc_start: 0.9744 (mp) cc_final: 0.9483 (mp) REVERT: B 954 GLN cc_start: 0.9108 (mt0) cc_final: 0.8704 (mt0) REVERT: B 995 ARG cc_start: 0.9240 (mtt180) cc_final: 0.8867 (mmm-85) REVERT: B 1041 ASP cc_start: 0.8077 (t70) cc_final: 0.7754 (t70) REVERT: C 334 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8015 (t0) REVERT: C 400 PHE cc_start: 0.9229 (p90) cc_final: 0.8844 (p90) REVERT: C 489 TYR cc_start: 0.8137 (m-10) cc_final: 0.7716 (m-80) REVERT: C 1002 GLN cc_start: 0.9188 (tp40) cc_final: 0.8647 (tp-100) REVERT: C 1029 MET cc_start: 0.9436 (tpp) cc_final: 0.8785 (tpp) outliers start: 76 outliers final: 69 residues processed: 162 average time/residue: 0.3094 time to fit residues: 85.3722 Evaluate side-chains 163 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 92 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LYS 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 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 0.0980 chunk 291 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 305 optimal weight: 7.9990 chunk 281 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24713 Z= 0.265 Angle : 0.592 12.054 33622 Z= 0.304 Chirality : 0.043 0.202 3831 Planarity : 0.004 0.066 4365 Dihedral : 4.816 38.745 3306 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.00 % Allowed : 18.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.15), residues: 3045 helix: 1.78 (0.21), residues: 650 sheet: -1.64 (0.21), residues: 595 loop : -2.39 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 353 HIS 0.004 0.001 HIS C 66 PHE 0.014 0.001 PHE B 329 TYR 0.013 0.001 TYR A 365 ARG 0.003 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 90 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8290 (mmmt) REVERT: A 223 LEU cc_start: 0.7981 (mp) cc_final: 0.7765 (mt) REVERT: A 456 PHE cc_start: 0.9096 (m-80) cc_final: 0.8743 (m-80) REVERT: A 725 GLU cc_start: 0.8317 (tt0) cc_final: 0.8030 (tt0) REVERT: A 731 MET cc_start: 0.9201 (ptm) cc_final: 0.8877 (ptp) REVERT: A 773 GLU cc_start: 0.8713 (tp30) cc_final: 0.8331 (tp30) REVERT: A 869 MET cc_start: 0.9061 (mtt) cc_final: 0.8670 (mtp) REVERT: A 1050 MET cc_start: 0.9130 (ptp) cc_final: 0.8808 (ptm) REVERT: A 1138 TYR cc_start: 0.8464 (t80) cc_final: 0.7604 (t80) REVERT: B 737 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7000 (p0) REVERT: B 740 MET cc_start: 0.8962 (tpp) cc_final: 0.8396 (tpp) REVERT: B 858 LEU cc_start: 0.9757 (mp) cc_final: 0.9497 (mp) REVERT: B 995 ARG cc_start: 0.9232 (mtt180) cc_final: 0.8859 (mmm-85) REVERT: B 1041 ASP cc_start: 0.8106 (t70) cc_final: 0.7885 (t70) REVERT: C 334 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8019 (t0) REVERT: C 489 TYR cc_start: 0.8425 (m-10) cc_final: 0.7936 (m-80) REVERT: C 1002 GLN cc_start: 0.9233 (tp40) cc_final: 0.8683 (tp-100) REVERT: C 1029 MET cc_start: 0.9515 (tpp) cc_final: 0.8876 (tpp) outliers start: 81 outliers final: 73 residues processed: 165 average time/residue: 0.3134 time to fit residues: 87.5842 Evaluate side-chains 160 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 85 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LYS 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 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 0.7980 chunk 259 optimal weight: 8.9990 chunk 74 optimal weight: 0.0770 chunk 224 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.083625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053110 restraints weight = 99235.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055123 restraints weight = 48225.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056489 restraints weight = 30580.128| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24713 Z= 0.198 Angle : 0.564 11.837 33622 Z= 0.290 Chirality : 0.043 0.203 3831 Planarity : 0.003 0.066 4365 Dihedral : 4.723 37.828 3306 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.81 % Allowed : 18.76 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.15), residues: 3045 helix: 1.81 (0.21), residues: 652 sheet: -1.59 (0.21), residues: 597 loop : -2.36 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 353 HIS 0.005 0.001 HIS C 66 PHE 0.014 0.001 PHE B 329 TYR 0.012 0.001 TYR A 365 ARG 0.005 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.33 seconds wall clock time: 71 minutes 47.36 seconds (4307.36 seconds total)