Starting phenix.real_space_refine on Wed Jun 25 00:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtc_32778/06_2025/7wtc_32778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtc_32778/06_2025/7wtc_32778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtc_32778/06_2025/7wtc_32778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtc_32778/06_2025/7wtc_32778.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtc_32778/06_2025/7wtc_32778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtc_32778/06_2025/7wtc_32778.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 172 5.16 5 C 17994 2.51 5 N 4945 2.21 5 O 5301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'CIS': 1, 'PTRANS': 65, 'TRANS': 1079} Chain: "B" Number of atoms: 8877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8877 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 65, 'TRANS': 1081} Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'ACO': 1, 'BTI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'ACO': 1, 'BTI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.51, per 1000 atoms: 0.58 Number of scatterers: 28418 At special positions: 0 Unit cell: (161.7, 162.8, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 6 15.00 O 5301 8.00 N 4945 7.00 C 17994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 3.7 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 27 sheets defined 45.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 91 through 96 removed outlier: 4.186A pdb=" N TYR A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.604A pdb=" N ASN A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.890A pdb=" N ALA A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.569A pdb=" N MET A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 176 through 188 removed outlier: 4.031A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.591A pdb=" N GLU A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 303 Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.659A pdb=" N LEU A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 468 through 474 removed outlier: 4.120A pdb=" N GLY A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 4.008A pdb=" N ILE A 481 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 540 through 549 removed outlier: 4.312A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.824A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 608 through 618 Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.640A pdb=" N ARG A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.649A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.755A pdb=" N MET A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 removed outlier: 3.524A pdb=" N TYR A 723 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.539A pdb=" N ALA A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.564A pdb=" N LEU A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 843 removed outlier: 3.933A pdb=" N VAL A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.940A pdb=" N ASN A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 882 Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.609A pdb=" N LYS A 891 " --> pdb=" O PHE A 887 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 898 " --> pdb=" O TYR A 894 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 925 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 977 through 982 removed outlier: 4.056A pdb=" N SER A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.512A pdb=" N LEU A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1034 through 1040 Processing helix chain 'B' and resid 46 through 59 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 91 through 96 removed outlier: 4.232A pdb=" N TYR B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.720A pdb=" N ILE B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 151 through 162 removed outlier: 3.844A pdb=" N ALA B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.959A pdb=" N ALA B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 228 Processing helix chain 'B' and resid 284 through 303 Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.727A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.743A pdb=" N ALA B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 435 through 450 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 468 through 474 removed outlier: 4.022A pdb=" N LEU B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.531A pdb=" N PHE B 488 " --> pdb=" O PRO B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 removed outlier: 3.625A pdb=" N LYS B 499 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 571 through 578 removed outlier: 4.439A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.534A pdb=" N LEU B 587 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 597 Processing helix chain 'B' and resid 608 through 618 Processing helix chain 'B' and resid 622 through 632 removed outlier: 3.611A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU B 632 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 669 Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.559A pdb=" N MET B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.540A pdb=" N TYR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 4.242A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.863A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 842 removed outlier: 3.573A pdb=" N TRP B 838 " --> pdb=" O TYR B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.731A pdb=" N THR B 853 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 870 through 882 Processing helix chain 'B' and resid 886 through 902 removed outlier: 4.264A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 925 Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.596A pdb=" N GLN B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 950 Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.509A pdb=" N LYS B 969 " --> pdb=" O SER B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.559A pdb=" N SER B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 999 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 549 through 560 removed outlier: 3.650A pdb=" N HIS C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 removed outlier: 4.069A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 608 through 618 Processing helix chain 'C' and resid 622 through 632 removed outlier: 3.668A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.785A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 697 Processing helix chain 'C' and resid 719 through 734 Processing helix chain 'C' and resid 748 through 762 removed outlier: 4.305A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 removed outlier: 3.567A pdb=" N ALA C 782 " --> pdb=" O ALA C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.507A pdb=" N MET C 801 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 802 " --> pdb=" O ASP C 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 798 through 802' Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.782A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 843 removed outlier: 3.956A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 849 through 853 Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.076A pdb=" N ASN C 864 " --> pdb=" O ASP C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 882 Processing helix chain 'C' and resid 886 through 902 removed outlier: 4.162A pdb=" N VAL C 895 " --> pdb=" O LYS C 891 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU C 896 " --> pdb=" O LYS C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 924 Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 Processing helix chain 'C' and resid 960 through 969 Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.714A pdb=" N SER C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 998 removed outlier: 3.611A pdb=" N GLU C 991 " --> pdb=" O LEU C 987 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1028 removed outlier: 3.593A pdb=" N THR C1026 " --> pdb=" O ASP C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1041 Processing helix chain 'D' and resid 496 through 511 Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.768A pdb=" N LEU D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.505A pdb=" N PHE D 553 " --> pdb=" O GLY D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 578 removed outlier: 3.694A pdb=" N GLN D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 4.014A pdb=" N LEU D 587 " --> pdb=" O ARG D 583 " (cutoff:3.500A) Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 608 through 618 Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 655 through 669 removed outlier: 3.660A pdb=" N VAL D 659 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 697 Processing helix chain 'D' and resid 719 through 733 removed outlier: 3.600A pdb=" N TYR D 723 " --> pdb=" O SER D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 removed outlier: 4.406A pdb=" N ARG D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.552A pdb=" N ALA D 782 " --> pdb=" O ALA D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 810 through 817 Processing helix chain 'D' and resid 827 through 843 removed outlier: 3.733A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 846 No H-bonds generated for 'chain 'D' and resid 844 through 846' Processing helix chain 'D' and resid 850 through 855 Processing helix chain 'D' and resid 860 through 865 Processing helix chain 'D' and resid 867 through 881 removed outlier: 4.645A pdb=" N THR D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN D 873 " --> pdb=" O GLY D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 885 No H-bonds generated for 'chain 'D' and resid 883 through 885' Processing helix chain 'D' and resid 886 through 902 removed outlier: 3.737A pdb=" N LYS D 891 " --> pdb=" O PHE D 887 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS D 892 " --> pdb=" O LYS D 888 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 893 " --> pdb=" O GLU D 889 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 898 " --> pdb=" O TYR D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 925 Processing helix chain 'D' and resid 927 through 934 Processing helix chain 'D' and resid 941 through 950 removed outlier: 3.704A pdb=" N VAL D 945 " --> pdb=" O PRO D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 968 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 988 through 998 Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 3.796A pdb=" N VAL D1007 " --> pdb=" O THR D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 Processing helix chain 'D' and resid 1034 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 removed outlier: 3.582A pdb=" N GLU A 82 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 42 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 66 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS A 39 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS A 115 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET A 41 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 207 removed outlier: 3.538A pdb=" N ILE A 192 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 264 removed outlier: 7.280A pdb=" N GLN A 248 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 262 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 246 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 245 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 313 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 322 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 277 removed outlier: 4.213A pdb=" N VAL A 427 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 564 through 567 removed outlier: 7.213A pdb=" N LEU A 565 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N GLU A 605 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP A 567 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TRP A 607 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ASN A 606 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 674 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA A 703 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 676 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N SER A 705 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU A 768 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ASP A 795 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ILE A 770 " --> pdb=" O ASP A 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1047 through 1051 removed outlier: 5.613A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A1064 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN A1075 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU A1068 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN A1073 " --> pdb=" O LEU A1068 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1146 through 1150 removed outlier: 3.708A pdb=" N CYS A1138 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A1137 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A1123 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1139 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1130 through 1131 removed outlier: 3.596A pdb=" N GLY A1155 " --> pdb=" O VAL A1131 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A1176 " --> pdb=" O ARG A1158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.700A pdb=" N VAL B 64 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 42 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 66 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 39 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N HIS B 115 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N MET B 41 " --> pdb=" O HIS B 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 204 through 207 Processing sheet with id=AB4, first strand: chain 'B' and resid 257 through 264 removed outlier: 6.788A pdb=" N GLN B 248 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 262 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU B 246 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 324 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 313 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 277 removed outlier: 4.167A pdb=" N VAL B 427 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.693A pdb=" N LEU B 565 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU B 605 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASP B 567 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N TRP B 607 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 642 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE B 677 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU B 643 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE B 674 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA B 703 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 676 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N SER B 705 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 704 " --> pdb=" O LYS B 741 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 768 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASP B 795 " --> pdb=" O LEU B 768 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE B 770 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 564 " --> pdb=" O VAL B 794 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 6.917A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1112 through 1113 removed outlier: 6.796A pdb=" N ILE B1112 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B1176 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS B1159 " --> pdb=" O GLU B1176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1146 through 1150 removed outlier: 3.526A pdb=" N THR B1147 " --> pdb=" O LEU B1140 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYS B1138 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B1137 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B1123 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B1139 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.303A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 796 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N MET C 566 " --> pdb=" O VAL C 796 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 768 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASP C 795 " --> pdb=" O LEU C 768 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE C 770 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 700 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N CYS C 739 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA C 702 " --> pdb=" O CYS C 739 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS C 741 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 701 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 676 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 703 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 639 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG C 675 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET C 641 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1047 through 1049 removed outlier: 5.703A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C1064 " --> pdb=" O PHE C1077 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1146 through 1151 removed outlier: 6.125A pdb=" N SER C1151 " --> pdb=" O PRO C1136 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU C1137 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C1123 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C1139 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1130 through 1131 removed outlier: 6.720A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 564 through 566 removed outlier: 6.709A pdb=" N LEU D 564 " --> pdb=" O VAL D 794 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 604 through 607 removed outlier: 6.062A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.676A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 1111 through 1113 removed outlier: 7.665A pdb=" N ILE D1112 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE D1174 " --> pdb=" O VAL D1160 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL D1160 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU D1176 " --> pdb=" O ARG D1158 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D1156 " --> pdb=" O GLU D1178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA D1129 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 1146 through 1150 removed outlier: 7.501A pdb=" N THR D1147 " --> pdb=" O VAL D1139 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL D1139 " --> pdb=" O THR D1147 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL D1149 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) 1183 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.59 Time building geometry restraints manager: 8.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4816 1.31 - 1.43: 7257 1.43 - 1.56: 16642 1.56 - 1.69: 31 1.69 - 1.82: 298 Bond restraints: 29044 Sorted by residual: bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.441 0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" C6 BTI B2002 " pdb=" S1 BTI B2002 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI A1201 " pdb=" S1 BTI A1201 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.444 0.367 2.00e-02 2.50e+03 3.37e+02 bond pdb=" C3 BTI A1201 " pdb=" N3 BTI A1201 " ideal model delta sigma weight residual 1.356 1.577 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 29039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 39012 3.32 - 6.63: 329 6.63 - 9.95: 26 9.95 - 13.26: 3 13.26 - 16.58: 5 Bond angle restraints: 39375 Sorted by residual: angle pdb=" N PRO C 536 " pdb=" CD PRO C 536 " pdb=" CG PRO C 536 " ideal model delta sigma weight residual 103.20 86.62 16.58 1.50e+00 4.44e-01 1.22e+02 angle pdb=" CA PRO C 536 " pdb=" N PRO C 536 " pdb=" CD PRO C 536 " ideal model delta sigma weight residual 112.00 102.32 9.68 1.40e+00 5.10e-01 4.78e+01 angle pdb=" CA PRO C 536 " pdb=" CB PRO C 536 " pdb=" CG PRO C 536 " ideal model delta sigma weight residual 104.50 92.39 12.11 1.90e+00 2.77e-01 4.07e+01 angle pdb=" C LEU B 260 " pdb=" N TYR B 261 " pdb=" CA TYR B 261 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.42e+01 angle pdb=" N VAL D1065 " pdb=" CA VAL D1065 " pdb=" C VAL D1065 " ideal model delta sigma weight residual 112.90 107.47 5.43 9.60e-01 1.09e+00 3.21e+01 ... (remaining 39370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 15968 17.79 - 35.58: 1446 35.58 - 53.37: 204 53.37 - 71.16: 45 71.16 - 88.95: 28 Dihedral angle restraints: 17691 sinusoidal: 7194 harmonic: 10497 Sorted by residual: dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual -86.00 -174.83 88.83 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS C 752 " pdb=" SG CYS C 752 " pdb=" SG CYS C 786 " pdb=" CB CYS C 786 " ideal model delta sinusoidal sigma weight residual 93.00 177.92 -84.92 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 173.77 -80.77 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 17688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3472 0.055 - 0.110: 780 0.110 - 0.165: 107 0.165 - 0.220: 14 0.220 - 0.275: 5 Chirality restraints: 4378 Sorted by residual: chirality pdb=" CB THR B 908 " pdb=" CA THR B 908 " pdb=" OG1 THR B 908 " pdb=" CG2 THR B 908 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BTI B2002 " pdb=" C4 BTI B2002 " pdb=" C6 BTI B2002 " pdb=" N3 BTI B2002 " both_signs ideal model delta sigma weight residual False 2.73 2.99 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR B 908 " pdb=" N THR B 908 " pdb=" C THR B 908 " pdb=" CB THR B 908 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4375 not shown) Planarity restraints: 5171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 535 " -0.059 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 536 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 536 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 542 " -0.185 9.50e-02 1.11e+02 8.33e-02 4.93e+00 pdb=" NE ARG A 542 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 542 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 542 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 542 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 947 " -0.014 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE A 947 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 947 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 947 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 947 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 947 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 947 " -0.015 2.00e-02 2.50e+03 ... (remaining 5168 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 529 2.63 - 3.20: 27470 3.20 - 3.76: 46762 3.76 - 4.33: 61568 4.33 - 4.90: 97454 Nonbonded interactions: 233783 Sorted by model distance: nonbonded pdb=" NH1 ARG A 542 " pdb=" O ILE A 634 " model vdw 2.060 3.120 nonbonded pdb=" OD2 ASP B 586 " pdb=" OH TYR B 845 " model vdw 2.070 3.040 nonbonded pdb=" OD2 ASP B 343 " pdb=" ND1 HIS B 346 " model vdw 2.102 3.120 nonbonded pdb=" O ALA C1132 " pdb=" OG SER C1151 " model vdw 2.109 3.040 nonbonded pdb=" O SER D 523 " pdb=" NH1 ARG D1036 " model vdw 2.117 3.120 ... (remaining 233778 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 33 through 1178) selection = (chain 'B' and resid 33 through 1178) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 65.130 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 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 : 0.009 0.805 29053 Z= 0.601 Angle : 0.825 16.581 39383 Z= 0.442 Chirality : 0.048 0.275 4378 Planarity : 0.006 0.083 5171 Dihedral : 13.845 88.949 10941 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.95 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3653 helix: 0.61 (0.14), residues: 1415 sheet: -0.08 (0.23), residues: 511 loop : -1.63 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 624 HIS 0.012 0.002 HIS C1019 PHE 0.031 0.002 PHE B 848 TYR 0.021 0.002 TYR D 723 ARG 0.015 0.001 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.17407 ( 1183) hydrogen bonds : angle 7.21730 ( 3453) SS BOND : bond 0.00871 ( 4) SS BOND : angle 4.20715 ( 8) covalent geometry : bond 0.00762 (29044) covalent geometry : angle 0.82337 (39375) Misc. bond : bond 0.36022 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 3.147 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: B 801 MET cc_start: 0.6900 (mmt) cc_final: 0.6430 (mmt) REVERT: C 671 MET cc_start: 0.5308 (tpt) cc_final: 0.4893 (tpt) REVERT: C 686 MET cc_start: 0.4577 (tpp) cc_final: 0.3845 (tpp) REVERT: C 854 MET cc_start: 0.8561 (tpt) cc_final: 0.8236 (tpp) REVERT: C 894 TYR cc_start: 0.8083 (t80) cc_final: 0.7726 (t80) REVERT: D 555 ARG cc_start: 0.7703 (tpm170) cc_final: 0.7313 (tmm160) REVERT: D 754 MET cc_start: 0.6247 (ppp) cc_final: 0.5330 (ppp) REVERT: D 1095 MET cc_start: 0.2386 (ppp) cc_final: 0.2155 (ppp) outliers start: 3 outliers final: 1 residues processed: 278 average time/residue: 0.4229 time to fit residues: 185.9991 Evaluate side-chains 218 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1144 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 285 optimal weight: 0.0020 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 330 optimal weight: 7.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 653 ASN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 ASN A1075 GLN B 248 GLN B 350 HIS B 470 GLN B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN B1040 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN C1093 GLN D 498 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.107312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.090601 restraints weight = 231979.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.090563 restraints weight = 217490.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.090912 restraints weight = 210448.336| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29053 Z= 0.144 Angle : 0.665 9.483 39383 Z= 0.342 Chirality : 0.045 0.266 4378 Planarity : 0.005 0.048 5171 Dihedral : 6.689 58.846 4145 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 0.66 % Allowed : 8.50 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3653 helix: 0.73 (0.13), residues: 1462 sheet: -0.09 (0.23), residues: 502 loop : -1.60 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 838 HIS 0.008 0.001 HIS C1019 PHE 0.024 0.002 PHE B 848 TYR 0.016 0.001 TYR A 651 ARG 0.013 0.001 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 1183) hydrogen bonds : angle 5.67908 ( 3453) SS BOND : bond 0.00214 ( 4) SS BOND : angle 1.64816 ( 8) covalent geometry : bond 0.00316 (29044) covalent geometry : angle 0.66444 (39375) Misc. bond : bond 0.00032 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8422 (m-10) cc_final: 0.8158 (m-10) REVERT: A 604 MET cc_start: 0.7189 (ptm) cc_final: 0.6817 (tmm) REVERT: B 108 GLU cc_start: 0.8910 (pt0) cc_final: 0.8556 (pp20) REVERT: B 690 MET cc_start: 0.7884 (mmt) cc_final: 0.7625 (tpt) REVERT: B 801 MET cc_start: 0.7103 (mmt) cc_final: 0.6668 (mmt) REVERT: B 1040 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7460 (pp30) REVERT: C 671 MET cc_start: 0.5270 (tpt) cc_final: 0.4777 (tpt) REVERT: C 686 MET cc_start: 0.5064 (tpp) cc_final: 0.4457 (tpp) REVERT: C 854 MET cc_start: 0.8391 (tpt) cc_final: 0.7927 (tpp) REVERT: C 894 TYR cc_start: 0.8424 (t80) cc_final: 0.8094 (t80) REVERT: C 1093 GLN cc_start: 0.5215 (OUTLIER) cc_final: 0.4849 (mp10) REVERT: C 1145 MET cc_start: 0.1997 (tpt) cc_final: 0.1517 (tpp) REVERT: D 555 ARG cc_start: 0.7529 (tpm170) cc_final: 0.7136 (tmm160) REVERT: D 754 MET cc_start: 0.6479 (ppp) cc_final: 0.5543 (ppp) REVERT: D 1095 MET cc_start: 0.2811 (ppp) cc_final: 0.2506 (ppp) outliers start: 20 outliers final: 9 residues processed: 246 average time/residue: 0.4168 time to fit residues: 163.7469 Evaluate side-chains 225 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1040 GLN Chi-restraints excluded: chain C residue 1093 GLN Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 305 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 129 optimal weight: 0.0570 chunk 30 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 310 optimal weight: 9.9990 chunk 230 optimal weight: 30.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 208 HIS ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 ASN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.103654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.084697 restraints weight = 236843.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.085353 restraints weight = 199261.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.086220 restraints weight = 177095.246| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 29053 Z= 0.218 Angle : 0.742 12.018 39383 Z= 0.381 Chirality : 0.046 0.210 4378 Planarity : 0.005 0.055 5171 Dihedral : 6.872 59.314 4141 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 1.79 % Allowed : 12.84 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3653 helix: 0.41 (0.13), residues: 1477 sheet: -0.38 (0.23), residues: 506 loop : -1.72 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 838 HIS 0.009 0.002 HIS B 875 PHE 0.024 0.002 PHE A 387 TYR 0.019 0.002 TYR D 723 ARG 0.010 0.001 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 1183) hydrogen bonds : angle 5.77679 ( 3453) SS BOND : bond 0.00230 ( 4) SS BOND : angle 1.35364 ( 8) covalent geometry : bond 0.00472 (29044) covalent geometry : angle 0.74176 (39375) Misc. bond : bond 0.00172 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 224 time to evaluate : 3.109 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 450 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7382 (t80) REVERT: A 604 MET cc_start: 0.7258 (ptm) cc_final: 0.6636 (tmm) REVERT: A 900 MET cc_start: 0.7547 (mpp) cc_final: 0.7292 (mpp) REVERT: B 108 GLU cc_start: 0.8944 (pt0) cc_final: 0.8627 (pp20) REVERT: B 277 ILE cc_start: 0.3788 (OUTLIER) cc_final: 0.3423 (tt) REVERT: B 690 MET cc_start: 0.7703 (mmt) cc_final: 0.7481 (tpt) REVERT: B 801 MET cc_start: 0.7333 (mmt) cc_final: 0.6803 (mmt) REVERT: B 939 SER cc_start: 0.7462 (p) cc_final: 0.7255 (t) REVERT: B 971 LEU cc_start: 0.8622 (pp) cc_final: 0.8400 (mm) REVERT: B 1058 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7675 (pp) REVERT: C 671 MET cc_start: 0.4948 (tpt) cc_final: 0.4540 (tpt) REVERT: C 804 MET cc_start: 0.9049 (tpp) cc_final: 0.8802 (mmt) REVERT: C 881 MET cc_start: 0.8713 (mmm) cc_final: 0.8406 (mmm) REVERT: C 894 TYR cc_start: 0.8424 (t80) cc_final: 0.8097 (t80) REVERT: C 910 SER cc_start: 0.7304 (OUTLIER) cc_final: 0.6826 (p) REVERT: D 555 ARG cc_start: 0.7320 (tpm170) cc_final: 0.6843 (tmm160) REVERT: D 754 MET cc_start: 0.6659 (ppp) cc_final: 0.5769 (ppp) outliers start: 54 outliers final: 33 residues processed: 262 average time/residue: 0.4008 time to fit residues: 169.7615 Evaluate side-chains 246 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1043 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1145 MET Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 248 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 166 optimal weight: 0.0870 chunk 117 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 282 optimal weight: 8.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 771 HIS ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.105664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.086504 restraints weight = 236320.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.087168 restraints weight = 200354.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.087890 restraints weight = 176763.089| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29053 Z= 0.126 Angle : 0.625 9.072 39383 Z= 0.315 Chirality : 0.043 0.213 4378 Planarity : 0.004 0.047 5171 Dihedral : 6.616 59.066 4141 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.76 % Favored : 93.18 % Rotamer: Outliers : 1.63 % Allowed : 14.54 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3653 helix: 0.76 (0.14), residues: 1478 sheet: -0.27 (0.23), residues: 506 loop : -1.61 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 607 HIS 0.008 0.001 HIS B 208 PHE 0.032 0.002 PHE D 920 TYR 0.015 0.001 TYR D 503 ARG 0.008 0.000 ARG D1070 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 1183) hydrogen bonds : angle 5.35752 ( 3453) SS BOND : bond 0.01533 ( 4) SS BOND : angle 1.32647 ( 8) covalent geometry : bond 0.00275 (29044) covalent geometry : angle 0.62518 (39375) Misc. bond : bond 0.00057 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 3.496 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 53 PHE cc_start: 0.8267 (m-10) cc_final: 0.7965 (m-10) REVERT: A 450 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7287 (t80) REVERT: A 616 MET cc_start: 0.8253 (tpp) cc_final: 0.7883 (tpp) REVERT: A 900 MET cc_start: 0.7622 (mpp) cc_final: 0.7266 (mpp) REVERT: A 1001 GLU cc_start: 0.8396 (pp20) cc_final: 0.8002 (pm20) REVERT: B 108 GLU cc_start: 0.8875 (pt0) cc_final: 0.8655 (pp20) REVERT: B 261 TYR cc_start: 0.5505 (OUTLIER) cc_final: 0.5080 (m-10) REVERT: B 690 MET cc_start: 0.7866 (mmt) cc_final: 0.7640 (tpt) REVERT: B 801 MET cc_start: 0.7317 (mmt) cc_final: 0.6822 (mmt) REVERT: B 939 SER cc_start: 0.7310 (p) cc_final: 0.7094 (t) REVERT: B 1166 MET cc_start: 0.3513 (ptt) cc_final: 0.2890 (pmm) REVERT: C 671 MET cc_start: 0.4954 (tpt) cc_final: 0.4521 (tpt) REVERT: C 686 MET cc_start: 0.5647 (tpp) cc_final: 0.5402 (tpp) REVERT: C 804 MET cc_start: 0.9092 (tpp) cc_final: 0.8767 (mmt) REVERT: C 810 MET cc_start: 0.8323 (mmt) cc_final: 0.8025 (mmm) REVERT: C 881 MET cc_start: 0.8769 (mmm) cc_final: 0.8264 (mmm) REVERT: C 894 TYR cc_start: 0.8423 (t80) cc_final: 0.8019 (t80) REVERT: C 910 SER cc_start: 0.7221 (OUTLIER) cc_final: 0.6835 (p) REVERT: D 555 ARG cc_start: 0.7314 (tpm170) cc_final: 0.7071 (tpm170) REVERT: D 629 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7356 (pp20) REVERT: D 754 MET cc_start: 0.6716 (ppp) cc_final: 0.5952 (ppp) REVERT: D 854 MET cc_start: 0.5247 (mmp) cc_final: 0.4176 (mmm) outliers start: 49 outliers final: 28 residues processed: 265 average time/residue: 0.4425 time to fit residues: 190.6628 Evaluate side-chains 247 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 690 MET Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 184 optimal weight: 0.0670 chunk 351 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 192 optimal weight: 0.0980 chunk 123 optimal weight: 4.9990 chunk 306 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 211 optimal weight: 0.9990 overall best weight: 2.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 HIS A 923 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.104989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.086688 restraints weight = 232556.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.087352 restraints weight = 195525.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.087515 restraints weight = 171622.315| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29053 Z= 0.135 Angle : 0.627 10.588 39383 Z= 0.316 Chirality : 0.043 0.209 4378 Planarity : 0.004 0.047 5171 Dihedral : 6.532 59.887 4141 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.50 % Favored : 92.47 % Rotamer: Outliers : 2.16 % Allowed : 15.83 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3653 helix: 0.79 (0.14), residues: 1490 sheet: -0.26 (0.23), residues: 505 loop : -1.61 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 624 HIS 0.006 0.001 HIS B 208 PHE 0.016 0.001 PHE C 947 TYR 0.014 0.001 TYR D 503 ARG 0.005 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 1183) hydrogen bonds : angle 5.30125 ( 3453) SS BOND : bond 0.00250 ( 4) SS BOND : angle 1.39281 ( 8) covalent geometry : bond 0.00303 (29044) covalent geometry : angle 0.62668 (39375) Misc. bond : bond 0.00037 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8327 (m-10) cc_final: 0.8108 (m-10) REVERT: A 450 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7429 (t80) REVERT: A 900 MET cc_start: 0.7668 (mpp) cc_final: 0.7272 (mpp) REVERT: A 1001 GLU cc_start: 0.8406 (pp20) cc_final: 0.7972 (pm20) REVERT: B 105 VAL cc_start: 0.9551 (m) cc_final: 0.9003 (p) REVERT: B 108 GLU cc_start: 0.8896 (pt0) cc_final: 0.8664 (pp20) REVERT: B 261 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.5095 (m-10) REVERT: B 690 MET cc_start: 0.7862 (mmt) cc_final: 0.7635 (tpt) REVERT: B 801 MET cc_start: 0.7307 (mmt) cc_final: 0.6801 (mmt) REVERT: B 1166 MET cc_start: 0.3289 (ptt) cc_final: 0.2528 (pmm) REVERT: C 671 MET cc_start: 0.5036 (tpt) cc_final: 0.4593 (tpt) REVERT: C 804 MET cc_start: 0.8965 (tpp) cc_final: 0.8744 (mmt) REVERT: C 881 MET cc_start: 0.8808 (mmm) cc_final: 0.8338 (mmm) REVERT: C 894 TYR cc_start: 0.8392 (t80) cc_final: 0.8033 (t80) REVERT: C 910 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6637 (p) REVERT: D 555 ARG cc_start: 0.7418 (tpm170) cc_final: 0.7134 (tpm170) REVERT: D 604 MET cc_start: 0.3346 (ttt) cc_final: 0.2781 (ptm) REVERT: D 629 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7306 (pp20) REVERT: D 754 MET cc_start: 0.6755 (ppp) cc_final: 0.6002 (ppp) outliers start: 65 outliers final: 42 residues processed: 273 average time/residue: 0.4005 time to fit residues: 178.6378 Evaluate side-chains 259 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 258 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 338 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN B 178 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.101134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.082226 restraints weight = 241037.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.083011 restraints weight = 202399.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.083461 restraints weight = 176547.452| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29053 Z= 0.221 Angle : 0.762 12.289 39383 Z= 0.391 Chirality : 0.047 0.321 4378 Planarity : 0.006 0.059 5171 Dihedral : 6.898 59.867 4141 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.73 % Favored : 91.24 % Rotamer: Outliers : 3.29 % Allowed : 16.30 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3653 helix: 0.19 (0.13), residues: 1481 sheet: -0.68 (0.23), residues: 505 loop : -1.83 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 838 HIS 0.010 0.002 HIS A 76 PHE 0.033 0.002 PHE A 387 TYR 0.018 0.002 TYR D 723 ARG 0.014 0.001 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 1183) hydrogen bonds : angle 5.82350 ( 3453) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.51829 ( 8) covalent geometry : bond 0.00477 (29044) covalent geometry : angle 0.76209 (39375) Misc. bond : bond 0.00191 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 224 time to evaluate : 3.391 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 283 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5436 (tp) REVERT: A 450 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 616 MET cc_start: 0.8123 (tpp) cc_final: 0.7882 (tpp) REVERT: A 871 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6717 (t80) REVERT: A 900 MET cc_start: 0.8014 (mpp) cc_final: 0.7639 (mpp) REVERT: A 1001 GLU cc_start: 0.8350 (pp20) cc_final: 0.8058 (pm20) REVERT: A 1093 GLN cc_start: 0.8722 (pp30) cc_final: 0.8477 (pp30) REVERT: A 1111 GLN cc_start: 0.6921 (mt0) cc_final: 0.6670 (pp30) REVERT: B 108 GLU cc_start: 0.9038 (pt0) cc_final: 0.8811 (pp20) REVERT: B 261 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.5181 (m-10) REVERT: B 677 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.5810 (t80) REVERT: B 783 MET cc_start: 0.8815 (tpp) cc_final: 0.8401 (tpp) REVERT: B 801 MET cc_start: 0.7390 (mmt) cc_final: 0.6950 (mmt) REVERT: C 566 MET cc_start: 0.0197 (ttp) cc_final: -0.0188 (ttm) REVERT: C 671 MET cc_start: 0.5117 (tpt) cc_final: 0.4586 (tpt) REVERT: C 783 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5072 (mmt) REVERT: C 804 MET cc_start: 0.9096 (tpp) cc_final: 0.8691 (mmt) REVERT: C 854 MET cc_start: 0.8491 (tpt) cc_final: 0.7976 (tpt) REVERT: C 855 LYS cc_start: 0.8351 (tmmt) cc_final: 0.7914 (mtmt) REVERT: C 879 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7007 (t70) REVERT: C 881 MET cc_start: 0.8883 (mmm) cc_final: 0.8468 (mmm) REVERT: C 910 SER cc_start: 0.7304 (OUTLIER) cc_final: 0.6721 (p) REVERT: D 604 MET cc_start: 0.3223 (ttt) cc_final: 0.2817 (ptm) REVERT: D 637 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.6702 (mp) outliers start: 99 outliers final: 59 residues processed: 305 average time/residue: 0.4275 time to fit residues: 214.6274 Evaluate side-chains 278 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 210 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 947 PHE Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 294 optimal weight: 30.0000 chunk 362 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 295 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 346 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1073 GLN ** C1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.101532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.082897 restraints weight = 237843.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.083542 restraints weight = 197636.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.084276 restraints weight = 171923.904| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29053 Z= 0.175 Angle : 0.697 10.092 39383 Z= 0.355 Chirality : 0.045 0.226 4378 Planarity : 0.005 0.056 5171 Dihedral : 6.811 59.874 4141 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.99 % Favored : 91.98 % Rotamer: Outliers : 2.75 % Allowed : 18.45 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3653 helix: 0.31 (0.13), residues: 1487 sheet: -0.62 (0.24), residues: 490 loop : -1.83 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 624 HIS 0.009 0.001 HIS A 76 PHE 0.019 0.002 PHE B 848 TYR 0.015 0.002 TYR D 503 ARG 0.011 0.001 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 1183) hydrogen bonds : angle 5.69722 ( 3453) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.39126 ( 8) covalent geometry : bond 0.00383 (29044) covalent geometry : angle 0.69699 (39375) Misc. bond : bond 0.00108 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.7041 (ttpt) cc_final: 0.6220 (mmmt) REVERT: A 450 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 871 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6532 (t80) REVERT: A 881 MET cc_start: 0.8242 (tmm) cc_final: 0.7990 (mmt) REVERT: A 1001 GLU cc_start: 0.8354 (pp20) cc_final: 0.8058 (pm20) REVERT: A 1111 GLN cc_start: 0.7070 (mt0) cc_final: 0.6828 (pp30) REVERT: B 108 GLU cc_start: 0.9048 (pt0) cc_final: 0.8831 (pp20) REVERT: B 261 TYR cc_start: 0.5624 (OUTLIER) cc_final: 0.5192 (m-10) REVERT: B 677 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.5673 (t80) REVERT: B 801 MET cc_start: 0.7441 (mmt) cc_final: 0.6982 (mmt) REVERT: B 891 LYS cc_start: 0.7039 (tptp) cc_final: 0.6300 (tttt) REVERT: B 1166 MET cc_start: 0.3551 (ptt) cc_final: 0.3232 (pmm) REVERT: C 566 MET cc_start: -0.0361 (ttp) cc_final: -0.0700 (ttm) REVERT: C 671 MET cc_start: 0.5064 (tpt) cc_final: 0.4570 (tpt) REVERT: C 804 MET cc_start: 0.9088 (tpp) cc_final: 0.8780 (mmt) REVERT: C 854 MET cc_start: 0.8467 (tpt) cc_final: 0.7810 (tpt) REVERT: C 881 MET cc_start: 0.8883 (mmm) cc_final: 0.8430 (mmm) REVERT: C 910 SER cc_start: 0.7349 (OUTLIER) cc_final: 0.7145 (p) REVERT: C 988 GLN cc_start: 0.8290 (tp40) cc_final: 0.8013 (mp10) REVERT: D 604 MET cc_start: 0.3357 (ttt) cc_final: 0.2855 (ptm) REVERT: D 754 MET cc_start: 0.6607 (ppp) cc_final: 0.5622 (ppp) outliers start: 83 outliers final: 56 residues processed: 278 average time/residue: 0.4045 time to fit residues: 180.1601 Evaluate side-chains 267 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1043 LYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 574 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 71 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 chunk 224 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 341 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.102205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.083392 restraints weight = 237035.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.084078 restraints weight = 198451.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.084769 restraints weight = 174484.847| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29053 Z= 0.141 Angle : 0.685 11.768 39383 Z= 0.343 Chirality : 0.045 0.286 4378 Planarity : 0.005 0.053 5171 Dihedral : 6.657 59.785 4141 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.88 % Favored : 92.09 % Rotamer: Outliers : 2.62 % Allowed : 19.15 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3653 helix: 0.51 (0.13), residues: 1480 sheet: -0.53 (0.24), residues: 485 loop : -1.78 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 624 HIS 0.007 0.001 HIS A 76 PHE 0.035 0.002 PHE C 662 TYR 0.016 0.001 TYR D 503 ARG 0.005 0.001 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 1183) hydrogen bonds : angle 5.53229 ( 3453) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.09658 ( 8) covalent geometry : bond 0.00315 (29044) covalent geometry : angle 0.68467 (39375) Misc. bond : bond 0.00055 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 214 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8352 (m-10) cc_final: 0.8129 (m-10) REVERT: A 283 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.4992 (tp) REVERT: A 428 LYS cc_start: 0.6890 (ttpt) cc_final: 0.6086 (mmmt) REVERT: A 450 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7620 (t80) REVERT: A 508 MET cc_start: 0.8582 (mmt) cc_final: 0.8143 (mmt) REVERT: A 616 MET cc_start: 0.7984 (tpp) cc_final: 0.7511 (tpp) REVERT: A 871 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6575 (t80) REVERT: A 881 MET cc_start: 0.8185 (tmm) cc_final: 0.7952 (mmt) REVERT: A 1001 GLU cc_start: 0.8351 (pp20) cc_final: 0.8051 (pm20) REVERT: A 1111 GLN cc_start: 0.7231 (mt0) cc_final: 0.6974 (pp30) REVERT: A 1168 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.5076 (mp) REVERT: B 105 VAL cc_start: 0.9618 (m) cc_final: 0.9102 (p) REVERT: B 108 GLU cc_start: 0.9127 (pt0) cc_final: 0.8866 (pp20) REVERT: B 261 TYR cc_start: 0.5565 (OUTLIER) cc_final: 0.5094 (m-10) REVERT: B 634 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7908 (mp) REVERT: B 677 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.5557 (t80) REVERT: B 891 LYS cc_start: 0.7036 (tptp) cc_final: 0.6318 (tttt) REVERT: C 566 MET cc_start: -0.0654 (ttp) cc_final: -0.1001 (ttm) REVERT: C 671 MET cc_start: 0.5137 (tpt) cc_final: 0.4573 (tpt) REVERT: C 801 MET cc_start: 0.8043 (mtp) cc_final: 0.7799 (mtt) REVERT: C 804 MET cc_start: 0.9077 (tpp) cc_final: 0.8829 (mmt) REVERT: C 810 MET cc_start: 0.8564 (mmm) cc_final: 0.8344 (mmm) REVERT: C 855 LYS cc_start: 0.8182 (tmmt) cc_final: 0.7646 (mtmt) REVERT: C 881 MET cc_start: 0.8857 (mmm) cc_final: 0.8422 (mmp) REVERT: C 910 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7100 (p) REVERT: C 988 GLN cc_start: 0.8420 (tp40) cc_final: 0.8089 (mp10) REVERT: D 604 MET cc_start: 0.3397 (ttt) cc_final: 0.2725 (ptm) REVERT: D 754 MET cc_start: 0.6456 (ppp) cc_final: 0.5514 (ppp) outliers start: 79 outliers final: 58 residues processed: 272 average time/residue: 0.4075 time to fit residues: 177.7184 Evaluate side-chains 274 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 203 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 308 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 6 optimal weight: 0.0030 chunk 103 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1040 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 = 0.4458 r_free = 0.4458 target = 0.103140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.084560 restraints weight = 234634.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.085187 restraints weight = 202082.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.085699 restraints weight = 177214.891| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29053 Z= 0.125 Angle : 0.670 18.175 39383 Z= 0.331 Chirality : 0.044 0.217 4378 Planarity : 0.005 0.050 5171 Dihedral : 6.475 59.399 4141 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.61 % Favored : 92.34 % Rotamer: Outliers : 2.22 % Allowed : 19.71 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3653 helix: 0.65 (0.14), residues: 1481 sheet: -0.35 (0.25), residues: 461 loop : -1.71 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 624 HIS 0.005 0.001 HIS A 76 PHE 0.023 0.001 PHE A 53 TYR 0.017 0.001 TYR D 503 ARG 0.005 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 1183) hydrogen bonds : angle 5.34000 ( 3453) SS BOND : bond 0.00246 ( 4) SS BOND : angle 1.20654 ( 8) covalent geometry : bond 0.00281 (29044) covalent geometry : angle 0.67025 (39375) Misc. bond : bond 0.00021 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 218 time to evaluate : 3.133 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 53 PHE cc_start: 0.8236 (m-10) cc_final: 0.7983 (m-10) REVERT: A 115 HIS cc_start: 0.6370 (m90) cc_final: 0.6140 (m90) REVERT: A 428 LYS cc_start: 0.6676 (ttpt) cc_final: 0.5958 (mmmt) REVERT: A 508 MET cc_start: 0.8692 (mmt) cc_final: 0.8349 (mmt) REVERT: A 616 MET cc_start: 0.7883 (tpp) cc_final: 0.7490 (tpp) REVERT: A 871 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6569 (t80) REVERT: A 921 MET cc_start: 0.7115 (mmt) cc_final: 0.6686 (mmt) REVERT: A 1001 GLU cc_start: 0.8340 (pp20) cc_final: 0.7989 (pm20) REVERT: A 1111 GLN cc_start: 0.7204 (mt0) cc_final: 0.6896 (pp30) REVERT: A 1168 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5522 (mp) REVERT: B 105 VAL cc_start: 0.9593 (m) cc_final: 0.9068 (p) REVERT: B 108 GLU cc_start: 0.9082 (pt0) cc_final: 0.8857 (pp20) REVERT: B 261 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.4984 (m-10) REVERT: B 677 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5399 (t80) REVERT: B 891 LYS cc_start: 0.6958 (tptp) cc_final: 0.6224 (tttt) REVERT: C 566 MET cc_start: -0.0583 (ttp) cc_final: -0.1172 (ttm) REVERT: C 671 MET cc_start: 0.4828 (tpt) cc_final: 0.4367 (tpt) REVERT: C 855 LYS cc_start: 0.8081 (tmmt) cc_final: 0.7784 (mttp) REVERT: C 910 SER cc_start: 0.7370 (OUTLIER) cc_final: 0.6963 (p) REVERT: C 988 GLN cc_start: 0.8355 (tp40) cc_final: 0.8027 (mp10) REVERT: D 555 ARG cc_start: 0.7333 (tpm170) cc_final: 0.6947 (tpm170) REVERT: D 604 MET cc_start: 0.3338 (ttt) cc_final: 0.2706 (ptm) REVERT: D 754 MET cc_start: 0.6448 (ppp) cc_final: 0.5524 (ppp) REVERT: D 1143 MET cc_start: 0.6885 (ptt) cc_final: 0.6092 (pmm) outliers start: 67 outliers final: 50 residues processed: 265 average time/residue: 0.4148 time to fit residues: 175.4049 Evaluate side-chains 266 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 265 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 877 GLN B 110 ASN B 370 ASN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN B 924 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 956 HIS ** D1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.099214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.080859 restraints weight = 239432.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.081530 restraints weight = 199494.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.082055 restraints weight = 176009.879| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 29053 Z= 0.254 Angle : 0.815 15.528 39383 Z= 0.415 Chirality : 0.048 0.259 4378 Planarity : 0.006 0.063 5171 Dihedral : 6.958 59.638 4141 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.23 % Favored : 90.72 % Rotamer: Outliers : 2.32 % Allowed : 19.95 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 3653 helix: 0.13 (0.13), residues: 1476 sheet: -0.75 (0.24), residues: 479 loop : -1.90 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 624 HIS 0.010 0.002 HIS B 875 PHE 0.017 0.002 PHE C 662 TYR 0.015 0.002 TYR D 723 ARG 0.014 0.001 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 1183) hydrogen bonds : angle 5.93907 ( 3453) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.75331 ( 8) covalent geometry : bond 0.00546 (29044) covalent geometry : angle 0.81471 (39375) Misc. bond : bond 0.00219 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5170 (tp) REVERT: A 428 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6202 (mmmt) REVERT: A 871 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6505 (t80) REVERT: A 921 MET cc_start: 0.7145 (mmt) cc_final: 0.6745 (mmt) REVERT: A 1001 GLU cc_start: 0.8307 (pp20) cc_final: 0.8063 (pm20) REVERT: B 108 GLU cc_start: 0.9195 (pt0) cc_final: 0.8989 (pp20) REVERT: B 261 TYR cc_start: 0.5660 (OUTLIER) cc_final: 0.5349 (m-10) REVERT: B 508 MET cc_start: 0.8180 (mmt) cc_final: 0.7891 (mmp) REVERT: B 566 MET cc_start: 0.5800 (tpp) cc_final: 0.5463 (mmm) REVERT: B 634 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7896 (mp) REVERT: B 677 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.5188 (t80) REVERT: B 690 MET cc_start: 0.8318 (mmt) cc_final: 0.8112 (tpt) REVERT: B 891 LYS cc_start: 0.7080 (tptp) cc_final: 0.6313 (tttt) REVERT: C 566 MET cc_start: -0.0540 (ttp) cc_final: -0.0931 (ttm) REVERT: C 783 MET cc_start: 0.6336 (mmt) cc_final: 0.5606 (mmt) REVERT: C 855 LYS cc_start: 0.8125 (tmmt) cc_final: 0.7672 (mtmt) REVERT: C 900 MET cc_start: 0.0735 (OUTLIER) cc_final: 0.0497 (tpp) REVERT: C 910 SER cc_start: 0.7478 (OUTLIER) cc_final: 0.6978 (p) REVERT: C 988 GLN cc_start: 0.8514 (tp40) cc_final: 0.8076 (mp10) REVERT: D 754 MET cc_start: 0.6196 (ppp) cc_final: 0.5180 (ppp) outliers start: 70 outliers final: 56 residues processed: 268 average time/residue: 0.4361 time to fit residues: 187.1431 Evaluate side-chains 274 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 651 TYR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 839 GLU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1040 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 = 0.4422 r_free = 0.4422 target = 0.101140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.082543 restraints weight = 237835.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.083323 restraints weight = 198715.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.083753 restraints weight = 173480.163| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29053 Z= 0.144 Angle : 0.726 15.529 39383 Z= 0.360 Chirality : 0.045 0.240 4378 Planarity : 0.005 0.077 5171 Dihedral : 6.766 59.575 4141 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.36 % Rotamer: Outliers : 2.16 % Allowed : 20.35 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3653 helix: 0.36 (0.13), residues: 1480 sheet: -0.58 (0.24), residues: 468 loop : -1.85 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 624 HIS 0.006 0.001 HIS B 875 PHE 0.023 0.002 PHE C 662 TYR 0.016 0.001 TYR C 654 ARG 0.008 0.001 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 1183) hydrogen bonds : angle 5.62618 ( 3453) SS BOND : bond 0.00370 ( 4) SS BOND : angle 2.20146 ( 8) covalent geometry : bond 0.00324 (29044) covalent geometry : angle 0.72501 (39375) Misc. bond : bond 0.00059 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10951.12 seconds wall clock time: 191 minutes 37.01 seconds (11497.01 seconds total)