Starting phenix.real_space_refine on Sun Oct 12 12:04:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x5b_6705/10_2025/5x5b_6705.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x5b_6705/10_2025/5x5b_6705.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/cci-nas-00/data/ceres_data/5x5b_6705/10_2025/5x5b_6705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x5b_6705/10_2025/5x5b_6705.map" model { file = "/net/cci-nas-00/data/ceres_data/5x5b_6705/10_2025/5x5b_6705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x5b_6705/10_2025/5x5b_6705.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.007 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 131 5.16 5 C 15678 2.51 5 N 4062 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24541 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8085 Classifications: {'peptide': 1033} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 983} Chain breaks: 5 Chain: "B" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8228 Classifications: {'peptide': 1053} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Restraints were copied for chains: C Time building chain proxies: 11.15, per 1000 atoms: 0.45 Number of scatterers: 24541 At special positions: 0 Unit cell: (149.5, 136.5, 179.4, 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 131 16.00 O 4670 8.00 N 4062 7.00 C 15678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 953.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 45 sheets defined 22.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.861A pdb=" N LEU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.640A pdb=" N GLY A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.191A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.639A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.560A pdb=" N ASN A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 749 through 764 removed outlier: 3.672A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 868 through 873 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.082A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.555A pdb=" N SER A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 945 removed outlier: 3.546A pdb=" N GLY A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 965 removed outlier: 3.619A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 Processing helix chain 'A' and resid 975 through 1014 removed outlier: 3.610A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.573A pdb=" N CYS B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.536A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 removed outlier: 3.590A pdb=" N LEU B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.889A pdb=" N ASN B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.793A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.672A pdb=" N GLY B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.896A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 757 removed outlier: 3.837A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 765 Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 868 through 873 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.136A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 958 through 967 removed outlier: 3.590A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1014 removed outlier: 4.062A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 986 " --> pdb=" O ARG B 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.573A pdb=" N CYS C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.536A pdb=" N ASN C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.590A pdb=" N LEU C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.889A pdb=" N ASN C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 608 removed outlier: 3.793A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.672A pdb=" N GLY C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.896A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 757 removed outlier: 3.836A pdb=" N LEU C 749 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 765 Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 868 through 873 Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.137A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 919 Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 958 through 967 removed outlier: 3.590A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1014 removed outlier: 4.062A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 986 " --> pdb=" O ARG C 982 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.115A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 190 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.659A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.728A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 128 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 removed outlier: 5.437A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.681A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 526 removed outlier: 3.671A pdb=" N LEU A 571 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.401A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 652 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB1, first strand: chain 'A' and resid 693 through 700 removed outlier: 3.590A pdb=" N ILE A 696 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 706 through 710 Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 716 removed outlier: 4.202A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.436A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1071 through 1072 Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 34 removed outlier: 4.278A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.681A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.567A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 112 through 116 removed outlier: 4.722A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 141 removed outlier: 6.485A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AC3, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.440A pdb=" N ASN B 321 " --> pdb=" O VAL B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.555A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 384 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 570 through 572 removed outlier: 7.102A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC7, first strand: chain 'B' and resid 684 through 685 Processing sheet with id=AC8, first strand: chain 'B' and resid 695 through 697 removed outlier: 3.572A pdb=" N ILE B 696 " --> pdb=" O ARG B1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.283A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1058 through 1059 removed outlier: 4.200A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN B1088 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B1093 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1071 through 1072 Processing sheet with id=AD4, first strand: chain 'C' and resid 31 through 34 removed outlier: 4.278A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS C 180 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.681A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.567A pdb=" N GLY C 104 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 112 through 116 removed outlier: 4.722A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 6.485A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AE1, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.439A pdb=" N ASN C 321 " --> pdb=" O VAL C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.556A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 384 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 651 Processing sheet with id=AE5, first strand: chain 'C' and resid 695 through 697 removed outlier: 3.573A pdb=" N ILE C 696 " --> pdb=" O ARG C1055 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 704 through 710 Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.282A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1058 through 1059 removed outlier: 4.199A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C1083 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN C1088 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER C1093 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1071 through 1072 746 hydrogen bonds defined for protein. 2082 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: 5.42 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7807 1.34 - 1.46: 5407 1.46 - 1.58: 11736 1.58 - 1.69: 0 1.69 - 1.81: 179 Bond restraints: 25129 Sorted by residual: bond pdb=" C LEU A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.334 1.242 0.092 2.34e-02 1.83e+03 1.55e+01 bond pdb=" C ASP A 790 " pdb=" N PRO A 791 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C ASP C 790 " pdb=" N PRO C 791 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.336 1.381 -0.046 1.23e-02 6.61e+03 1.38e+01 bond pdb=" C LYS B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.337 1.379 -0.041 1.24e-02 6.50e+03 1.12e+01 ... (remaining 25124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 33415 3.16 - 6.32: 671 6.32 - 9.48: 80 9.48 - 12.64: 14 12.64 - 15.80: 11 Bond angle restraints: 34191 Sorted by residual: angle pdb=" N SER A 303 " pdb=" CA SER A 303 " pdb=" C SER A 303 " ideal model delta sigma weight residual 111.04 126.16 -15.12 1.55e+00 4.16e-01 9.51e+01 angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 110.91 120.02 -9.11 1.17e+00 7.31e-01 6.06e+01 angle pdb=" N VAL A 969 " pdb=" CA VAL A 969 " pdb=" C VAL A 969 " ideal model delta sigma weight residual 113.71 107.06 6.65 9.50e-01 1.11e+00 4.90e+01 angle pdb=" N PHE B 305 " pdb=" CA PHE B 305 " pdb=" C PHE B 305 " ideal model delta sigma weight residual 108.76 119.74 -10.98 1.58e+00 4.01e-01 4.83e+01 angle pdb=" N PHE C 305 " pdb=" CA PHE C 305 " pdb=" C PHE C 305 " ideal model delta sigma weight residual 108.76 119.67 -10.91 1.58e+00 4.01e-01 4.77e+01 ... (remaining 34186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 14158 16.46 - 32.91: 566 32.91 - 49.37: 119 49.37 - 65.82: 15 65.82 - 82.28: 25 Dihedral angle restraints: 14883 sinusoidal: 5721 harmonic: 9162 Sorted by residual: dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -165.24 79.24 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS B 524 " pdb=" SG CYS B 524 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual -86.00 -159.32 73.32 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CB CYS C 524 " pdb=" SG CYS C 524 " pdb=" SG CYS C 576 " pdb=" CB CYS C 576 " ideal model delta sinusoidal sigma weight residual -86.00 -159.29 73.29 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 14880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3454 0.095 - 0.190: 366 0.190 - 0.285: 26 0.285 - 0.380: 10 0.380 - 0.475: 2 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CB ILE A1097 " pdb=" CA ILE A1097 " pdb=" CG1 ILE A1097 " pdb=" CG2 ILE A1097 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB ILE A 787 " pdb=" CA ILE A 787 " pdb=" CG1 ILE A 787 " pdb=" CG2 ILE A 787 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 3855 not shown) Planarity restraints: 4427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 616 " -0.058 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 617 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 616 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO C 617 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 617 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 617 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 469 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO C 470 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " -0.034 5.00e-02 4.00e+02 ... (remaining 4424 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5162 2.77 - 3.30: 22639 3.30 - 3.84: 41136 3.84 - 4.37: 48496 4.37 - 4.90: 81134 Nonbonded interactions: 198567 Sorted by model distance: nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 41 " pdb=" O LEU B 58 " model vdw 2.242 3.040 nonbonded pdb=" O GLU A 647 " pdb=" OH TYR A 677 " model vdw 2.247 3.040 nonbonded pdb=" O ASP A 564 " pdb=" N SER A 568 " model vdw 2.255 3.120 nonbonded pdb=" O GLU B 647 " pdb=" OH TYR B 677 " model vdw 2.261 3.040 ... (remaining 198562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 809 or resid 831 through 1104)) selection = (chain 'B' and (resid 18 through 315 or resid 322 through 502 or resid 518 throu \ gh 1104)) selection = (chain 'C' and (resid 18 through 315 or resid 322 through 502 or resid 518 throu \ gh 1104)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.090 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.006 0.092 25147 Z= 0.302 Angle : 1.133 15.798 34227 Z= 0.646 Chirality : 0.060 0.475 3858 Planarity : 0.007 0.087 4427 Dihedral : 10.423 82.277 8933 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.96 % Favored : 88.01 % Rotamer: Outliers : 0.66 % Allowed : 5.06 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.67 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.94 (0.12), residues: 3111 helix: -3.82 (0.10), residues: 630 sheet: -2.74 (0.20), residues: 493 loop : -3.42 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1089 TYR 0.034 0.003 TYR A 481 PHE 0.044 0.003 PHE B1077 TRP 0.031 0.003 TRP B 423 HIS 0.014 0.003 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00626 (25129) covalent geometry : angle 1.13269 (34191) SS BOND : bond 0.00801 ( 18) SS BOND : angle 1.63850 ( 36) hydrogen bonds : bond 0.28267 ( 746) hydrogen bonds : angle 11.05603 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 680 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9193 (mm) cc_final: 0.8620 (tt) REVERT: A 74 HIS cc_start: 0.7040 (m-70) cc_final: 0.6621 (t-90) REVERT: A 190 LYS cc_start: 0.8516 (tttp) cc_final: 0.8159 (tptp) REVERT: A 232 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.6951 (ttt180) REVERT: A 294 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8597 (tm-30) REVERT: A 524 CYS cc_start: 0.8600 (m) cc_final: 0.7339 (m) REVERT: A 554 ASP cc_start: 0.8953 (t70) cc_final: 0.8686 (t70) REVERT: A 563 ARG cc_start: 0.6878 (mtp180) cc_final: 0.6413 (tpp80) REVERT: A 582 SER cc_start: 0.9085 (m) cc_final: 0.8848 (t) REVERT: A 730 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9003 (mp0) REVERT: A 733 ASN cc_start: 0.9245 (t160) cc_final: 0.8935 (p0) REVERT: A 742 CYS cc_start: 0.8559 (t) cc_final: 0.8271 (p) REVERT: A 747 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8513 (ttp-170) REVERT: A 755 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 768 LYS cc_start: 0.9077 (tttp) cc_final: 0.8598 (tppt) REVERT: A 849 ASP cc_start: 0.9372 (m-30) cc_final: 0.9145 (p0) REVERT: A 850 ASP cc_start: 0.9383 (m-30) cc_final: 0.9068 (t0) REVERT: A 936 GLN cc_start: 0.8991 (tt0) cc_final: 0.8704 (pt0) REVERT: A 939 GLN cc_start: 0.8909 (tm130) cc_final: 0.8663 (tm-30) REVERT: A 955 ILE cc_start: 0.9091 (mm) cc_final: 0.8890 (mm) REVERT: A 963 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8971 (mm) REVERT: A 967 ASP cc_start: 0.8839 (m-30) cc_final: 0.8563 (t0) REVERT: A 972 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8974 (pp20) REVERT: A 1049 TYR cc_start: 0.8495 (t80) cc_final: 0.8271 (t80) REVERT: B 89 PHE cc_start: 0.8659 (t80) cc_final: 0.8443 (t80) REVERT: B 179 PHE cc_start: 0.6022 (m-10) cc_final: 0.5543 (m-80) REVERT: B 197 TYR cc_start: 0.6285 (m-10) cc_final: 0.6070 (m-10) REVERT: B 214 ASN cc_start: 0.6662 (t0) cc_final: 0.6069 (p0) REVERT: B 231 PHE cc_start: 0.7739 (p90) cc_final: 0.7503 (p90) REVERT: B 256 TYR cc_start: 0.7432 (m-80) cc_final: 0.6915 (m-10) REVERT: B 261 THR cc_start: 0.8680 (m) cc_final: 0.8087 (p) REVERT: B 289 SER cc_start: 0.9209 (m) cc_final: 0.8999 (p) REVERT: B 305 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: B 322 LEU cc_start: 0.7926 (pt) cc_final: 0.7191 (tt) REVERT: B 389 VAL cc_start: 0.8487 (m) cc_final: 0.8272 (p) REVERT: B 394 VAL cc_start: 0.8604 (t) cc_final: 0.8353 (p) REVERT: B 407 ASP cc_start: 0.6948 (t70) cc_final: 0.6600 (t70) REVERT: B 447 LYS cc_start: 0.8691 (mttt) cc_final: 0.8039 (mmmt) REVERT: B 522 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8403 (t0) REVERT: B 675 VAL cc_start: 0.8982 (t) cc_final: 0.8706 (p) REVERT: B 721 ASN cc_start: 0.9380 (t160) cc_final: 0.8908 (m-40) REVERT: B 722 MET cc_start: 0.9409 (tpt) cc_final: 0.9207 (tpp) REVERT: B 758 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8697 (tmt170) REVERT: B 768 LYS cc_start: 0.8861 (tptt) cc_final: 0.8381 (mtmm) REVERT: B 770 MET cc_start: 0.8568 (mmp) cc_final: 0.8054 (mpp) REVERT: B 787 ILE cc_start: 0.9172 (tt) cc_final: 0.8854 (tt) REVERT: B 882 MET cc_start: 0.8896 (mmm) cc_final: 0.8357 (mmt) REVERT: B 925 THR cc_start: 0.8019 (m) cc_final: 0.7716 (p) REVERT: B 942 ASN cc_start: 0.9175 (t0) cc_final: 0.8963 (m-40) REVERT: B 951 ASN cc_start: 0.8077 (t0) cc_final: 0.7753 (t0) REVERT: B 987 GLN cc_start: 0.8640 (tp40) cc_final: 0.8328 (tp40) REVERT: B 999 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9029 (tt0) REVERT: B 1022 VAL cc_start: 0.8990 (m) cc_final: 0.8766 (m) REVERT: B 1027 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7468 (tptp) REVERT: B 1029 TYR cc_start: 0.8834 (m-80) cc_final: 0.8164 (m-80) REVERT: B 1055 ARG cc_start: 0.9008 (mmm160) cc_final: 0.8674 (mmm-85) REVERT: B 1066 GLU cc_start: 0.9011 (tt0) cc_final: 0.8767 (pm20) REVERT: B 1090 ASN cc_start: 0.9070 (m-40) cc_final: 0.8684 (m-40) REVERT: C 56 GLN cc_start: 0.9068 (tt0) cc_final: 0.8614 (pp30) REVERT: C 191 ASP cc_start: 0.8760 (m-30) cc_final: 0.8543 (p0) REVERT: C 214 ASN cc_start: 0.7781 (t0) cc_final: 0.7527 (m-40) REVERT: C 268 GLU cc_start: 0.9296 (tt0) cc_final: 0.9046 (pp20) REVERT: C 278 CYS cc_start: 0.8677 (t) cc_final: 0.8036 (m) REVERT: C 387 PHE cc_start: 0.8294 (p90) cc_final: 0.7910 (p90) REVERT: C 457 ASN cc_start: 0.8166 (t0) cc_final: 0.7741 (m-40) REVERT: C 647 GLU cc_start: 0.7552 (tt0) cc_final: 0.7329 (pm20) REVERT: C 745 LEU cc_start: 0.9308 (tm) cc_final: 0.9066 (mt) REVERT: C 776 LEU cc_start: 0.9188 (mt) cc_final: 0.8975 (tp) REVERT: C 796 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8476 (ttpp) REVERT: C 840 LEU cc_start: 0.9476 (mm) cc_final: 0.9023 (mm) REVERT: C 868 TRP cc_start: 0.8285 (m100) cc_final: 0.7120 (t60) REVERT: C 956 SER cc_start: 0.9266 (t) cc_final: 0.8875 (m) REVERT: C 987 GLN cc_start: 0.8916 (tp40) cc_final: 0.8511 (tt0) REVERT: C 999 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8820 (tm-30) outliers start: 18 outliers final: 5 residues processed: 695 average time/residue: 0.1861 time to fit residues: 197.3541 Evaluate side-chains 382 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 374 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 920 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.0070 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 135 ASN A 201 GLN A 269 ASN A 409 ASN A 522 ASN A 528 ASN A 614 GLN A 733 ASN A 746 ASN A 835 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN A 915 GLN A 942 ASN B 96 ASN B 129 ASN B 522 ASN B 528 ASN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN B 550 GLN B 599 GLN B 611 HIS B 641 HIS B 661 HIS B 721 ASN B 783 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B 917 GLN B 947 GLN B1036 GLN B1065 HIS C 96 ASN C 201 GLN C 227 ASN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 ASN C 599 GLN C 611 HIS C 661 HIS C 721 ASN C 766 GLN C 783 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1065 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.145106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.115910 restraints weight = 59461.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114666 restraints weight = 42665.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.115576 restraints weight = 31875.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115957 restraints weight = 25243.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116111 restraints weight = 22911.742| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 25147 Z= 0.167 Angle : 0.727 11.762 34227 Z= 0.380 Chirality : 0.047 0.223 3858 Planarity : 0.005 0.083 4427 Dihedral : 7.130 53.501 3388 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.08 % Allowed : 10.61 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.67 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.13), residues: 3111 helix: -1.40 (0.17), residues: 662 sheet: -2.09 (0.21), residues: 554 loop : -3.06 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 306 TYR 0.026 0.002 TYR C 598 PHE 0.036 0.002 PHE A 909 TRP 0.025 0.002 TRP B 423 HIS 0.004 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00369 (25129) covalent geometry : angle 0.72520 (34191) SS BOND : bond 0.00393 ( 18) SS BOND : angle 1.71168 ( 36) hydrogen bonds : bond 0.04762 ( 746) hydrogen bonds : angle 6.82465 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 430 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9213 (mm) cc_final: 0.8894 (tt) REVERT: A 200 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5439 (t80) REVERT: A 955 ILE cc_start: 0.8236 (mm) cc_final: 0.7972 (mm) REVERT: A 963 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8219 (mt) REVERT: A 1021 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8249 (ptm-80) REVERT: B 305 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: B 322 LEU cc_start: 0.7361 (pt) cc_final: 0.6498 (tt) REVERT: B 525 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 582 SER cc_start: 0.9086 (m) cc_final: 0.8202 (p) REVERT: B 598 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: B 1027 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7770 (tptp) REVERT: C 323 CYS cc_start: 0.5213 (OUTLIER) cc_final: 0.4687 (t) REVERT: C 417 MET cc_start: 0.7224 (ptt) cc_final: 0.6676 (ppp) REVERT: C 449 ARG cc_start: 0.4668 (mtm180) cc_final: 0.4416 (mtm180) REVERT: C 457 ASN cc_start: 0.7037 (t0) cc_final: 0.6200 (m-40) REVERT: C 559 THR cc_start: 0.8579 (m) cc_final: 0.8234 (t) REVERT: C 886 TYR cc_start: 0.7586 (t80) cc_final: 0.7159 (t80) REVERT: C 956 SER cc_start: 0.9008 (t) cc_final: 0.8265 (m) REVERT: C 1102 THR cc_start: 0.8381 (p) cc_final: 0.8174 (t) outliers start: 84 outliers final: 44 residues processed: 490 average time/residue: 0.1661 time to fit residues: 129.5970 Evaluate side-chains 357 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 408 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 947 GLN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 246 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A 993 GLN B 70 HIS ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 181 HIS B 201 GLN B 473 ASN B 526 ASN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 766 GLN B 835 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN B1101 ASN C 108 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 GLN ** C 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.137252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.105303 restraints weight = 59890.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105635 restraints weight = 44277.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106224 restraints weight = 29368.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106640 restraints weight = 24946.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106827 restraints weight = 22976.359| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 25147 Z= 0.323 Angle : 0.825 16.243 34227 Z= 0.433 Chirality : 0.049 0.242 3858 Planarity : 0.006 0.090 4427 Dihedral : 7.222 59.591 3381 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 4.92 % Allowed : 12.07 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.67 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.14), residues: 3111 helix: -0.72 (0.19), residues: 660 sheet: -2.04 (0.21), residues: 526 loop : -3.00 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1021 TYR 0.030 0.002 TYR B 442 PHE 0.026 0.002 PHE A 551 TRP 0.013 0.002 TRP A 619 HIS 0.007 0.002 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00718 (25129) covalent geometry : angle 0.82281 (34191) SS BOND : bond 0.00713 ( 18) SS BOND : angle 2.12366 ( 36) hydrogen bonds : bond 0.04895 ( 746) hydrogen bonds : angle 6.66063 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 322 time to evaluate : 0.892 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 54 LEU cc_start: 0.9270 (mm) cc_final: 0.8896 (tt) REVERT: A 151 MET cc_start: 0.5789 (mpp) cc_final: 0.5241 (ptp) REVERT: A 200 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.5213 (t80) REVERT: A 222 LEU cc_start: 0.8525 (mt) cc_final: 0.8123 (mt) REVERT: A 598 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: A 741 PHE cc_start: 0.7763 (m-10) cc_final: 0.7298 (m-10) REVERT: A 955 ILE cc_start: 0.8382 (mm) cc_final: 0.8180 (mm) REVERT: A 963 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8196 (mm) REVERT: A 1074 GLU cc_start: 0.7460 (tp30) cc_final: 0.7189 (tp30) REVERT: A 1086 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8554 (pp) REVERT: B 44 ASP cc_start: 0.3921 (p0) cc_final: 0.3467 (p0) REVERT: B 305 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: B 582 SER cc_start: 0.9055 (m) cc_final: 0.8340 (p) REVERT: B 598 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: B 745 LEU cc_start: 0.9242 (tp) cc_final: 0.9041 (tp) REVERT: B 755 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: B 846 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8948 (tt) REVERT: B 850 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7836 (t0) REVERT: B 851 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7815 (mtp) REVERT: B 1027 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8118 (tptp) REVERT: C 37 MET cc_start: 0.8176 (mmm) cc_final: 0.7891 (mmm) REVERT: C 214 ASN cc_start: 0.6428 (t0) cc_final: 0.6193 (m-40) REVERT: C 345 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7172 (mm) REVERT: C 396 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7239 (mp10) REVERT: C 417 MET cc_start: 0.7268 (ptt) cc_final: 0.6608 (ppp) REVERT: C 713 MET cc_start: 0.8564 (ptm) cc_final: 0.8322 (ptp) REVERT: C 772 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7994 (mppt) REVERT: C 956 SER cc_start: 0.9142 (t) cc_final: 0.8533 (m) REVERT: C 957 SER cc_start: 0.9088 (p) cc_final: 0.8794 (p) REVERT: C 1088 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7833 (pm20) outliers start: 134 outliers final: 83 residues processed: 425 average time/residue: 0.1616 time to fit residues: 110.0441 Evaluate side-chains 361 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 265 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 408 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 947 GLN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 550 GLN ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN B 877 GLN B 883 GLN B 947 GLN C 201 GLN C 550 GLN C 614 GLN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 GLN ** C 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.139871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110671 restraints weight = 59125.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109560 restraints weight = 42889.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.110413 restraints weight = 33625.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.110701 restraints weight = 26833.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110962 restraints weight = 24458.989| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25147 Z= 0.170 Angle : 0.685 12.384 34227 Z= 0.356 Chirality : 0.046 0.213 3858 Planarity : 0.005 0.088 4427 Dihedral : 6.723 58.403 3381 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.59 % Allowed : 14.35 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.14), residues: 3111 helix: -0.03 (0.20), residues: 649 sheet: -1.80 (0.22), residues: 514 loop : -2.80 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 306 TYR 0.023 0.002 TYR C 598 PHE 0.023 0.002 PHE A 909 TRP 0.023 0.001 TRP B 868 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00374 (25129) covalent geometry : angle 0.68245 (34191) SS BOND : bond 0.00360 ( 18) SS BOND : angle 1.84696 ( 36) hydrogen bonds : bond 0.04064 ( 746) hydrogen bonds : angle 6.15935 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 322 time to evaluate : 1.017 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: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9297 (mm) cc_final: 0.8676 (tp) REVERT: A 151 MET cc_start: 0.5804 (mpp) cc_final: 0.4865 (ptm) REVERT: A 222 LEU cc_start: 0.8381 (mt) cc_final: 0.8057 (mt) REVERT: A 262 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7928 (t80) REVERT: A 598 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.5865 (m-80) REVERT: A 955 ILE cc_start: 0.8226 (mm) cc_final: 0.7994 (mm) REVERT: A 1021 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8031 (ptm-80) REVERT: A 1086 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8385 (pp) REVERT: B 254 VAL cc_start: 0.8495 (t) cc_final: 0.8232 (p) REVERT: B 256 TYR cc_start: 0.6904 (m-10) cc_final: 0.6544 (m-80) REVERT: B 305 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: B 582 SER cc_start: 0.9038 (m) cc_final: 0.8188 (p) REVERT: B 598 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: B 647 GLU cc_start: 0.6793 (tp30) cc_final: 0.6473 (tp30) REVERT: B 677 TYR cc_start: 0.8648 (p90) cc_final: 0.7766 (p90) REVERT: B 755 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7375 (pt0) REVERT: B 846 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8722 (tt) REVERT: B 855 TYR cc_start: 0.8785 (m-80) cc_final: 0.8321 (m-80) REVERT: B 882 MET cc_start: 0.7992 (mmm) cc_final: 0.7675 (mmt) REVERT: B 886 TYR cc_start: 0.7879 (t80) cc_final: 0.7487 (t80) REVERT: C 37 MET cc_start: 0.7986 (mmm) cc_final: 0.7624 (mmm) REVERT: C 214 ASN cc_start: 0.6409 (t0) cc_final: 0.6190 (m-40) REVERT: C 263 MET cc_start: 0.8476 (ttt) cc_final: 0.8187 (ttt) REVERT: C 329 PHE cc_start: 0.8086 (m-80) cc_final: 0.7871 (m-10) REVERT: C 396 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7268 (mp10) REVERT: C 417 MET cc_start: 0.7050 (ptt) cc_final: 0.6700 (ppp) REVERT: C 481 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.5442 (t80) REVERT: C 681 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8763 (mm) REVERT: C 770 MET cc_start: 0.7958 (mmm) cc_final: 0.7458 (mmm) REVERT: C 772 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7742 (mppt) REVERT: C 849 ASP cc_start: 0.7958 (p0) cc_final: 0.7693 (p0) REVERT: C 956 SER cc_start: 0.9118 (t) cc_final: 0.8410 (m) outliers start: 125 outliers final: 73 residues processed: 414 average time/residue: 0.1642 time to fit residues: 109.9688 Evaluate side-chains 356 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 272 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1097 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 304 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 232 optimal weight: 0.5980 chunk 229 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 243 optimal weight: 0.0270 chunk 181 optimal weight: 5.9990 overall best weight: 2.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN B 614 GLN B 947 GLN C 381 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 GLN ** C 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN C1101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.139506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110437 restraints weight = 58896.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109578 restraints weight = 42700.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110070 restraints weight = 35106.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110645 restraints weight = 25974.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110802 restraints weight = 22976.124| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25147 Z= 0.179 Angle : 0.676 12.450 34227 Z= 0.349 Chirality : 0.046 0.248 3858 Planarity : 0.005 0.091 4427 Dihedral : 6.463 59.081 3379 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 4.99 % Allowed : 15.23 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.14), residues: 3111 helix: 0.19 (0.20), residues: 650 sheet: -1.63 (0.22), residues: 525 loop : -2.70 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 315 TYR 0.023 0.002 TYR C 598 PHE 0.027 0.002 PHE B 89 TRP 0.014 0.001 TRP B 868 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00399 (25129) covalent geometry : angle 0.67290 (34191) SS BOND : bond 0.00310 ( 18) SS BOND : angle 2.00203 ( 36) hydrogen bonds : bond 0.04003 ( 746) hydrogen bonds : angle 5.98749 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 308 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7366 (tpp) cc_final: 0.6593 (tpp) REVERT: A 54 LEU cc_start: 0.9279 (mm) cc_final: 0.8844 (tt) REVERT: A 151 MET cc_start: 0.5543 (mpp) cc_final: 0.4989 (ptm) REVERT: A 262 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8100 (t80) REVERT: A 598 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: A 1021 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8049 (ptm-80) REVERT: A 1032 MET cc_start: 0.7865 (ptm) cc_final: 0.7665 (ptp) REVERT: A 1086 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8278 (pp) REVERT: B 58 LEU cc_start: 0.8461 (mt) cc_final: 0.8147 (mt) REVERT: B 254 VAL cc_start: 0.8483 (t) cc_final: 0.8239 (p) REVERT: B 256 TYR cc_start: 0.6881 (m-10) cc_final: 0.6528 (m-80) REVERT: B 305 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6760 (m-80) REVERT: B 582 SER cc_start: 0.9089 (m) cc_final: 0.8257 (p) REVERT: B 598 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6720 (m-80) REVERT: B 647 GLU cc_start: 0.6936 (tp30) cc_final: 0.6520 (tp30) REVERT: B 677 TYR cc_start: 0.8744 (p90) cc_final: 0.7891 (p90) REVERT: B 855 TYR cc_start: 0.8794 (m-80) cc_final: 0.8176 (m-80) REVERT: B 859 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8872 (mm) REVERT: B 882 MET cc_start: 0.8054 (mmm) cc_final: 0.7705 (mmt) REVERT: B 948 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8483 (tt) REVERT: C 37 MET cc_start: 0.8009 (mmm) cc_final: 0.7684 (mmm) REVERT: C 214 ASN cc_start: 0.6482 (t0) cc_final: 0.6235 (m-40) REVERT: C 574 SER cc_start: 0.9329 (m) cc_final: 0.9049 (p) REVERT: C 598 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: C 681 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8771 (mm) REVERT: C 707 GLU cc_start: 0.7875 (tt0) cc_final: 0.7374 (pt0) REVERT: C 772 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7710 (mppt) REVERT: C 849 ASP cc_start: 0.8016 (p0) cc_final: 0.7768 (p0) REVERT: C 905 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8935 (mt) REVERT: C 956 SER cc_start: 0.9220 (t) cc_final: 0.8515 (m) outliers start: 136 outliers final: 90 residues processed: 411 average time/residue: 0.1500 time to fit residues: 101.2287 Evaluate side-chains 378 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 276 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 165 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 288 optimal weight: 0.7980 chunk 296 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN C 473 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.137379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.105802 restraints weight = 59252.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.106349 restraints weight = 41939.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.107098 restraints weight = 27482.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107435 restraints weight = 24491.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107516 restraints weight = 22441.198| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25147 Z= 0.223 Angle : 0.708 13.334 34227 Z= 0.364 Chirality : 0.047 0.238 3858 Planarity : 0.005 0.091 4427 Dihedral : 6.492 57.277 3379 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 5.10 % Allowed : 15.56 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.14), residues: 3111 helix: 0.29 (0.21), residues: 643 sheet: -1.53 (0.22), residues: 523 loop : -2.65 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 306 TYR 0.028 0.002 TYR B 53 PHE 0.027 0.002 PHE B 185 TRP 0.012 0.001 TRP B 101 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00495 (25129) covalent geometry : angle 0.70541 (34191) SS BOND : bond 0.00344 ( 18) SS BOND : angle 2.05752 ( 36) hydrogen bonds : bond 0.04095 ( 746) hydrogen bonds : angle 5.99484 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 298 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7426 (tpp) cc_final: 0.6571 (tpp) REVERT: A 54 LEU cc_start: 0.9288 (mm) cc_final: 0.8841 (tt) REVERT: A 151 MET cc_start: 0.5404 (mpp) cc_final: 0.4728 (ptm) REVERT: A 200 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.5396 (t80) REVERT: A 262 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8273 (t80) REVERT: A 524 CYS cc_start: 0.2079 (m) cc_final: 0.0797 (m) REVERT: A 598 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: A 1021 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7345 (ptp90) REVERT: A 1086 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8408 (pp) REVERT: B 305 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.6918 (m-80) REVERT: B 532 LEU cc_start: 0.7866 (mt) cc_final: 0.7602 (mm) REVERT: B 582 SER cc_start: 0.9124 (m) cc_final: 0.8312 (p) REVERT: B 647 GLU cc_start: 0.7167 (tp30) cc_final: 0.6736 (tp30) REVERT: B 677 TYR cc_start: 0.8744 (p90) cc_final: 0.7816 (p90) REVERT: B 747 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7394 (ttm-80) REVERT: B 850 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7764 (t0) REVERT: B 855 TYR cc_start: 0.8915 (m-80) cc_final: 0.8334 (m-80) REVERT: B 859 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8865 (mm) REVERT: B 882 MET cc_start: 0.8228 (mmm) cc_final: 0.7954 (mmt) REVERT: C 37 MET cc_start: 0.8200 (mmm) cc_final: 0.7841 (mmm) REVERT: C 214 ASN cc_start: 0.6600 (t0) cc_final: 0.6320 (m-40) REVERT: C 379 PHE cc_start: 0.7264 (m-80) cc_final: 0.6711 (m-80) REVERT: C 598 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: C 707 GLU cc_start: 0.8009 (tt0) cc_final: 0.7419 (pt0) REVERT: C 772 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7675 (mppt) REVERT: C 837 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: C 905 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9066 (mt) REVERT: C 956 SER cc_start: 0.9297 (t) cc_final: 0.8586 (m) outliers start: 139 outliers final: 96 residues processed: 405 average time/residue: 0.1513 time to fit residues: 100.7215 Evaluate side-chains 390 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 281 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1097 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 109 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 177 optimal weight: 0.0370 chunk 67 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 409 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 ASN ** 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 = 0.4074 r_free = 0.4074 target = 0.136178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107506 restraints weight = 58773.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106030 restraints weight = 42958.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.106977 restraints weight = 34140.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107320 restraints weight = 26579.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107613 restraints weight = 24024.973| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 25147 Z= 0.246 Angle : 0.726 14.292 34227 Z= 0.375 Chirality : 0.047 0.209 3858 Planarity : 0.005 0.093 4427 Dihedral : 6.574 58.061 3379 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 4.92 % Allowed : 16.18 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.14), residues: 3111 helix: 0.25 (0.21), residues: 642 sheet: -1.54 (0.22), residues: 538 loop : -2.66 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 306 TYR 0.024 0.002 TYR A1049 PHE 0.021 0.002 PHE B 952 TRP 0.012 0.002 TRP B 101 HIS 0.006 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00551 (25129) covalent geometry : angle 0.72380 (34191) SS BOND : bond 0.00367 ( 18) SS BOND : angle 1.81168 ( 36) hydrogen bonds : bond 0.04162 ( 746) hydrogen bonds : angle 6.05873 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 290 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7505 (tpp) cc_final: 0.6822 (tpp) REVERT: A 151 MET cc_start: 0.5802 (mpp) cc_final: 0.5140 (ptm) REVERT: A 968 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7329 (tmtt) REVERT: A 1086 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8411 (pp) REVERT: B 89 PHE cc_start: 0.8405 (t80) cc_final: 0.8172 (t80) REVERT: B 163 TYR cc_start: 0.6171 (t80) cc_final: 0.5809 (t80) REVERT: B 187 PHE cc_start: 0.6707 (m-10) cc_final: 0.6438 (m-10) REVERT: B 256 TYR cc_start: 0.7182 (m-80) cc_final: 0.6927 (m-80) REVERT: B 305 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: B 451 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: B 677 TYR cc_start: 0.8726 (p90) cc_final: 0.7800 (p90) REVERT: B 747 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7333 (ttm-80) REVERT: B 859 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.8938 (mm) REVERT: C 37 MET cc_start: 0.8187 (mmm) cc_final: 0.7833 (mmm) REVERT: C 214 ASN cc_start: 0.6785 (t0) cc_final: 0.6548 (m-40) REVERT: C 355 LEU cc_start: 0.8501 (tp) cc_final: 0.8294 (tt) REVERT: C 379 PHE cc_start: 0.7282 (m-80) cc_final: 0.6803 (m-80) REVERT: C 598 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: C 837 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: C 956 SER cc_start: 0.9244 (t) cc_final: 0.8582 (m) outliers start: 134 outliers final: 105 residues processed: 396 average time/residue: 0.1508 time to fit residues: 97.4212 Evaluate side-chains 384 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 271 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1031 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 198 optimal weight: 0.6980 chunk 239 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.135442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105871 restraints weight = 58735.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.104941 restraints weight = 42636.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105595 restraints weight = 31371.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.105901 restraints weight = 26061.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106109 restraints weight = 23789.157| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 25147 Z= 0.252 Angle : 0.730 13.731 34227 Z= 0.380 Chirality : 0.047 0.219 3858 Planarity : 0.005 0.092 4427 Dihedral : 6.630 58.140 3379 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.38 % Favored : 87.59 % Rotamer: Outliers : 4.99 % Allowed : 16.77 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.14), residues: 3111 helix: 0.17 (0.21), residues: 642 sheet: -1.58 (0.22), residues: 530 loop : -2.66 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 306 TYR 0.026 0.002 TYR A1049 PHE 0.029 0.002 PHE B 185 TRP 0.014 0.002 TRP B 423 HIS 0.004 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00564 (25129) covalent geometry : angle 0.72811 (34191) SS BOND : bond 0.00309 ( 18) SS BOND : angle 1.96104 ( 36) hydrogen bonds : bond 0.04198 ( 746) hydrogen bonds : angle 6.09106 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 292 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7329 (tpp) cc_final: 0.6727 (tpp) REVERT: A 151 MET cc_start: 0.5756 (mpp) cc_final: 0.4956 (ptm) REVERT: A 200 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.5322 (t80) REVERT: A 306 ARG cc_start: 0.6971 (mmm160) cc_final: 0.6744 (mmm160) REVERT: A 968 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7481 (tmtt) REVERT: A 1086 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8511 (pp) REVERT: B 53 TYR cc_start: 0.8194 (t80) cc_final: 0.7889 (t80) REVERT: B 305 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.6837 (m-10) REVERT: B 402 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.7174 (p) REVERT: B 451 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: B 582 SER cc_start: 0.9013 (m) cc_final: 0.8019 (p) REVERT: B 677 TYR cc_start: 0.8748 (p90) cc_final: 0.7681 (p90) REVERT: B 747 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7197 (ttm-80) REVERT: B 855 TYR cc_start: 0.8774 (m-10) cc_final: 0.8558 (m-80) REVERT: B 859 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8891 (mm) REVERT: B 882 MET cc_start: 0.8231 (mmm) cc_final: 0.8028 (mmt) REVERT: C 37 MET cc_start: 0.8236 (mmm) cc_final: 0.7948 (mmm) REVERT: C 214 ASN cc_start: 0.6732 (t0) cc_final: 0.6498 (m-40) REVERT: C 379 PHE cc_start: 0.7361 (m-80) cc_final: 0.6996 (m-80) REVERT: C 481 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5837 (t80) REVERT: C 707 GLU cc_start: 0.7960 (tt0) cc_final: 0.7720 (pt0) REVERT: C 837 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: C 956 SER cc_start: 0.9239 (t) cc_final: 0.8550 (m) outliers start: 136 outliers final: 113 residues processed: 388 average time/residue: 0.1533 time to fit residues: 97.1804 Evaluate side-chains 398 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 275 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1097 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1031 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 43 optimal weight: 0.8980 chunk 299 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 208 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B 835 GLN B 883 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.139685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110867 restraints weight = 59027.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.110479 restraints weight = 39558.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111385 restraints weight = 29668.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111660 restraints weight = 24415.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111774 restraints weight = 22633.049| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25147 Z= 0.129 Angle : 0.665 11.752 34227 Z= 0.340 Chirality : 0.045 0.257 3858 Planarity : 0.005 0.089 4427 Dihedral : 6.136 59.299 3379 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.68 % Favored : 90.29 % Rotamer: Outliers : 3.52 % Allowed : 18.28 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.15), residues: 3111 helix: 0.57 (0.21), residues: 634 sheet: -1.50 (0.22), residues: 518 loop : -2.46 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 306 TYR 0.026 0.001 TYR B 408 PHE 0.045 0.001 PHE B 89 TRP 0.014 0.001 TRP A 423 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00285 (25129) covalent geometry : angle 0.66318 (34191) SS BOND : bond 0.00199 ( 18) SS BOND : angle 1.54187 ( 36) hydrogen bonds : bond 0.03693 ( 746) hydrogen bonds : angle 5.75831 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 333 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6884 (tpp) cc_final: 0.6508 (tpp) REVERT: A 151 MET cc_start: 0.5724 (mpp) cc_final: 0.5152 (ptm) REVERT: A 966 LEU cc_start: 0.7313 (mt) cc_final: 0.6512 (tp) REVERT: A 968 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7465 (tmtt) REVERT: A 1027 LYS cc_start: 0.8364 (mmmt) cc_final: 0.7550 (tptt) REVERT: A 1086 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8266 (pp) REVERT: B 44 ASP cc_start: 0.7253 (p0) cc_final: 0.7003 (p0) REVERT: B 54 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8148 (tp) REVERT: B 187 PHE cc_start: 0.6691 (m-10) cc_final: 0.6450 (m-10) REVERT: B 256 TYR cc_start: 0.7371 (m-80) cc_final: 0.7077 (m-80) REVERT: B 286 LEU cc_start: 0.8992 (tt) cc_final: 0.8738 (tt) REVERT: B 305 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: B 582 SER cc_start: 0.8966 (m) cc_final: 0.7881 (p) REVERT: B 855 TYR cc_start: 0.8685 (m-10) cc_final: 0.8455 (m-10) REVERT: B 859 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8896 (mm) REVERT: B 970 GLU cc_start: 0.7065 (pm20) cc_final: 0.6781 (pm20) REVERT: B 1010 LYS cc_start: 0.8924 (mttp) cc_final: 0.8698 (mttt) REVERT: B 1023 ASP cc_start: 0.7485 (t0) cc_final: 0.7103 (t0) REVERT: C 37 MET cc_start: 0.8075 (mmm) cc_final: 0.7584 (mmm) REVERT: C 214 ASN cc_start: 0.6632 (t0) cc_final: 0.6423 (m-40) REVERT: C 263 MET cc_start: 0.8293 (ttp) cc_final: 0.7989 (ptm) REVERT: C 598 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: C 707 GLU cc_start: 0.7872 (tt0) cc_final: 0.7610 (pt0) REVERT: C 837 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: C 902 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 956 SER cc_start: 0.9000 (t) cc_final: 0.8419 (m) REVERT: C 980 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8591 (p) outliers start: 96 outliers final: 79 residues processed: 409 average time/residue: 0.1539 time to fit residues: 102.5796 Evaluate side-chains 370 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 283 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 980 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 229 optimal weight: 0.0000 chunk 247 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 163 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 overall best weight: 0.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN B 883 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.141258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.111422 restraints weight = 58902.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.111148 restraints weight = 38520.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.112078 restraints weight = 27759.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.112283 restraints weight = 23937.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112437 restraints weight = 22032.761| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25147 Z= 0.123 Angle : 0.663 11.344 34227 Z= 0.340 Chirality : 0.045 0.276 3858 Planarity : 0.005 0.087 4427 Dihedral : 5.939 58.499 3379 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.68 % Favored : 90.29 % Rotamer: Outliers : 3.19 % Allowed : 19.16 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.15), residues: 3111 helix: 0.69 (0.21), residues: 648 sheet: -1.33 (0.22), residues: 527 loop : -2.47 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 232 TYR 0.024 0.001 TYR B 408 PHE 0.030 0.002 PHE A1071 TRP 0.012 0.001 TRP A 423 HIS 0.005 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00268 (25129) covalent geometry : angle 0.66145 (34191) SS BOND : bond 0.00359 ( 18) SS BOND : angle 1.59951 ( 36) hydrogen bonds : bond 0.03686 ( 746) hydrogen bonds : angle 5.60969 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 314 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6941 (tpp) cc_final: 0.6563 (tpp) REVERT: A 40 VAL cc_start: 0.9127 (t) cc_final: 0.8909 (p) REVERT: A 151 MET cc_start: 0.5722 (mpp) cc_final: 0.4995 (ptm) REVERT: A 966 LEU cc_start: 0.7191 (mt) cc_final: 0.6264 (tp) REVERT: A 968 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7456 (tmtt) REVERT: A 1027 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7864 (tptt) REVERT: A 1032 MET cc_start: 0.7799 (ptm) cc_final: 0.7569 (ptm) REVERT: A 1086 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8197 (pp) REVERT: B 44 ASP cc_start: 0.7341 (p0) cc_final: 0.7112 (p0) REVERT: B 53 TYR cc_start: 0.7966 (t80) cc_final: 0.7753 (t80) REVERT: B 54 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8104 (tt) REVERT: B 187 PHE cc_start: 0.6802 (m-10) cc_final: 0.6471 (m-10) REVERT: B 256 TYR cc_start: 0.7363 (m-80) cc_final: 0.7094 (m-80) REVERT: B 286 LEU cc_start: 0.8979 (tt) cc_final: 0.8764 (tt) REVERT: B 305 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.6598 (m-80) REVERT: B 582 SER cc_start: 0.8932 (m) cc_final: 0.7815 (p) REVERT: B 677 TYR cc_start: 0.8563 (p90) cc_final: 0.7485 (p90) REVERT: B 721 ASN cc_start: 0.7263 (m110) cc_final: 0.7004 (m-40) REVERT: B 855 TYR cc_start: 0.8808 (m-10) cc_final: 0.8595 (m-10) REVERT: B 859 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8884 (mm) REVERT: B 1010 LYS cc_start: 0.8896 (mttp) cc_final: 0.8662 (mttt) REVERT: B 1023 ASP cc_start: 0.7421 (t0) cc_final: 0.7088 (t0) REVERT: C 37 MET cc_start: 0.8030 (mmm) cc_final: 0.7576 (mmm) REVERT: C 214 ASN cc_start: 0.6594 (t0) cc_final: 0.6337 (m-40) REVERT: C 263 MET cc_start: 0.8284 (ttp) cc_final: 0.7940 (ppp) REVERT: C 379 PHE cc_start: 0.7237 (m-80) cc_final: 0.6834 (m-80) REVERT: C 451 PHE cc_start: 0.7639 (m-80) cc_final: 0.7398 (m-80) REVERT: C 570 ILE cc_start: 0.8446 (mp) cc_final: 0.8139 (pt) REVERT: C 598 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: C 837 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: C 891 ILE cc_start: 0.8719 (mt) cc_final: 0.8412 (mt) REVERT: C 956 SER cc_start: 0.8846 (t) cc_final: 0.8304 (m) REVERT: C 980 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8540 (p) REVERT: C 1001 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7640 (ttp80) outliers start: 87 outliers final: 70 residues processed: 381 average time/residue: 0.1579 time to fit residues: 98.4563 Evaluate side-chains 364 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 286 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1031 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 146 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 306 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 300 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.140980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.112389 restraints weight = 59526.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112055 restraints weight = 39665.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112829 restraints weight = 29697.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113144 restraints weight = 23513.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.113307 restraints weight = 21405.968| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25147 Z= 0.142 Angle : 0.671 12.007 34227 Z= 0.345 Chirality : 0.045 0.269 3858 Planarity : 0.005 0.089 4427 Dihedral : 5.900 57.603 3379 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.45 % Favored : 90.52 % Rotamer: Outliers : 3.34 % Allowed : 19.60 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.15), residues: 3111 helix: 0.75 (0.21), residues: 644 sheet: -1.21 (0.22), residues: 534 loop : -2.45 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 306 TYR 0.026 0.002 TYR B 197 PHE 0.045 0.002 PHE B 185 TRP 0.014 0.001 TRP A 868 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00321 (25129) covalent geometry : angle 0.66981 (34191) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.56313 ( 36) hydrogen bonds : bond 0.03737 ( 746) hydrogen bonds : angle 5.57633 ( 2082) =============================================================================== Job complete usr+sys time: 4147.83 seconds wall clock time: 72 minutes 46.53 seconds (4366.53 seconds total)