Starting phenix.real_space_refine on Mon Jun 23 21:21:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtd_32779/06_2025/7wtd_32779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtd_32779/06_2025/7wtd_32779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtd_32779/06_2025/7wtd_32779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtd_32779/06_2025/7wtd_32779.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtd_32779/06_2025/7wtd_32779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtd_32779/06_2025/7wtd_32779.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 12 5.49 5 S 152 5.16 5 C 17157 2.51 5 N 4733 2.21 5 O 5083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 27137 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "B" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "C" 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: "D" Number of atoms: 8860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 8860 Classifications: {'peptide': 1145} Link IDs: {'PTRANS': 65, 'TRANS': 1079} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'ATP': 1, 'COA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'ATP': 1, 'COA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.75, per 1000 atoms: 0.58 Number of scatterers: 27137 At special positions: 0 Unit cell: (159.5, 152.9, 134.2, 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 152 16.00 P 12 15.00 O 5083 8.00 N 4733 7.00 C 17157 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=2.03 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.6 seconds 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6426 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 22 sheets defined 47.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.890A pdb=" N LEU A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.848A 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 571 through 577 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.710A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 Processing helix chain 'A' and resid 611 through 618 removed outlier: 3.744A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.766A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.536A pdb=" N MET A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.563A pdb=" N THR A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 843 removed outlier: 3.615A pdb=" N VAL A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.982A pdb=" N VAL A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 924 Processing helix chain 'A' and resid 928 through 934 removed outlier: 3.755A pdb=" N GLN A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.995A 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 removed outlier: 3.520A pdb=" N PHE A1017 " --> pdb=" O TYR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1040 Processing helix chain 'B' and resid 496 through 510 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: 3.830A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.600A pdb=" N LEU B 587 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 Processing helix chain 'B' and resid 608 through 611 removed outlier: 3.832A pdb=" N THR B 611 " --> pdb=" O GLY B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.720A pdb=" N GLU B 629 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.603A pdb=" N VAL B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 670 " --> pdb=" O ALA B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.630A pdb=" N MET B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.543A pdb=" N TYR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 4.194A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 removed outlier: 3.733A pdb=" N ALA B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.700A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 843 removed outlier: 3.792A pdb=" N PHE B 832 " --> pdb=" O MET B 828 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 867 through 881 removed outlier: 3.838A pdb=" N ASN B 873 " --> pdb=" O GLY B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 902 removed outlier: 3.549A pdb=" N VAL B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 894 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 924 removed outlier: 3.872A pdb=" N LYS B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 941 through 950 removed outlier: 3.722A pdb=" N GLY B 950 " --> pdb=" O GLU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.909A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 986 through 999 removed outlier: 4.068A pdb=" N LEU B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1013 removed outlier: 3.601A pdb=" N VAL B1007 " --> pdb=" O THR B1003 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.663A pdb=" N ILE C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.548A pdb=" N ASN C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.675A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 149 Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.848A pdb=" N ALA C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.548A pdb=" N TYR C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 227 removed outlier: 3.759A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 303 Processing helix chain 'C' and resid 332 through 341 removed outlier: 4.515A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 354 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 435 through 450 Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.621A pdb=" N LEU C 462 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 474 removed outlier: 3.516A pdb=" N GLY C 474 " --> pdb=" O GLN C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 481 removed outlier: 4.385A pdb=" N ILE C 481 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 511 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 549 through 559 Processing helix chain 'C' and resid 571 through 578 removed outlier: 4.397A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 589 removed outlier: 3.643A pdb=" N LYS C 589 " --> pdb=" O ASP C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 586 through 589' Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 608 through 612 removed outlier: 4.412A pdb=" N PHE C 612 " --> pdb=" O GLY C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 634 removed outlier: 4.550A pdb=" N GLU C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.526A pdb=" N VAL C 659 " --> pdb=" O PRO C 655 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 697 removed outlier: 4.090A pdb=" N MET C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.660A pdb=" N TYR C 723 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 removed outlier: 4.150A pdb=" N ASP C 761 " --> pdb=" O SER C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.953A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 843 removed outlier: 3.577A pdb=" N ASP C 833 " --> pdb=" O GLU C 829 " (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 854 Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.983A pdb=" N ASN C 864 " --> pdb=" O ASP C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 881 removed outlier: 4.349A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 893 removed outlier: 3.536A pdb=" N VAL C 890 " --> pdb=" O LYS C 886 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 893 " --> pdb=" O GLU C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 901 Processing helix chain 'C' and resid 908 through 925 removed outlier: 4.255A pdb=" N LYS C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 934 removed outlier: 3.624A pdb=" N ALA C 931 " --> pdb=" O SER C 927 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 934 " --> pdb=" O GLU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 950 removed outlier: 3.861A pdb=" N GLY C 950 " --> pdb=" O GLU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 968 removed outlier: 3.733A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 987 through 998 removed outlier: 3.997A pdb=" N GLU C 991 " --> pdb=" O LEU C 987 " (cutoff:3.500A) removed outlier: 3.869A 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 1027 Processing helix chain 'C' and resid 1034 through 1040 Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.511A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.842A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 151 through 162 removed outlier: 3.954A pdb=" N ALA D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.596A pdb=" N TYR D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 228 removed outlier: 3.797A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 303 Processing helix chain 'D' and resid 332 through 340 removed outlier: 3.994A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 468 through 474 removed outlier: 3.538A pdb=" N LEU D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 481 removed outlier: 4.245A pdb=" N ILE D 481 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 removed outlier: 3.647A pdb=" N PHE D 488 " --> pdb=" O PRO D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 510 Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.652A pdb=" N LEU D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 571 through 577 removed outlier: 3.742A pdb=" N GLN D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.962A 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 617 removed outlier: 3.808A pdb=" N PHE D 612 " --> pdb=" O GLY D 608 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.546A pdb=" N GLY D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 697 Processing helix chain 'D' and resid 719 through 734 Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.528A pdb=" N ALA D 782 " --> pdb=" O ALA D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 816 Processing helix chain 'D' and resid 827 through 843 removed outlier: 4.057A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 848 removed outlier: 4.816A pdb=" N ALA D 847 " --> pdb=" O LEU D 844 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 848 " --> pdb=" O TYR D 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 844 through 848' Processing helix chain 'D' and resid 849 through 854 removed outlier: 3.852A pdb=" N THR D 853 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 881 removed outlier: 3.605A pdb=" N THR D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN D 873 " --> pdb=" O GLY D 869 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 874 " --> pdb=" O GLN D 870 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 4.093A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 901 " --> pdb=" O ALA D 897 " (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 Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 986 through 998 removed outlier: 4.367A pdb=" N LEU D 990 " --> pdb=" O ASP D 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU D 991 " --> pdb=" O LEU D 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 992 " --> pdb=" O GLN D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 4.080A 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 639 through 640 removed outlier: 8.135A pdb=" N GLN A 640 " --> pdb=" O PHE A 602 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 565 " --> pdb=" O PHE A 602 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET A 604 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP A 567 " --> pdb=" O MET A 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 642 through 644 removed outlier: 7.020A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 3.611A pdb=" N VAL A1050 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A1058 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 564 through 567 removed outlier: 7.717A pdb=" N LEU B 565 " --> pdb=" O PHE B 602 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET B 604 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 567 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLN B 640 " --> pdb=" O PHE B 602 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 674 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 704 " --> pdb=" O LYS B 741 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 768 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP B 795 " --> pdb=" O LEU B 768 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE B 770 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 796 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 3.581A pdb=" N VAL B1050 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B1058 " --> pdb=" O VAL B1050 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA B1062 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B1064 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B1077 " --> pdb=" O ALA B1064 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 85 removed outlier: 6.486A pdb=" N VAL C 40 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE C 66 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL C 42 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 39 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS C 115 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N MET C 41 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.771A pdb=" N GLU C 236 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 326 removed outlier: 6.323A pdb=" N GLU C 246 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU C 262 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN C 248 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER C 266 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL C 275 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 268 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS C 273 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL C 274 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG C 377 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 372 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS C 432 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 374 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 430 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS C 376 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS C 428 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 378 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 381 through 382 removed outlier: 3.701A pdb=" N GLN C 388 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.137A pdb=" N GLY C 392 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.078A pdb=" N ARG C 451 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 564 through 566 removed outlier: 6.169A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 770 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 795 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR C 772 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 700 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS C 739 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA C 702 " --> pdb=" O CYS C 739 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS C 741 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 703 " --> pdb=" O VAL C 676 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 604 through 605 removed outlier: 6.338A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 1047 through 1053 removed outlier: 7.336A pdb=" N GLU C1047 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ALA C1062 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU C1049 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE C1060 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLU C1051 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU C1058 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C1053 " --> pdb=" O LYS C1056 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C1076 " --> pdb=" O ILE C1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.340A pdb=" N VAL D 40 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE D 66 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL D 42 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 113 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.510A pdb=" N ARG D 205 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.843A pdb=" N GLU D 324 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.657A pdb=" N VAL D 427 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 381 through 382 removed outlier: 3.802A pdb=" N GLN D 388 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 564 through 567 removed outlier: 8.588A pdb=" N GLU D 605 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP D 567 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 674 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 700 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS D 739 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 702 " --> pdb=" O CYS D 739 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS D 741 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE D 704 " --> pdb=" O LYS D 741 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1047 through 1051 removed outlier: 6.512A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL D1065 " --> pdb=" O GLN D1075 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN D1075 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1112 through 1114 removed outlier: 5.635A pdb=" N ALA D1114 " --> pdb=" O LEU D1173 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU D1173 " --> pdb=" O ALA D1114 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3210 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: 11.53 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4583 1.30 - 1.44: 7057 1.44 - 1.57: 15813 1.57 - 1.70: 30 1.70 - 1.84: 262 Bond restraints: 27745 Sorted by residual: bond pdb=" C1B COA C2001 " pdb=" C2B COA C2001 " ideal model delta sigma weight residual 1.533 1.328 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C1B COA D2001 " pdb=" C2B COA D2001 " ideal model delta sigma weight residual 1.533 1.329 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C1B COA D2001 " pdb=" O4B COA D2001 " ideal model delta sigma weight residual 1.418 1.595 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C1B COA C2001 " pdb=" O4B COA C2001 " ideal model delta sigma weight residual 1.418 1.592 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" C3B COA C2001 " pdb=" C4B COA C2001 " ideal model delta sigma weight residual 1.529 1.358 0.171 2.00e-02 2.50e+03 7.28e+01 ... (remaining 27740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 37453 4.18 - 8.35: 170 8.35 - 12.53: 15 12.53 - 16.71: 1 16.71 - 20.88: 7 Bond angle restraints: 37646 Sorted by residual: angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 132.69 7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" C1B COA C2001 " pdb=" N9A COA C2001 " pdb=" C8A COA C2001 " ideal model delta sigma weight residual 124.69 103.81 20.88 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C1B COA D2001 " pdb=" N9A COA D2001 " pdb=" C8A COA D2001 " ideal model delta sigma weight residual 124.69 104.65 20.04 3.00e+00 1.11e-01 4.46e+01 angle pdb=" N1A COA D2001 " pdb=" C6A COA D2001 " pdb=" N6A COA D2001 " ideal model delta sigma weight residual 119.19 99.57 19.62 3.00e+00 1.11e-01 4.28e+01 angle pdb=" N1A COA C2001 " pdb=" C6A COA C2001 " pdb=" N6A COA C2001 " ideal model delta sigma weight residual 119.19 100.08 19.11 3.00e+00 1.11e-01 4.06e+01 ... (remaining 37641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 15171 18.09 - 36.19: 1315 36.19 - 54.28: 268 54.28 - 72.37: 88 72.37 - 90.47: 30 Dihedral angle restraints: 16872 sinusoidal: 6857 harmonic: 10015 Sorted by residual: dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 -176.53 -90.47 1 1.00e+01 1.00e-02 9.68e+01 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 93.00 174.82 -81.82 1 1.00e+01 1.00e-02 8.23e+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 93.00 154.22 -61.22 1 1.00e+01 1.00e-02 4.98e+01 ... (remaining 16869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3666 0.074 - 0.147: 467 0.147 - 0.221: 26 0.221 - 0.294: 1 0.294 - 0.368: 3 Chirality restraints: 4163 Sorted by residual: chirality pdb=" CB VAL C 164 " pdb=" CA VAL C 164 " pdb=" CG1 VAL C 164 " pdb=" CG2 VAL C 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C3B COA C2001 " pdb=" C2B COA C2001 " pdb=" C4B COA C2001 " pdb=" O3B COA C2001 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4160 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 199 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C GLY C 199 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY C 199 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 200 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D1030 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C LEU D1030 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU D1030 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP D1031 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 908 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO C 909 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 909 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 909 " 0.037 5.00e-02 4.00e+02 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 6 1.77 - 2.55: 344 2.55 - 3.34: 35186 3.34 - 4.12: 66127 4.12 - 4.90: 116215 Warning: very small nonbonded interaction distances. Nonbonded interactions: 217878 Sorted by model distance: nonbonded pdb=" NH2 ARG C 393 " pdb=" OE1 GLN C1075 " model vdw 0.990 3.120 nonbonded pdb=" OE2 GLU C 395 " pdb=" N LEU C1088 " model vdw 1.323 3.120 nonbonded pdb=" NE2 GLN C 78 " pdb=" OD1 ASN D1081 " model vdw 1.374 3.120 nonbonded pdb=" OE1 GLN D 388 " pdb=" CE MET D1145 " model vdw 1.463 3.460 nonbonded pdb=" O ASN C1081 " pdb=" OE1 GLN D 78 " model vdw 1.580 3.040 ... (remaining 217873 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 34 through 1178) selection = (chain 'D' and resid 34 through 1178) } 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: 0.010 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 62.350 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 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 : 0.008 0.825 27755 Z= 0.653 Angle : 0.841 20.884 37654 Z= 0.442 Chirality : 0.047 0.368 4163 Planarity : 0.005 0.071 4950 Dihedral : 14.981 89.743 10434 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 1.15 % Allowed : 0.87 % Favored : 97.98 % Cbeta Deviations : 0.03 % 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: -0.88 (0.14), residues: 3483 helix: 0.63 (0.14), residues: 1407 sheet: -0.40 (0.24), residues: 471 loop : -1.77 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 624 HIS 0.019 0.001 HIS C 998 PHE 0.028 0.001 PHE A 876 TYR 0.023 0.002 TYR D 304 ARG 0.008 0.001 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.19062 ( 1095) hydrogen bonds : angle 7.18956 ( 3210) SS BOND : bond 0.00455 ( 4) SS BOND : angle 2.70188 ( 8) covalent geometry : bond 0.00548 (27745) covalent geometry : angle 0.83999 (37646) Misc. bond : bond 0.39493 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 502 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 600 LYS cc_start: 0.7347 (mttt) cc_final: 0.6917 (mttt) REVERT: A 641 MET cc_start: 0.6574 (ptp) cc_final: 0.6223 (ptt) REVERT: A 675 ARG cc_start: 0.6946 (ttm170) cc_final: 0.6222 (mtt-85) REVERT: A 686 MET cc_start: 0.9322 (mpp) cc_final: 0.9116 (mpp) REVERT: A 828 MET cc_start: 0.8521 (ttt) cc_final: 0.8279 (tpp) REVERT: A 986 ASP cc_start: 0.8679 (t0) cc_final: 0.8334 (t0) REVERT: A 992 LYS cc_start: 0.7461 (mmpt) cc_final: 0.7073 (mmtt) REVERT: B 504 LEU cc_start: 0.9080 (mm) cc_final: 0.8703 (pp) REVERT: B 724 MET cc_start: 0.9310 (mpp) cc_final: 0.8960 (mpp) REVERT: C 92 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8679 (Cg_endo) REVERT: C 204 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.5895 (mtt) REVERT: C 492 PRO cc_start: 0.7413 (Cg_endo) cc_final: 0.6527 (Cg_exo) REVERT: C 496 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7323 (mpp80) REVERT: C 502 HIS cc_start: 0.9031 (m90) cc_final: 0.8655 (m90) REVERT: C 686 MET cc_start: 0.8730 (mpp) cc_final: 0.7637 (mpp) REVERT: C 724 MET cc_start: 0.8872 (mmm) cc_final: 0.8449 (mmm) REVERT: C 754 MET cc_start: 0.9458 (pmm) cc_final: 0.9118 (pmm) REVERT: C 801 MET cc_start: 0.8127 (mpp) cc_final: 0.7721 (mpp) REVERT: C 854 MET cc_start: 0.7831 (mmm) cc_final: 0.7413 (mpp) REVERT: C 1032 SER cc_start: 0.8337 (m) cc_final: 0.8125 (t) REVERT: C 1038 PHE cc_start: 0.8563 (t80) cc_final: 0.8222 (t80) REVERT: C 1048 PHE cc_start: 0.8758 (p90) cc_final: 0.8484 (p90) REVERT: C 1098 MET cc_start: 0.7406 (tmm) cc_final: 0.7173 (tpp) REVERT: D 453 ARG cc_start: 0.4412 (OUTLIER) cc_final: 0.2005 (mmt180) REVERT: D 500 LEU cc_start: 0.9269 (mt) cc_final: 0.9055 (mm) REVERT: D 604 MET cc_start: 0.7219 (tpt) cc_final: 0.6670 (tpp) REVERT: D 641 MET cc_start: 0.6989 (ptm) cc_final: 0.5257 (tmm) REVERT: D 671 MET cc_start: 0.3812 (tpt) cc_final: 0.2996 (tpt) REVERT: D 784 LEU cc_start: 0.9233 (mm) cc_final: 0.8892 (pp) REVERT: D 920 PHE cc_start: 0.7319 (t80) cc_final: 0.7081 (t80) REVERT: D 1116 MET cc_start: 0.4981 (mpp) cc_final: 0.4673 (ptm) REVERT: D 1122 ASP cc_start: 0.8629 (m-30) cc_final: 0.8289 (p0) REVERT: D 1145 MET cc_start: 0.4614 (mtm) cc_final: 0.3340 (ttm) outliers start: 33 outliers final: 3 residues processed: 524 average time/residue: 0.4433 time to fit residues: 354.1448 Evaluate side-chains 309 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 303 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain D residue 453 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 316 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS C 348 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN C 506 HIS C 560 HIS ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 375 GLN D 436 HIS D 463 GLN D 467 ASN D 494 GLN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.072334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.058479 restraints weight = 207835.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.060015 restraints weight = 134063.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.061207 restraints weight = 97069.879| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27755 Z= 0.211 Angle : 0.761 11.260 37654 Z= 0.392 Chirality : 0.047 0.293 4163 Planarity : 0.006 0.085 4950 Dihedral : 8.758 87.037 3992 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 2.16 % Allowed : 11.36 % Favored : 86.48 % 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: -1.06 (0.14), residues: 3483 helix: 0.42 (0.13), residues: 1437 sheet: -0.59 (0.24), residues: 463 loop : -1.80 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 607 HIS 0.018 0.002 HIS C 574 PHE 0.028 0.002 PHE A 876 TYR 0.027 0.002 TYR B1013 ARG 0.011 0.001 ARG B 625 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 1095) hydrogen bonds : angle 5.95017 ( 3210) SS BOND : bond 0.00536 ( 4) SS BOND : angle 2.16736 ( 8) covalent geometry : bond 0.00453 (27745) covalent geometry : angle 0.76016 (37646) Misc. bond : bond 0.00313 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 565 LEU cc_start: 0.9310 (tp) cc_final: 0.9091 (pt) REVERT: A 577 LEU cc_start: 0.8890 (tp) cc_final: 0.8630 (tp) REVERT: A 583 ARG cc_start: 0.8383 (ttt180) cc_final: 0.8159 (ttm170) REVERT: A 641 MET cc_start: 0.7018 (ptp) cc_final: 0.6816 (ptm) REVERT: A 675 ARG cc_start: 0.7482 (ttm170) cc_final: 0.6553 (mtm-85) REVERT: A 686 MET cc_start: 0.9204 (mpp) cc_final: 0.9001 (mpp) REVERT: A 724 MET cc_start: 0.8515 (tpp) cc_final: 0.8149 (tpp) REVERT: A 743 MET cc_start: 0.7573 (tpt) cc_final: 0.7042 (tpp) REVERT: A 828 MET cc_start: 0.8879 (ttt) cc_final: 0.8662 (tpp) REVERT: A 986 ASP cc_start: 0.8599 (t0) cc_final: 0.8221 (t0) REVERT: B 828 MET cc_start: 0.8033 (ppp) cc_final: 0.7692 (ppp) REVERT: C 84 TYR cc_start: 0.7495 (m-80) cc_final: 0.7249 (m-80) REVERT: C 300 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.7005 (pptt) REVERT: C 422 TYR cc_start: 0.3854 (m-80) cc_final: 0.3172 (m-80) REVERT: C 442 LYS cc_start: 0.9261 (mttt) cc_final: 0.8852 (mttt) REVERT: C 686 MET cc_start: 0.8877 (mpp) cc_final: 0.8071 (mpp) REVERT: C 724 MET cc_start: 0.9241 (mmm) cc_final: 0.8849 (mmm) REVERT: C 804 MET cc_start: 0.7450 (tpt) cc_final: 0.7135 (mmp) REVERT: C 854 MET cc_start: 0.7787 (mmm) cc_final: 0.7491 (mpp) REVERT: C 874 LEU cc_start: 0.9103 (tp) cc_final: 0.8721 (mt) REVERT: C 1032 SER cc_start: 0.8742 (m) cc_final: 0.8487 (t) REVERT: C 1038 PHE cc_start: 0.8795 (t80) cc_final: 0.8385 (t80) REVERT: C 1048 PHE cc_start: 0.9175 (p90) cc_final: 0.8792 (p90) REVERT: D 239 ILE cc_start: 0.2270 (mp) cc_final: 0.1704 (mm) REVERT: D 353 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6864 (mm-30) REVERT: D 453 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.4680 (mmm-85) REVERT: D 500 LEU cc_start: 0.9348 (mt) cc_final: 0.9100 (mm) REVERT: D 604 MET cc_start: 0.7443 (tpt) cc_final: 0.6843 (tpp) REVERT: D 686 MET cc_start: 0.8567 (mmt) cc_final: 0.8337 (mmt) REVERT: D 728 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8924 (pt0) REVERT: D 784 LEU cc_start: 0.9208 (mm) cc_final: 0.8889 (pp) REVERT: D 920 PHE cc_start: 0.7804 (t80) cc_final: 0.7473 (t80) REVERT: D 1116 MET cc_start: 0.6791 (mpp) cc_final: 0.5988 (ptp) REVERT: D 1122 ASP cc_start: 0.8638 (m-30) cc_final: 0.8316 (p0) REVERT: D 1143 MET cc_start: 0.1399 (mmp) cc_final: 0.0229 (mmm) REVERT: D 1145 MET cc_start: 0.0654 (mtm) cc_final: -0.0538 (ttp) REVERT: D 1166 MET cc_start: 0.6755 (tmm) cc_final: 0.6157 (ppp) outliers start: 62 outliers final: 31 residues processed: 358 average time/residue: 0.4092 time to fit residues: 234.7947 Evaluate side-chains 312 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 18 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 HIS ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS D 44 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D1075 GLN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.071046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.057448 restraints weight = 208853.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.059030 restraints weight = 132959.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.060109 restraints weight = 95413.355| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27755 Z= 0.163 Angle : 0.685 12.139 37654 Z= 0.348 Chirality : 0.045 0.190 4163 Planarity : 0.005 0.058 4950 Dihedral : 8.313 87.309 3985 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.88 % Rotamer: Outliers : 2.65 % Allowed : 14.19 % Favored : 83.16 % 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: -1.00 (0.14), residues: 3483 helix: 0.48 (0.13), residues: 1438 sheet: -0.73 (0.24), residues: 471 loop : -1.72 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 624 HIS 0.016 0.002 HIS A 998 PHE 0.028 0.002 PHE A 876 TYR 0.022 0.002 TYR C 118 ARG 0.027 0.001 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 1095) hydrogen bonds : angle 5.64082 ( 3210) SS BOND : bond 0.00415 ( 4) SS BOND : angle 1.96691 ( 8) covalent geometry : bond 0.00357 (27745) covalent geometry : angle 0.68463 (37646) Misc. bond : bond 0.00191 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 289 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9281 (tp) cc_final: 0.9030 (pt) REVERT: A 566 MET cc_start: 0.6890 (ttp) cc_final: 0.5012 (ttm) REVERT: A 577 LEU cc_start: 0.8874 (tp) cc_final: 0.8632 (tp) REVERT: A 583 ARG cc_start: 0.8469 (ttt180) cc_final: 0.7712 (ttt180) REVERT: A 641 MET cc_start: 0.7126 (ptp) cc_final: 0.6906 (ptm) REVERT: A 675 ARG cc_start: 0.7560 (ttm170) cc_final: 0.6792 (mtt180) REVERT: A 686 MET cc_start: 0.9207 (mpp) cc_final: 0.8977 (mpp) REVERT: A 920 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9115 (m-80) REVERT: A 923 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8045 (pp30) REVERT: A 986 ASP cc_start: 0.8645 (t0) cc_final: 0.8288 (t0) REVERT: B 496 ARG cc_start: 0.8555 (mtt180) cc_final: 0.8051 (mmm160) REVERT: C 300 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6948 (pptt) REVERT: C 442 LYS cc_start: 0.9284 (mttt) cc_final: 0.9069 (mttt) REVERT: C 604 MET cc_start: 0.8690 (mmm) cc_final: 0.7719 (tpp) REVERT: C 686 MET cc_start: 0.8925 (mpp) cc_final: 0.8484 (mpp) REVERT: C 724 MET cc_start: 0.9219 (mmm) cc_final: 0.8791 (mmm) REVERT: C 1032 SER cc_start: 0.8874 (m) cc_final: 0.8664 (t) REVERT: C 1038 PHE cc_start: 0.8790 (t80) cc_final: 0.8395 (t80) REVERT: C 1048 PHE cc_start: 0.9228 (p90) cc_final: 0.8932 (p90) REVERT: C 1051 GLU cc_start: 0.8388 (tp30) cc_final: 0.8166 (tp30) REVERT: C 1088 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8899 (mm) REVERT: D 47 GLU cc_start: 0.8685 (pp20) cc_final: 0.8403 (tp30) REVERT: D 74 GLN cc_start: 0.8250 (tp40) cc_final: 0.7932 (tp40) REVERT: D 337 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8425 (tm-30) REVERT: D 500 LEU cc_start: 0.9344 (mt) cc_final: 0.9058 (mm) REVERT: D 604 MET cc_start: 0.7189 (tpt) cc_final: 0.6498 (tpp) REVERT: D 641 MET cc_start: 0.6648 (ptm) cc_final: 0.5498 (ppp) REVERT: D 671 MET cc_start: 0.4133 (tpt) cc_final: 0.3593 (tpt) REVERT: D 686 MET cc_start: 0.8604 (mmt) cc_final: 0.8380 (mmt) REVERT: D 784 LEU cc_start: 0.9150 (mm) cc_final: 0.8808 (pp) REVERT: D 854 MET cc_start: 0.8644 (mmm) cc_final: 0.8101 (tpp) REVERT: D 920 PHE cc_start: 0.7883 (t80) cc_final: 0.7581 (t80) REVERT: D 1012 MET cc_start: 0.8822 (mpp) cc_final: 0.8569 (mpp) REVERT: D 1116 MET cc_start: 0.6568 (mpp) cc_final: 0.5783 (ptp) REVERT: D 1122 ASP cc_start: 0.8620 (m-30) cc_final: 0.8312 (p0) REVERT: D 1143 MET cc_start: 0.1403 (mmp) cc_final: 0.0195 (mmm) REVERT: D 1145 MET cc_start: 0.1517 (mtm) cc_final: 0.0028 (ttp) REVERT: D 1166 MET cc_start: 0.6755 (tmm) cc_final: 0.5926 (ppp) outliers start: 76 outliers final: 41 residues processed: 342 average time/residue: 0.4519 time to fit residues: 254.3654 Evaluate side-chains 314 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 163 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 326 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS ** C 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 GLN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 HIS D 463 GLN D 467 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.064396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.051510 restraints weight = 233388.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.052832 restraints weight = 149463.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.053746 restraints weight = 108260.357| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 27755 Z= 0.282 Angle : 0.850 12.506 37654 Z= 0.445 Chirality : 0.049 0.229 4163 Planarity : 0.007 0.074 4950 Dihedral : 8.567 85.765 3983 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.84 % Favored : 91.13 % Rotamer: Outliers : 3.97 % Allowed : 17.04 % Favored : 78.98 % 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: -1.79 (0.14), residues: 3483 helix: -0.43 (0.13), residues: 1467 sheet: -1.19 (0.23), residues: 489 loop : -1.89 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 838 HIS 0.030 0.003 HIS D 773 PHE 0.030 0.003 PHE B 553 TYR 0.040 0.003 TYR B1013 ARG 0.014 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 1095) hydrogen bonds : angle 6.06944 ( 3210) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.89170 ( 8) covalent geometry : bond 0.00595 (27745) covalent geometry : angle 0.84998 (37646) Misc. bond : bond 0.00132 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 269 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9202 (tp) cc_final: 0.8949 (pt) REVERT: A 566 MET cc_start: 0.6936 (ttp) cc_final: 0.4665 (ttp) REVERT: A 583 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8506 (ttm170) REVERT: A 604 MET cc_start: 0.3014 (ppp) cc_final: 0.2349 (ppp) REVERT: A 675 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7239 (mtt180) REVERT: A 1044 ILE cc_start: 0.8863 (mm) cc_final: 0.8309 (tp) REVERT: B 496 ARG cc_start: 0.8847 (mtt180) cc_final: 0.8452 (mmm160) REVERT: B 566 MET cc_start: 0.8133 (tmm) cc_final: 0.7903 (tmm) REVERT: B 604 MET cc_start: 0.7642 (tpt) cc_final: 0.7300 (tpp) REVERT: B 754 MET cc_start: 0.9308 (mmm) cc_final: 0.9025 (mmm) REVERT: C 84 TYR cc_start: 0.7799 (m-80) cc_final: 0.7259 (m-80) REVERT: C 204 MET cc_start: 0.7570 (mmp) cc_final: 0.6952 (mmp) REVERT: C 300 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.7001 (pptt) REVERT: C 491 ARG cc_start: 0.9288 (ppt170) cc_final: 0.8960 (tmt170) REVERT: C 686 MET cc_start: 0.8911 (mpp) cc_final: 0.8045 (mpp) REVERT: C 724 MET cc_start: 0.9237 (mmm) cc_final: 0.8878 (mmm) REVERT: C 1048 PHE cc_start: 0.9322 (p90) cc_final: 0.9026 (p90) REVERT: C 1088 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8152 (mm) REVERT: D 56 CYS cc_start: 0.9313 (m) cc_final: 0.8904 (t) REVERT: D 74 GLN cc_start: 0.8432 (tp40) cc_final: 0.8075 (tp40) REVERT: D 294 ASP cc_start: 0.8409 (m-30) cc_final: 0.8038 (t70) REVERT: D 375 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: D 463 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8837 (tm-30) REVERT: D 500 LEU cc_start: 0.9328 (mt) cc_final: 0.9024 (mm) REVERT: D 604 MET cc_start: 0.7475 (tpt) cc_final: 0.6590 (tpp) REVERT: D 784 LEU cc_start: 0.9142 (mm) cc_final: 0.8709 (pp) REVERT: D 804 MET cc_start: 0.8843 (mmp) cc_final: 0.8477 (mmp) REVERT: D 848 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5843 (p90) REVERT: D 920 PHE cc_start: 0.8114 (t80) cc_final: 0.7839 (t80) REVERT: D 1116 MET cc_start: 0.6531 (mpp) cc_final: 0.6121 (ptp) REVERT: D 1122 ASP cc_start: 0.8560 (m-30) cc_final: 0.8345 (p0) REVERT: D 1143 MET cc_start: 0.1681 (mmp) cc_final: 0.0277 (mmm) REVERT: D 1166 MET cc_start: 0.6603 (tmm) cc_final: 0.5753 (ppp) outliers start: 114 outliers final: 70 residues processed: 355 average time/residue: 0.4261 time to fit residues: 247.0844 Evaluate side-chains 317 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 243 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1084 LEU Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 51 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 ASN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 773 HIS ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 HIS ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** 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 = 0.4304 r_free = 0.4304 target = 0.065090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.052137 restraints weight = 224535.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.053487 restraints weight = 144733.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.054483 restraints weight = 105136.734| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27755 Z= 0.176 Angle : 0.722 11.143 37654 Z= 0.367 Chirality : 0.046 0.302 4163 Planarity : 0.005 0.063 4950 Dihedral : 8.198 87.920 3975 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.85 % Rotamer: Outliers : 3.45 % Allowed : 19.48 % Favored : 77.07 % 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: -1.50 (0.14), residues: 3483 helix: -0.06 (0.13), residues: 1462 sheet: -1.11 (0.24), residues: 465 loop : -1.85 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 838 HIS 0.008 0.002 HIS C 574 PHE 0.027 0.002 PHE A 876 TYR 0.024 0.002 TYR B1013 ARG 0.013 0.001 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1095) hydrogen bonds : angle 5.74613 ( 3210) SS BOND : bond 0.00840 ( 4) SS BOND : angle 1.98415 ( 8) covalent geometry : bond 0.00385 (27745) covalent geometry : angle 0.72114 (37646) Misc. bond : bond 0.00118 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 259 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9289 (tp) cc_final: 0.9003 (pt) REVERT: A 566 MET cc_start: 0.6907 (ttp) cc_final: 0.4395 (ttp) REVERT: A 583 ARG cc_start: 0.8739 (ttt180) cc_final: 0.8199 (ttt180) REVERT: A 636 ASN cc_start: 0.7731 (t0) cc_final: 0.7134 (p0) REVERT: A 641 MET cc_start: 0.7330 (ptp) cc_final: 0.6449 (ptp) REVERT: A 675 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7282 (mtt180) REVERT: A 686 MET cc_start: 0.9148 (mpp) cc_final: 0.8942 (mpp) REVERT: A 854 MET cc_start: 0.7160 (ppp) cc_final: 0.6924 (ppp) REVERT: A 986 ASP cc_start: 0.8651 (t0) cc_final: 0.8311 (t0) REVERT: B 496 ARG cc_start: 0.8569 (mtt180) cc_final: 0.8182 (mmm160) REVERT: B 604 MET cc_start: 0.7535 (tpt) cc_final: 0.7219 (tpt) REVERT: B 754 MET cc_start: 0.9326 (mmm) cc_final: 0.9009 (mmm) REVERT: C 204 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.6967 (mmp) REVERT: C 300 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.7019 (pptt) REVERT: C 491 ARG cc_start: 0.9166 (ppt170) cc_final: 0.8880 (tmt170) REVERT: C 604 MET cc_start: 0.8396 (mmm) cc_final: 0.7513 (tpp) REVERT: C 641 MET cc_start: 0.7084 (mtm) cc_final: 0.6827 (mtm) REVERT: C 724 MET cc_start: 0.9225 (mmm) cc_final: 0.8874 (mmm) REVERT: C 1022 ASP cc_start: 0.7622 (m-30) cc_final: 0.6468 (p0) REVERT: C 1048 PHE cc_start: 0.9204 (p90) cc_final: 0.8781 (p90) REVERT: D 47 GLU cc_start: 0.8777 (pp20) cc_final: 0.8543 (tp30) REVERT: D 294 ASP cc_start: 0.8288 (m-30) cc_final: 0.8040 (t70) REVERT: D 326 ASN cc_start: 0.8397 (m-40) cc_final: 0.7443 (t0) REVERT: D 604 MET cc_start: 0.7241 (tpt) cc_final: 0.6371 (tpp) REVERT: D 686 MET cc_start: 0.8614 (mmt) cc_final: 0.8344 (mmt) REVERT: D 724 MET cc_start: 0.9000 (mmm) cc_final: 0.8611 (mmm) REVERT: D 728 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8840 (mp0) REVERT: D 784 LEU cc_start: 0.9067 (mm) cc_final: 0.8644 (pp) REVERT: D 804 MET cc_start: 0.8647 (mmp) cc_final: 0.8239 (mmp) REVERT: D 920 PHE cc_start: 0.8204 (t80) cc_final: 0.7966 (t80) REVERT: D 1012 MET cc_start: 0.8841 (mpp) cc_final: 0.8641 (mpp) REVERT: D 1116 MET cc_start: 0.6507 (mpp) cc_final: 0.6144 (ptp) REVERT: D 1122 ASP cc_start: 0.8665 (m-30) cc_final: 0.8386 (p0) REVERT: D 1143 MET cc_start: 0.1819 (mmp) cc_final: 0.0506 (mmm) REVERT: D 1166 MET cc_start: 0.6255 (tmm) cc_final: 0.5363 (ppp) outliers start: 99 outliers final: 69 residues processed: 332 average time/residue: 0.5169 time to fit residues: 283.8615 Evaluate side-chains 318 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 246 time to evaluate : 5.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 171 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 ASN ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** 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 = 0.4274 r_free = 0.4274 target = 0.063900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.051090 restraints weight = 228930.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.052410 restraints weight = 148146.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.053327 restraints weight = 107631.007| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27755 Z= 0.186 Angle : 0.731 17.460 37654 Z= 0.371 Chirality : 0.046 0.279 4163 Planarity : 0.005 0.084 4950 Dihedral : 8.071 85.478 3975 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.42 % Rotamer: Outliers : 4.39 % Allowed : 19.28 % Favored : 76.33 % 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: -1.51 (0.14), residues: 3483 helix: -0.02 (0.13), residues: 1478 sheet: -1.12 (0.24), residues: 469 loop : -1.92 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 838 HIS 0.008 0.002 HIS D 76 PHE 0.043 0.002 PHE D 387 TYR 0.022 0.002 TYR B1013 ARG 0.021 0.001 ARG D 269 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 1095) hydrogen bonds : angle 5.66667 ( 3210) SS BOND : bond 0.00430 ( 4) SS BOND : angle 2.17486 ( 8) covalent geometry : bond 0.00404 (27745) covalent geometry : angle 0.73073 (37646) Misc. bond : bond 0.00110 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 246 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9241 (tp) cc_final: 0.8988 (pt) REVERT: A 566 MET cc_start: 0.6769 (ttp) cc_final: 0.4297 (ttp) REVERT: A 583 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8143 (ttt180) REVERT: A 675 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7212 (mtt180) REVERT: A 681 ASN cc_start: 0.8437 (p0) cc_final: 0.8220 (p0) REVERT: A 724 MET cc_start: 0.9031 (tpt) cc_final: 0.8727 (tpp) REVERT: B 496 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8208 (mmm160) REVERT: B 604 MET cc_start: 0.7786 (tpt) cc_final: 0.7391 (tpt) REVERT: B 754 MET cc_start: 0.9361 (mmm) cc_final: 0.9016 (mmm) REVERT: B 1008 LEU cc_start: 0.9266 (tp) cc_final: 0.8799 (pp) REVERT: C 204 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6981 (mmp) REVERT: C 300 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7085 (pptt) REVERT: C 724 MET cc_start: 0.9207 (mmm) cc_final: 0.8844 (mmm) REVERT: C 1022 ASP cc_start: 0.7953 (m-30) cc_final: 0.6786 (p0) REVERT: C 1048 PHE cc_start: 0.9211 (p90) cc_final: 0.8796 (p90) REVERT: D 47 GLU cc_start: 0.8865 (pp20) cc_final: 0.8500 (tp30) REVERT: D 268 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: D 326 ASN cc_start: 0.8315 (m-40) cc_final: 0.7306 (t0) REVERT: D 374 ILE cc_start: 0.8834 (mm) cc_final: 0.8476 (pt) REVERT: D 375 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: D 604 MET cc_start: 0.7272 (tpt) cc_final: 0.6394 (tpp) REVERT: D 641 MET cc_start: 0.6779 (ptm) cc_final: 0.5879 (ppp) REVERT: D 671 MET cc_start: 0.5347 (tpt) cc_final: 0.5120 (tpt) REVERT: D 686 MET cc_start: 0.8513 (mmt) cc_final: 0.8248 (mmt) REVERT: D 784 LEU cc_start: 0.9015 (mm) cc_final: 0.8574 (pp) REVERT: D 804 MET cc_start: 0.8693 (mmp) cc_final: 0.8282 (mmp) REVERT: D 820 THR cc_start: 0.6333 (m) cc_final: 0.6094 (t) REVERT: D 848 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.5735 (p90) REVERT: D 920 PHE cc_start: 0.8315 (t80) cc_final: 0.8062 (t80) REVERT: D 1116 MET cc_start: 0.7120 (mpp) cc_final: 0.6084 (ptm) REVERT: D 1143 MET cc_start: 0.2729 (mmp) cc_final: 0.1229 (mmm) REVERT: D 1166 MET cc_start: 0.6536 (tmm) cc_final: 0.5673 (ppp) outliers start: 126 outliers final: 90 residues processed: 339 average time/residue: 0.3490 time to fit residues: 194.9832 Evaluate side-chains 336 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 241 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 12 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS C 669 ASN ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 282 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.064340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.051311 restraints weight = 225529.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.052655 restraints weight = 146409.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.053671 restraints weight = 106877.309| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 27755 Z= 0.149 Angle : 0.707 13.254 37654 Z= 0.352 Chirality : 0.045 0.256 4163 Planarity : 0.005 0.059 4950 Dihedral : 7.928 86.672 3975 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.61 % Favored : 92.36 % Rotamer: Outliers : 3.49 % Allowed : 21.02 % Favored : 75.50 % 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: -1.35 (0.14), residues: 3483 helix: 0.15 (0.13), residues: 1481 sheet: -1.06 (0.24), residues: 468 loop : -1.88 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 838 HIS 0.007 0.001 HIS D 76 PHE 0.023 0.002 PHE A 876 TYR 0.020 0.002 TYR B1013 ARG 0.013 0.001 ARG C 385 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 1095) hydrogen bonds : angle 5.56036 ( 3210) SS BOND : bond 0.00315 ( 4) SS BOND : angle 2.03258 ( 8) covalent geometry : bond 0.00335 (27745) covalent geometry : angle 0.70672 (37646) Misc. bond : bond 0.00092 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 254 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9244 (tp) cc_final: 0.9010 (pt) REVERT: A 566 MET cc_start: 0.6650 (ttp) cc_final: 0.4402 (ttp) REVERT: A 583 ARG cc_start: 0.8678 (ttt180) cc_final: 0.7722 (ttt180) REVERT: A 636 ASN cc_start: 0.7748 (t0) cc_final: 0.7131 (p0) REVERT: A 675 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7165 (mtm180) REVERT: A 686 MET cc_start: 0.9017 (mpp) cc_final: 0.8754 (mpp) REVERT: A 724 MET cc_start: 0.9074 (tpt) cc_final: 0.8750 (tpp) REVERT: A 986 ASP cc_start: 0.8538 (t0) cc_final: 0.8199 (t0) REVERT: B 496 ARG cc_start: 0.8537 (mtt180) cc_final: 0.8141 (mmm160) REVERT: B 604 MET cc_start: 0.7782 (tpt) cc_final: 0.7515 (tpt) REVERT: B 754 MET cc_start: 0.9380 (mmm) cc_final: 0.9052 (mmm) REVERT: B 1008 LEU cc_start: 0.9192 (tp) cc_final: 0.8698 (pp) REVERT: C 204 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6950 (mmp) REVERT: C 300 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7125 (pptt) REVERT: C 616 MET cc_start: 0.8684 (mmp) cc_final: 0.8212 (mmp) REVERT: C 724 MET cc_start: 0.9183 (mmm) cc_final: 0.8787 (mmm) REVERT: C 1022 ASP cc_start: 0.7921 (m-30) cc_final: 0.6781 (p0) REVERT: C 1048 PHE cc_start: 0.9176 (p90) cc_final: 0.8753 (p90) REVERT: C 1077 PHE cc_start: 0.8727 (m-10) cc_final: 0.8469 (m-10) REVERT: D 326 ASN cc_start: 0.8314 (m-40) cc_final: 0.7336 (t0) REVERT: D 374 ILE cc_start: 0.8781 (mm) cc_final: 0.8416 (pt) REVERT: D 375 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: D 641 MET cc_start: 0.6751 (ptm) cc_final: 0.5748 (ppp) REVERT: D 671 MET cc_start: 0.5348 (tpt) cc_final: 0.4858 (tpt) REVERT: D 686 MET cc_start: 0.8573 (mmt) cc_final: 0.8218 (mmt) REVERT: D 784 LEU cc_start: 0.8989 (mm) cc_final: 0.8556 (pp) REVERT: D 804 MET cc_start: 0.8630 (mmp) cc_final: 0.8115 (mmp) REVERT: D 820 THR cc_start: 0.6356 (m) cc_final: 0.6095 (t) REVERT: D 848 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.5463 (p90) REVERT: D 920 PHE cc_start: 0.8381 (t80) cc_final: 0.8121 (t80) REVERT: D 1081 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7330 (m-40) REVERT: D 1116 MET cc_start: 0.6915 (mpp) cc_final: 0.5871 (ptt) REVERT: D 1143 MET cc_start: 0.2592 (mmp) cc_final: 0.1105 (mmm) outliers start: 100 outliers final: 79 residues processed: 327 average time/residue: 0.3679 time to fit residues: 198.1290 Evaluate side-chains 330 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 246 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 316 ARG Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1081 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 15 optimal weight: 20.0000 chunk 246 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 212 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 317 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 HIS B 575 GLN B 597 ASN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.065924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.052557 restraints weight = 217079.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.053982 restraints weight = 139937.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.054960 restraints weight = 101052.830| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 27755 Z= 0.123 Angle : 0.698 13.825 37654 Z= 0.342 Chirality : 0.045 0.206 4163 Planarity : 0.005 0.056 4950 Dihedral : 7.699 88.428 3975 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.94 % Rotamer: Outliers : 2.82 % Allowed : 21.92 % Favored : 75.25 % 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: 3483 helix: 0.37 (0.13), residues: 1475 sheet: -0.93 (0.24), residues: 468 loop : -1.82 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.009 0.001 HIS B 879 PHE 0.029 0.002 PHE C 450 TYR 0.018 0.001 TYR B1013 ARG 0.012 0.001 ARG C 385 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1095) hydrogen bonds : angle 5.33375 ( 3210) SS BOND : bond 0.00295 ( 4) SS BOND : angle 2.08716 ( 8) covalent geometry : bond 0.00282 (27745) covalent geometry : angle 0.69740 (37646) Misc. bond : bond 0.00077 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9273 (tp) cc_final: 0.9050 (pt) REVERT: A 566 MET cc_start: 0.6411 (ttp) cc_final: 0.5843 (ttp) REVERT: A 583 ARG cc_start: 0.8594 (ttt180) cc_final: 0.7642 (ttt180) REVERT: A 636 ASN cc_start: 0.7658 (t0) cc_final: 0.7011 (p0) REVERT: A 641 MET cc_start: 0.7198 (ptp) cc_final: 0.6764 (ptp) REVERT: A 724 MET cc_start: 0.9093 (tpt) cc_final: 0.8253 (tpp) REVERT: A 986 ASP cc_start: 0.8567 (t0) cc_final: 0.8220 (t0) REVERT: B 496 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8003 (mmm160) REVERT: B 604 MET cc_start: 0.7398 (tpt) cc_final: 0.6994 (tpt) REVERT: B 754 MET cc_start: 0.9381 (mmm) cc_final: 0.9040 (mmm) REVERT: C 149 MET cc_start: 0.8213 (mmt) cc_final: 0.6987 (ppp) REVERT: C 204 MET cc_start: 0.7614 (mmp) cc_final: 0.6976 (mmp) REVERT: C 300 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7113 (pptt) REVERT: C 409 ASN cc_start: 0.7826 (t0) cc_final: 0.7546 (t0) REVERT: C 604 MET cc_start: 0.8196 (mmm) cc_final: 0.7166 (tpp) REVERT: C 724 MET cc_start: 0.9190 (mmm) cc_final: 0.8777 (mmm) REVERT: C 804 MET cc_start: 0.6245 (tpp) cc_final: 0.5765 (tpp) REVERT: C 959 PHE cc_start: 0.4476 (OUTLIER) cc_final: 0.3178 (p90) REVERT: C 1022 ASP cc_start: 0.7837 (m-30) cc_final: 0.6763 (p0) REVERT: C 1048 PHE cc_start: 0.9138 (p90) cc_final: 0.8810 (p90) REVERT: C 1077 PHE cc_start: 0.8817 (m-10) cc_final: 0.8562 (m-10) REVERT: D 263 ARG cc_start: 0.7424 (mpt-90) cc_final: 0.7139 (mpt180) REVERT: D 326 ASN cc_start: 0.8222 (m-40) cc_final: 0.7273 (t0) REVERT: D 374 ILE cc_start: 0.8786 (mm) cc_final: 0.8391 (pt) REVERT: D 465 VAL cc_start: 0.8030 (t) cc_final: 0.7760 (t) REVERT: D 604 MET cc_start: 0.8204 (mmm) cc_final: 0.6756 (tpp) REVERT: D 641 MET cc_start: 0.6690 (ptm) cc_final: 0.5612 (ppp) REVERT: D 671 MET cc_start: 0.5339 (tpt) cc_final: 0.4993 (tpt) REVERT: D 686 MET cc_start: 0.8546 (mmt) cc_final: 0.8180 (mmt) REVERT: D 784 LEU cc_start: 0.9012 (mm) cc_final: 0.8591 (pp) REVERT: D 804 MET cc_start: 0.8564 (mmp) cc_final: 0.8141 (mmp) REVERT: D 848 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.5398 (p90) REVERT: D 920 PHE cc_start: 0.8406 (t80) cc_final: 0.8188 (t80) REVERT: D 1116 MET cc_start: 0.6821 (mpp) cc_final: 0.5748 (ptt) REVERT: D 1143 MET cc_start: 0.2550 (mmp) cc_final: 0.0768 (mmm) REVERT: D 1166 MET cc_start: 0.5441 (ppp) cc_final: 0.4564 (ppp) outliers start: 81 outliers final: 66 residues processed: 326 average time/residue: 0.3547 time to fit residues: 189.6638 Evaluate side-chains 322 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 253 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 959 PHE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 316 ARG Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1080 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 286 optimal weight: 0.0050 chunk 166 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 343 optimal weight: 0.0570 chunk 75 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.064903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.051878 restraints weight = 225902.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.053250 restraints weight = 145218.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.054221 restraints weight = 104961.805| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 27755 Z= 0.139 Angle : 0.715 16.543 37654 Z= 0.350 Chirality : 0.045 0.238 4163 Planarity : 0.005 0.119 4950 Dihedral : 7.578 87.377 3975 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.78 % Favored : 92.19 % Rotamer: Outliers : 3.28 % Allowed : 21.89 % Favored : 74.83 % 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: 3483 helix: 0.34 (0.14), residues: 1485 sheet: -0.89 (0.25), residues: 460 loop : -1.83 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 624 HIS 0.008 0.001 HIS D 76 PHE 0.030 0.002 PHE D 53 TYR 0.026 0.002 TYR B 593 ARG 0.009 0.001 ARG C 385 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1095) hydrogen bonds : angle 5.37239 ( 3210) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.99885 ( 8) covalent geometry : bond 0.00319 (27745) covalent geometry : angle 0.71429 (37646) Misc. bond : bond 0.00080 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 259 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9277 (tp) cc_final: 0.9038 (pt) REVERT: A 566 MET cc_start: 0.6500 (ttp) cc_final: 0.5785 (ttp) REVERT: A 583 ARG cc_start: 0.8692 (ttt180) cc_final: 0.7777 (ttt180) REVERT: A 636 ASN cc_start: 0.7579 (t0) cc_final: 0.6910 (p0) REVERT: A 724 MET cc_start: 0.9156 (tpt) cc_final: 0.8865 (tpp) REVERT: A 986 ASP cc_start: 0.8531 (t0) cc_final: 0.8175 (t0) REVERT: A 998 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.7016 (t-90) REVERT: A 1043 LYS cc_start: 0.8957 (pttm) cc_final: 0.8584 (pptt) REVERT: B 496 ARG cc_start: 0.8481 (mtt180) cc_final: 0.8048 (mmm160) REVERT: B 604 MET cc_start: 0.7638 (tpt) cc_final: 0.7119 (tpt) REVERT: B 754 MET cc_start: 0.9386 (mmm) cc_final: 0.9059 (mmm) REVERT: B 1008 LEU cc_start: 0.9010 (tp) cc_final: 0.8477 (pp) REVERT: C 204 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6998 (mmp) REVERT: C 300 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7131 (pptt) REVERT: C 409 ASN cc_start: 0.7866 (t0) cc_final: 0.7606 (t0) REVERT: C 604 MET cc_start: 0.8270 (mmm) cc_final: 0.7103 (tpp) REVERT: C 724 MET cc_start: 0.9204 (mmm) cc_final: 0.8796 (mmm) REVERT: C 804 MET cc_start: 0.7032 (tpp) cc_final: 0.6268 (tpp) REVERT: C 1048 PHE cc_start: 0.9210 (p90) cc_final: 0.8926 (p90) REVERT: C 1077 PHE cc_start: 0.8846 (m-10) cc_final: 0.8549 (m-10) REVERT: D 268 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: D 326 ASN cc_start: 0.8171 (m-40) cc_final: 0.7264 (t0) REVERT: D 374 ILE cc_start: 0.8833 (mm) cc_final: 0.8419 (pt) REVERT: D 465 VAL cc_start: 0.8058 (t) cc_final: 0.7781 (t) REVERT: D 604 MET cc_start: 0.8190 (mmm) cc_final: 0.6657 (tpp) REVERT: D 641 MET cc_start: 0.6830 (ptm) cc_final: 0.5670 (ppp) REVERT: D 671 MET cc_start: 0.5346 (tpt) cc_final: 0.4990 (tpt) REVERT: D 686 MET cc_start: 0.8570 (mmt) cc_final: 0.8149 (mmt) REVERT: D 804 MET cc_start: 0.8671 (mmp) cc_final: 0.8200 (mmp) REVERT: D 820 THR cc_start: 0.6378 (m) cc_final: 0.6149 (t) REVERT: D 848 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.5460 (p90) REVERT: D 920 PHE cc_start: 0.8368 (t80) cc_final: 0.8144 (t80) REVERT: D 1012 MET cc_start: 0.8675 (mpp) cc_final: 0.7504 (mpp) REVERT: D 1116 MET cc_start: 0.6872 (mpp) cc_final: 0.5743 (ptt) REVERT: D 1143 MET cc_start: 0.2557 (mmp) cc_final: 0.0714 (mmm) REVERT: D 1166 MET cc_start: 0.5199 (ppp) cc_final: 0.4292 (ppp) outliers start: 94 outliers final: 70 residues processed: 326 average time/residue: 0.3514 time to fit residues: 188.5739 Evaluate side-chains 330 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 157 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 327 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.062103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.049639 restraints weight = 234797.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.050902 restraints weight = 152189.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.051786 restraints weight = 110994.107| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 27755 Z= 0.213 Angle : 0.796 15.433 37654 Z= 0.400 Chirality : 0.047 0.262 4163 Planarity : 0.006 0.066 4950 Dihedral : 7.718 86.080 3975 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.76 % Favored : 91.21 % Rotamer: Outliers : 3.03 % Allowed : 22.10 % Favored : 74.87 % Cbeta Deviations : 0.03 % 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: -1.57 (0.14), residues: 3483 helix: -0.08 (0.13), residues: 1488 sheet: -1.18 (0.24), residues: 462 loop : -1.94 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 838 HIS 0.010 0.002 HIS C 436 PHE 0.046 0.002 PHE D 53 TYR 0.025 0.002 TYR D 503 ARG 0.024 0.001 ARG A 997 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 1095) hydrogen bonds : angle 5.74697 ( 3210) SS BOND : bond 0.00350 ( 4) SS BOND : angle 1.96476 ( 8) covalent geometry : bond 0.00466 (27745) covalent geometry : angle 0.79588 (37646) Misc. bond : bond 0.00111 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 248 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9182 (tp) cc_final: 0.8940 (pt) REVERT: A 566 MET cc_start: 0.6611 (ttp) cc_final: 0.5469 (ttp) REVERT: A 583 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8346 (ttt180) REVERT: A 675 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7197 (ttm170) REVERT: A 1043 LYS cc_start: 0.9040 (pttm) cc_final: 0.8602 (pptt) REVERT: B 496 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8244 (mmm160) REVERT: B 604 MET cc_start: 0.7834 (tpt) cc_final: 0.7314 (tpt) REVERT: B 754 MET cc_start: 0.9397 (mmm) cc_final: 0.9053 (mmm) REVERT: B 921 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8691 (tpt) REVERT: C 204 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7060 (mmp) REVERT: C 300 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7231 (pptt) REVERT: C 583 ARG cc_start: 0.8852 (mtp180) cc_final: 0.8428 (mtp180) REVERT: C 604 MET cc_start: 0.8391 (mmm) cc_final: 0.7981 (mmm) REVERT: C 724 MET cc_start: 0.9205 (mmm) cc_final: 0.8844 (mmm) REVERT: C 804 MET cc_start: 0.7356 (tpp) cc_final: 0.6418 (tpp) REVERT: C 1048 PHE cc_start: 0.9275 (p90) cc_final: 0.8937 (p90) REVERT: D 47 GLU cc_start: 0.8790 (pp20) cc_final: 0.8357 (tp30) REVERT: D 263 ARG cc_start: 0.7380 (mpt-90) cc_final: 0.7007 (mpt180) REVERT: D 326 ASN cc_start: 0.8174 (m-40) cc_final: 0.7327 (t0) REVERT: D 374 ILE cc_start: 0.8772 (mm) cc_final: 0.8348 (pt) REVERT: D 375 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: D 500 LEU cc_start: 0.9486 (tp) cc_final: 0.9176 (mm) REVERT: D 508 MET cc_start: 0.9273 (ptp) cc_final: 0.9069 (ptp) REVERT: D 604 MET cc_start: 0.8256 (mmm) cc_final: 0.6734 (tpp) REVERT: D 641 MET cc_start: 0.7093 (ptm) cc_final: 0.5853 (ppp) REVERT: D 671 MET cc_start: 0.5634 (tpt) cc_final: 0.5254 (tpt) REVERT: D 686 MET cc_start: 0.8664 (mmt) cc_final: 0.8243 (mmt) REVERT: D 804 MET cc_start: 0.8795 (mmp) cc_final: 0.8418 (mmp) REVERT: D 820 THR cc_start: 0.6400 (m) cc_final: 0.6161 (t) REVERT: D 848 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5748 (p90) REVERT: D 920 PHE cc_start: 0.8537 (t80) cc_final: 0.8248 (t80) REVERT: D 1012 MET cc_start: 0.8881 (mpp) cc_final: 0.8473 (mpp) REVERT: D 1116 MET cc_start: 0.6889 (mpp) cc_final: 0.5845 (ptp) REVERT: D 1143 MET cc_start: 0.2965 (mmp) cc_final: 0.1228 (mmm) outliers start: 87 outliers final: 77 residues processed: 309 average time/residue: 0.3672 time to fit residues: 186.7461 Evaluate side-chains 328 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 246 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 921 MET Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 876 PHE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 89 optimal weight: 0.1980 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 271 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 342 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.064330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.051088 restraints weight = 224706.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.052546 restraints weight = 144666.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.053545 restraints weight = 104680.033| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.164 27755 Z= 0.127 Angle : 0.741 16.955 37654 Z= 0.359 Chirality : 0.045 0.194 4163 Planarity : 0.005 0.056 4950 Dihedral : 7.425 86.895 3975 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.80 % Favored : 93.17 % Rotamer: Outliers : 2.75 % Allowed : 22.52 % Favored : 74.73 % Cbeta Deviations : 0.03 % 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: -1.23 (0.14), residues: 3483 helix: 0.26 (0.13), residues: 1491 sheet: -0.97 (0.25), residues: 455 loop : -1.84 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.011 0.001 HIS A 998 PHE 0.039 0.002 PHE D 53 TYR 0.020 0.001 TYR B1013 ARG 0.009 0.001 ARG C 385 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 1095) hydrogen bonds : angle 5.42525 ( 3210) SS BOND : bond 0.00267 ( 4) SS BOND : angle 2.09324 ( 8) covalent geometry : bond 0.00299 (27745) covalent geometry : angle 0.74090 (37646) Misc. bond : bond 0.00076 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11100.83 seconds wall clock time: 196 minutes 51.50 seconds (11811.50 seconds total)