Starting phenix.real_space_refine on Sun May 18 01:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pd8_17605/05_2025/8pd8_17605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pd8_17605/05_2025/8pd8_17605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pd8_17605/05_2025/8pd8_17605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pd8_17605/05_2025/8pd8_17605.map" model { file = "/net/cci-nas-00/data/ceres_data/8pd8_17605/05_2025/8pd8_17605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pd8_17605/05_2025/8pd8_17605.cif" } resolution = 3.3 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= 0.024 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 2 5.49 5 S 82 5.16 5 C 10520 2.51 5 N 2678 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16122 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 8039 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 29, 'TRANS': 988} Chain breaks: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B Time building chain proxies: 18.18, per 1000 atoms: 1.13 Number of scatterers: 16122 At special positions: 0 Unit cell: (115.486, 158.41, 126.728, 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 82 16.00 P 2 15.00 O 2840 8.00 N 2678 7.00 C 10520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 2.0 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 8 sheets defined 77.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 72 through 95 removed outlier: 4.152A pdb=" N LYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.040A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.077A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.876A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.925A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.963A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.689A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.511A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.580A pdb=" N VAL A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 411 removed outlier: 3.804A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.649A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 469 removed outlier: 4.256A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 5.335A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.706A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 600 removed outlier: 3.571A pdb=" N HIS A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.646A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 678 through 705 removed outlier: 4.050A pdb=" N VAL A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 726 through 743 removed outlier: 3.720A pdb=" N ASP A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 removed outlier: 4.511A pdb=" N VAL A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 4.004A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 780 removed outlier: 3.754A pdb=" N LYS A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 771 " --> pdb=" O ASP A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 795 through 812 removed outlier: 3.741A pdb=" N LYS A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 854 Proline residue: A 819 - end of helix removed outlier: 3.950A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 862 through 889 removed outlier: 4.258A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 878 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.503A pdb=" N GLN A 900 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 942 removed outlier: 3.642A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1045 through 1050 Processing helix chain 'A' and resid 1070 through 1080 removed outlier: 3.881A pdb=" N ILE A1075 " --> pdb=" O GLU A1071 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A1076 " --> pdb=" O ASP A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1108 removed outlier: 3.698A pdb=" N ARG A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Proline residue: A1101 - end of helix removed outlier: 3.605A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.802A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 4.192A pdb=" N GLU A1183 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 95 Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.040A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.077A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.876A pdb=" N MET B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 162 through 188 removed outlier: 3.925A pdb=" N VAL B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.963A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.688A pdb=" N TYR B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.511A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.581A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 411 removed outlier: 3.804A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.649A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 469 removed outlier: 4.256A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 removed outlier: 5.335A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.706A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 600 removed outlier: 3.571A pdb=" N HIS B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.646A pdb=" N LYS B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 653 Processing helix chain 'B' and resid 678 through 705 removed outlier: 4.050A pdb=" N VAL B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 689 " --> pdb=" O ASN B 685 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 726 through 743 removed outlier: 3.720A pdb=" N ASP B 730 " --> pdb=" O GLN B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 removed outlier: 4.512A pdb=" N VAL B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 removed outlier: 4.003A pdb=" N ILE B 759 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 780 removed outlier: 3.754A pdb=" N LYS B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 766 " --> pdb=" O HIS B 762 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 771 " --> pdb=" O ASP B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 783 No H-bonds generated for 'chain 'B' and resid 781 through 783' Processing helix chain 'B' and resid 795 through 812 removed outlier: 3.741A pdb=" N LYS B 800 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 803 " --> pdb=" O VAL B 799 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 806 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 854 Proline residue: B 819 - end of helix removed outlier: 3.951A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 862 through 889 removed outlier: 4.258A pdb=" N GLN B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 878 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 883 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 887 " --> pdb=" O GLY B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.503A pdb=" N GLN B 900 " --> pdb=" O VAL B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 942 removed outlier: 3.642A pdb=" N THR B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET B 942 " --> pdb=" O MET B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 958 Processing helix chain 'B' and resid 966 through 976 Processing helix chain 'B' and resid 1045 through 1050 Processing helix chain 'B' and resid 1070 through 1080 removed outlier: 3.881A pdb=" N ILE B1075 " --> pdb=" O GLU B1071 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B1076 " --> pdb=" O ASP B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1108 removed outlier: 3.698A pdb=" N ARG B1097 " --> pdb=" O VAL B1093 " (cutoff:3.500A) Proline residue: B1101 - end of helix removed outlier: 3.605A pdb=" N GLN B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1123 removed outlier: 3.802A pdb=" N ARG B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1183 removed outlier: 4.192A pdb=" N GLU B1183 " --> pdb=" O ALA B1180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.339A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.443A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.680A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.340A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.443A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 6.681A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1134 through 1136 1162 hydrogen bonds defined for protein. 3414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4272 1.33 - 1.45: 2725 1.45 - 1.58: 9285 1.58 - 1.70: 4 1.70 - 1.82: 152 Bond restraints: 16438 Sorted by residual: bond pdb=" CZ ARG B 583 " pdb=" NH2 ARG B 583 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.56e+00 bond pdb=" CZ ARG A 583 " pdb=" NH2 ARG A 583 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.41e+00 bond pdb=" CZ ARG B 865 " pdb=" NH2 ARG B 865 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.66e+00 bond pdb=" CZ ARG A 865 " pdb=" NH2 ARG A 865 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.60e+00 bond pdb=" CZ ARG A 856 " pdb=" NH2 ARG A 856 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.58e+00 ... (remaining 16433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21520 2.06 - 4.12: 674 4.12 - 6.18: 79 6.18 - 8.23: 17 8.23 - 10.29: 14 Bond angle restraints: 22304 Sorted by residual: angle pdb=" CA LYS B 224 " pdb=" CB LYS B 224 " pdb=" CG LYS B 224 " ideal model delta sigma weight residual 114.10 123.66 -9.56 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA LYS A 224 " pdb=" CB LYS A 224 " pdb=" CG LYS A 224 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA ARG B 128 " pdb=" CB ARG B 128 " pdb=" CG ARG B 128 " ideal model delta sigma weight residual 114.10 123.06 -8.96 2.00e+00 2.50e-01 2.01e+01 angle pdb=" CA ARG A 128 " pdb=" CB ARG A 128 " pdb=" CG ARG A 128 " ideal model delta sigma weight residual 114.10 123.05 -8.95 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA ARG A 756 " pdb=" CB ARG A 756 " pdb=" CG ARG A 756 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.95e+01 ... (remaining 22299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 9582 29.58 - 59.17: 194 59.17 - 88.75: 24 88.75 - 118.34: 0 118.34 - 147.92: 6 Dihedral angle restraints: 9806 sinusoidal: 3886 harmonic: 5920 Sorted by residual: dihedral pdb=" C5' CMP A1401 " pdb=" O5' CMP A1401 " pdb=" P CMP A1401 " pdb=" O1P CMP A1401 " ideal model delta sinusoidal sigma weight residual 60.00 -152.08 -147.92 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' CMP B1401 " pdb=" O5' CMP B1401 " pdb=" P CMP B1401 " pdb=" O1P CMP B1401 " ideal model delta sinusoidal sigma weight residual 60.00 -152.10 -147.90 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C3' CMP B1401 " pdb=" O3' CMP B1401 " pdb=" P CMP B1401 " pdb=" O1P CMP B1401 " ideal model delta sinusoidal sigma weight residual 300.00 159.68 140.32 1 2.00e+01 2.50e-03 4.25e+01 ... (remaining 9803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1715 0.039 - 0.077: 710 0.077 - 0.116: 214 0.116 - 0.155: 34 0.155 - 0.193: 11 Chirality restraints: 2684 Sorted by residual: chirality pdb=" CA LYS B 861 " pdb=" N LYS B 861 " pdb=" C LYS B 861 " pdb=" CB LYS B 861 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA LYS A 861 " pdb=" N LYS A 861 " pdb=" C LYS A 861 " pdb=" CB LYS A 861 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA GLU B 616 " pdb=" N GLU B 616 " pdb=" C GLU B 616 " pdb=" CB GLU B 616 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 2681 not shown) Planarity restraints: 2738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 843 " 0.023 2.00e-02 2.50e+03 1.91e-02 7.31e+00 pdb=" CG TYR A 843 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 843 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 843 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 843 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 843 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR A 843 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 843 " 0.023 2.00e-02 2.50e+03 1.91e-02 7.27e+00 pdb=" CG TYR B 843 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 843 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 843 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 843 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 843 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 843 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR B 843 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 614 " 0.029 2.00e-02 2.50e+03 2.17e-02 7.07e+00 pdb=" CG HIS B 614 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS B 614 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS B 614 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS B 614 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS B 614 " 0.016 2.00e-02 2.50e+03 ... (remaining 2735 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2971 2.77 - 3.30: 16714 3.30 - 3.84: 25999 3.84 - 4.37: 30223 4.37 - 4.90: 52092 Nonbonded interactions: 127999 Sorted by model distance: nonbonded pdb=" O ASP A 534 " pdb=" OD1 ASP A 534 " model vdw 2.240 3.040 nonbonded pdb=" O ASP B 534 " pdb=" OD1 ASP B 534 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU A 233 " pdb=" NH2 ARG A 399 " model vdw 2.339 3.120 nonbonded pdb=" OE2 GLU B 233 " pdb=" NH2 ARG B 399 " model vdw 2.340 3.120 nonbonded pdb=" O ILE B 81 " pdb=" OG SER B 84 " model vdw 2.344 3.040 ... (remaining 127994 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 46.650 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 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 : 0.005 0.044 16438 Z= 0.273 Angle : 0.848 10.292 22304 Z= 0.479 Chirality : 0.046 0.193 2684 Planarity : 0.005 0.050 2738 Dihedral : 13.011 147.921 5966 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.77 (0.19), residues: 2012 helix: 0.82 (0.13), residues: 1416 sheet: -0.02 (0.52), residues: 82 loop : 0.04 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 643 HIS 0.007 0.001 HIS A 928 PHE 0.021 0.002 PHE B 625 TYR 0.034 0.003 TYR B 984 ARG 0.011 0.001 ARG B1169 Details of bonding type rmsd hydrogen bonds : bond 0.12976 ( 1162) hydrogen bonds : angle 5.55026 ( 3414) covalent geometry : bond 0.00547 (16438) covalent geometry : angle 0.84799 (22304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6696 (mmm) cc_final: 0.6060 (mmm) REVERT: A 149 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 155 ASP cc_start: 0.7110 (t70) cc_final: 0.6670 (t70) REVERT: A 164 SER cc_start: 0.8254 (m) cc_final: 0.7699 (t) REVERT: A 209 ASP cc_start: 0.7641 (t0) cc_final: 0.7123 (t0) REVERT: A 300 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 338 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7558 (mtpt) REVERT: A 344 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7028 (mt-10) REVERT: A 375 LYS cc_start: 0.8078 (mttt) cc_final: 0.7652 (mtpp) REVERT: A 380 VAL cc_start: 0.8634 (t) cc_final: 0.8309 (m) REVERT: A 383 MET cc_start: 0.6925 (mmp) cc_final: 0.6433 (mmm) REVERT: A 448 ASN cc_start: 0.8635 (m-40) cc_final: 0.8397 (m110) REVERT: A 485 ASP cc_start: 0.7960 (m-30) cc_final: 0.7646 (p0) REVERT: A 515 ASP cc_start: 0.7650 (t70) cc_final: 0.7340 (t70) REVERT: A 522 ASP cc_start: 0.7097 (t0) cc_final: 0.6579 (t0) REVERT: A 525 ILE cc_start: 0.7205 (mm) cc_final: 0.6839 (mt) REVERT: A 531 GLU cc_start: 0.7957 (tt0) cc_final: 0.7131 (tm-30) REVERT: A 534 ASP cc_start: 0.6889 (p0) cc_final: 0.6507 (p0) REVERT: A 578 MET cc_start: 0.6531 (mmm) cc_final: 0.6033 (mmm) REVERT: A 580 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7519 (tp30) REVERT: A 584 LEU cc_start: 0.8064 (mt) cc_final: 0.7686 (mt) REVERT: A 591 LYS cc_start: 0.8066 (mttp) cc_final: 0.7708 (mtpp) REVERT: A 613 GLN cc_start: 0.7978 (tt0) cc_final: 0.7640 (tm-30) REVERT: A 634 SER cc_start: 0.8462 (m) cc_final: 0.8104 (p) REVERT: A 635 TRP cc_start: 0.7405 (p90) cc_final: 0.7154 (p90) REVERT: A 645 LYS cc_start: 0.7595 (tttt) cc_final: 0.7265 (tttt) REVERT: A 828 LYS cc_start: 0.7315 (mmtt) cc_final: 0.7076 (mmtt) REVERT: A 857 MET cc_start: 0.7329 (ttm) cc_final: 0.6803 (ttm) REVERT: A 869 HIS cc_start: 0.6619 (t70) cc_final: 0.6414 (t-90) REVERT: A 887 ARG cc_start: 0.7249 (mmm-85) cc_final: 0.7019 (mmm-85) REVERT: A 958 LYS cc_start: 0.7961 (tttt) cc_final: 0.7655 (mttm) REVERT: A 991 GLU cc_start: 0.5641 (mt-10) cc_final: 0.5347 (mm-30) REVERT: A 998 LEU cc_start: 0.5553 (mp) cc_final: 0.5106 (mp) REVERT: A 1066 TYR cc_start: 0.6402 (m-80) cc_final: 0.6179 (m-10) REVERT: A 1068 ILE cc_start: 0.6230 (mp) cc_final: 0.5880 (pt) REVERT: B 133 MET cc_start: 0.6528 (mmm) cc_final: 0.5882 (mmm) REVERT: B 155 ASP cc_start: 0.7129 (t70) cc_final: 0.6690 (t70) REVERT: B 160 MET cc_start: 0.7427 (mmt) cc_final: 0.7127 (mmm) REVERT: B 164 SER cc_start: 0.8202 (m) cc_final: 0.7726 (t) REVERT: B 218 LYS cc_start: 0.7676 (mttt) cc_final: 0.7325 (mtpp) REVERT: B 268 PHE cc_start: 0.7618 (t80) cc_final: 0.7378 (t80) REVERT: B 300 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7672 (mt-10) REVERT: B 375 LYS cc_start: 0.8092 (mttt) cc_final: 0.7626 (mtpp) REVERT: B 380 VAL cc_start: 0.8592 (t) cc_final: 0.8276 (m) REVERT: B 383 MET cc_start: 0.7061 (mmp) cc_final: 0.6837 (mmm) REVERT: B 443 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 448 ASN cc_start: 0.8664 (m-40) cc_final: 0.8408 (m-40) REVERT: B 475 GLN cc_start: 0.7997 (tp40) cc_final: 0.7795 (mm-40) REVERT: B 479 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7355 (ttm-80) REVERT: B 485 ASP cc_start: 0.7982 (m-30) cc_final: 0.7661 (p0) REVERT: B 494 MET cc_start: 0.7417 (tpp) cc_final: 0.6959 (tpp) REVERT: B 500 ARG cc_start: 0.7453 (tpp80) cc_final: 0.7112 (tpp80) REVERT: B 515 ASP cc_start: 0.7519 (t70) cc_final: 0.7168 (t70) REVERT: B 522 ASP cc_start: 0.7252 (t0) cc_final: 0.6758 (t0) REVERT: B 525 ILE cc_start: 0.7189 (mm) cc_final: 0.6835 (mt) REVERT: B 534 ASP cc_start: 0.6730 (p0) cc_final: 0.6354 (p0) REVERT: B 578 MET cc_start: 0.6833 (mmm) cc_final: 0.6468 (mmm) REVERT: B 588 LYS cc_start: 0.7631 (ttmt) cc_final: 0.7385 (ttmt) REVERT: B 591 LYS cc_start: 0.8249 (mttp) cc_final: 0.8009 (mtpp) REVERT: B 606 GLU cc_start: 0.7423 (mp0) cc_final: 0.7221 (pm20) REVERT: B 610 LEU cc_start: 0.8041 (mp) cc_final: 0.7784 (mt) REVERT: B 613 GLN cc_start: 0.7807 (tt0) cc_final: 0.7519 (tm-30) REVERT: B 634 SER cc_start: 0.8672 (m) cc_final: 0.8005 (p) REVERT: B 635 TRP cc_start: 0.7447 (p90) cc_final: 0.6263 (p90) REVERT: B 644 LEU cc_start: 0.7971 (mt) cc_final: 0.7650 (mt) REVERT: B 645 LYS cc_start: 0.7959 (tttt) cc_final: 0.7479 (tttt) REVERT: B 828 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6685 (mmmm) REVERT: B 832 GLN cc_start: 0.6965 (tp40) cc_final: 0.6660 (tp-100) REVERT: B 839 VAL cc_start: 0.7759 (m) cc_final: 0.7460 (p) REVERT: B 852 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7450 (mmmm) REVERT: B 857 MET cc_start: 0.7473 (ttm) cc_final: 0.6993 (ttp) REVERT: B 860 ASN cc_start: 0.6801 (t0) cc_final: 0.6584 (t0) REVERT: B 863 ILE cc_start: 0.5962 (mm) cc_final: 0.4759 (tp) REVERT: B 867 LEU cc_start: 0.7526 (mp) cc_final: 0.7276 (mp) REVERT: B 925 MET cc_start: 0.7265 (tmm) cc_final: 0.6879 (tmm) REVERT: B 929 LYS cc_start: 0.7316 (tttt) cc_final: 0.7047 (ttmt) REVERT: B 958 LYS cc_start: 0.7930 (tttt) cc_final: 0.7621 (mttm) REVERT: B 962 TRP cc_start: 0.6463 (p-90) cc_final: 0.5994 (p90) REVERT: B 991 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5664 (mm-30) REVERT: B 998 LEU cc_start: 0.5557 (mp) cc_final: 0.5089 (mp) REVERT: B 1007 LYS cc_start: 0.5593 (tttt) cc_final: 0.5205 (ttpp) REVERT: B 1035 TYR cc_start: 0.7058 (m-80) cc_final: 0.6623 (m-80) REVERT: B 1066 TYR cc_start: 0.6482 (m-80) cc_final: 0.6273 (m-10) REVERT: B 1068 ILE cc_start: 0.6372 (mp) cc_final: 0.6155 (pt) REVERT: B 1104 MET cc_start: 0.6908 (tpp) cc_final: 0.6579 (mmm) REVERT: B 1122 GLU cc_start: 0.7588 (tp30) cc_final: 0.7288 (tp30) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.2842 time to fit residues: 219.3698 Evaluate side-chains 448 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 877 GLN B 126 HIS B 192 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 510 ASN B 900 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.175173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144606 restraints weight = 23742.951| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.31 r_work: 0.3562 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16438 Z= 0.193 Angle : 0.625 8.376 22304 Z= 0.329 Chirality : 0.043 0.148 2684 Planarity : 0.004 0.051 2738 Dihedral : 8.537 144.793 2194 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.23 % Allowed : 10.39 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.17 (0.18), residues: 2012 helix: 1.13 (0.13), residues: 1464 sheet: -0.36 (0.53), residues: 94 loop : 0.20 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 962 HIS 0.009 0.001 HIS B 928 PHE 0.016 0.002 PHE A 268 TYR 0.028 0.002 TYR A 309 ARG 0.005 0.001 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.05574 ( 1162) hydrogen bonds : angle 4.34232 ( 3414) covalent geometry : bond 0.00424 (16438) covalent geometry : angle 0.62542 (22304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 466 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6846 (mmm) cc_final: 0.6288 (mmm) REVERT: A 134 ASP cc_start: 0.7571 (m-30) cc_final: 0.7282 (m-30) REVERT: A 149 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 155 ASP cc_start: 0.7544 (t70) cc_final: 0.7137 (t70) REVERT: A 164 SER cc_start: 0.8754 (m) cc_final: 0.8463 (t) REVERT: A 380 VAL cc_start: 0.8707 (t) cc_final: 0.8367 (m) REVERT: A 383 MET cc_start: 0.7840 (mmp) cc_final: 0.7633 (mmm) REVERT: A 500 ARG cc_start: 0.8243 (tpp80) cc_final: 0.8028 (tpp80) REVERT: A 522 ASP cc_start: 0.8223 (t0) cc_final: 0.7902 (t0) REVERT: A 525 ILE cc_start: 0.9021 (mm) cc_final: 0.8494 (mt) REVERT: A 534 ASP cc_start: 0.7631 (p0) cc_final: 0.7374 (p0) REVERT: A 584 LEU cc_start: 0.8893 (mt) cc_final: 0.8524 (mt) REVERT: A 591 LYS cc_start: 0.8958 (mttp) cc_final: 0.8729 (mtpp) REVERT: A 602 MET cc_start: 0.5853 (mmp) cc_final: 0.5624 (mmm) REVERT: A 606 GLU cc_start: 0.7939 (pm20) cc_final: 0.7608 (pm20) REVERT: A 634 SER cc_start: 0.7987 (m) cc_final: 0.7744 (p) REVERT: A 647 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7603 (mmtt) REVERT: A 828 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7979 (mmtt) REVERT: A 887 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7965 (mmm-85) REVERT: A 938 MET cc_start: 0.8493 (tpp) cc_final: 0.8132 (ttt) REVERT: A 947 SER cc_start: 0.8354 (t) cc_final: 0.7820 (p) REVERT: A 954 GLU cc_start: 0.8010 (pm20) cc_final: 0.7796 (pm20) REVERT: A 986 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6562 (mt-10) REVERT: A 991 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6537 (mm-30) REVERT: A 998 LEU cc_start: 0.8109 (mp) cc_final: 0.7890 (mp) REVERT: A 1007 LYS cc_start: 0.7993 (tttt) cc_final: 0.7490 (tttp) REVERT: A 1068 ILE cc_start: 0.7857 (mp) cc_final: 0.7561 (tt) REVERT: A 1122 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6987 (tp30) REVERT: B 133 MET cc_start: 0.6612 (mmm) cc_final: 0.6171 (mmm) REVERT: B 155 ASP cc_start: 0.7687 (t70) cc_final: 0.7280 (t70) REVERT: B 164 SER cc_start: 0.8729 (m) cc_final: 0.8451 (t) REVERT: B 171 LEU cc_start: 0.8262 (mm) cc_final: 0.8058 (mm) REVERT: B 367 MET cc_start: 0.7924 (mtm) cc_final: 0.7689 (mtm) REVERT: B 380 VAL cc_start: 0.8742 (t) cc_final: 0.8453 (m) REVERT: B 398 ILE cc_start: 0.8643 (mm) cc_final: 0.8403 (mt) REVERT: B 500 ARG cc_start: 0.8298 (tpp80) cc_final: 0.8066 (tpp80) REVERT: B 522 ASP cc_start: 0.8123 (t0) cc_final: 0.7833 (t0) REVERT: B 525 ILE cc_start: 0.9028 (mm) cc_final: 0.8265 (mt) REVERT: B 531 GLU cc_start: 0.8395 (tt0) cc_final: 0.8046 (tm-30) REVERT: B 534 ASP cc_start: 0.7586 (p0) cc_final: 0.7329 (p0) REVERT: B 588 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7799 (ttmt) REVERT: B 590 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 613 GLN cc_start: 0.7875 (tt0) cc_final: 0.7577 (tm-30) REVERT: B 623 ASP cc_start: 0.7948 (t0) cc_final: 0.7627 (t0) REVERT: B 634 SER cc_start: 0.8121 (m) cc_final: 0.7827 (p) REVERT: B 645 LYS cc_start: 0.8544 (tttt) cc_final: 0.7871 (tptt) REVERT: B 828 LYS cc_start: 0.8350 (mmtt) cc_final: 0.8110 (mmtt) REVERT: B 852 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8622 (mmmm) REVERT: B 863 ILE cc_start: 0.7158 (mm) cc_final: 0.6303 (tp) REVERT: B 947 SER cc_start: 0.8356 (t) cc_final: 0.7734 (p) REVERT: B 954 GLU cc_start: 0.8045 (pm20) cc_final: 0.7845 (pm20) REVERT: B 981 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6832 (t-90) REVERT: B 991 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6798 (mm-30) REVERT: B 1068 ILE cc_start: 0.7840 (mp) cc_final: 0.7636 (tt) REVERT: B 1122 GLU cc_start: 0.7486 (tp30) cc_final: 0.7013 (tp30) outliers start: 39 outliers final: 19 residues processed: 484 average time/residue: 0.2749 time to fit residues: 195.3344 Evaluate side-chains 448 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 428 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 981 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 196 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 597 GLN A 886 GLN A1114 GLN B 510 ASN B 860 ASN B 900 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.178850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148697 restraints weight = 23297.041| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.21 r_work: 0.3553 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16438 Z= 0.206 Angle : 0.609 8.613 22304 Z= 0.317 Chirality : 0.042 0.162 2684 Planarity : 0.004 0.044 2738 Dihedral : 8.401 143.695 2194 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.80 % Allowed : 13.24 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.29 (0.18), residues: 2012 helix: 1.25 (0.13), residues: 1466 sheet: -0.36 (0.61), residues: 74 loop : 0.09 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 962 HIS 0.005 0.001 HIS B 928 PHE 0.026 0.002 PHE B 982 TYR 0.025 0.001 TYR A 309 ARG 0.005 0.000 ARG B 812 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 1162) hydrogen bonds : angle 4.19790 ( 3414) covalent geometry : bond 0.00459 (16438) covalent geometry : angle 0.60878 (22304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 433 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6915 (mmm) cc_final: 0.6472 (mmm) REVERT: A 134 ASP cc_start: 0.7487 (m-30) cc_final: 0.7286 (m-30) REVERT: A 149 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 155 ASP cc_start: 0.7503 (t70) cc_final: 0.7046 (t70) REVERT: A 164 SER cc_start: 0.8714 (m) cc_final: 0.8355 (t) REVERT: A 209 ASP cc_start: 0.7972 (t0) cc_final: 0.7545 (t70) REVERT: A 380 VAL cc_start: 0.8734 (t) cc_final: 0.8399 (m) REVERT: A 531 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 534 ASP cc_start: 0.7667 (p0) cc_final: 0.7428 (p0) REVERT: A 591 LYS cc_start: 0.8955 (mttp) cc_final: 0.8737 (mtpp) REVERT: A 602 MET cc_start: 0.5965 (mmp) cc_final: 0.5702 (mmm) REVERT: A 606 GLU cc_start: 0.7852 (pm20) cc_final: 0.7522 (pm20) REVERT: A 647 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7606 (mmtt) REVERT: A 678 MET cc_start: 0.1722 (ppp) cc_final: 0.0656 (ppp) REVERT: A 828 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7918 (mmtt) REVERT: A 863 ILE cc_start: 0.7185 (mm) cc_final: 0.6904 (mm) REVERT: A 887 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7851 (mmm-85) REVERT: A 947 SER cc_start: 0.8393 (t) cc_final: 0.7841 (p) REVERT: A 986 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6736 (mt-10) REVERT: A 1007 LYS cc_start: 0.8049 (tttt) cc_final: 0.7610 (tttp) REVERT: A 1068 ILE cc_start: 0.7772 (mp) cc_final: 0.7458 (tt) REVERT: A 1122 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6928 (tp30) REVERT: B 133 MET cc_start: 0.6697 (mmm) cc_final: 0.6283 (mmm) REVERT: B 155 ASP cc_start: 0.7667 (t70) cc_final: 0.7206 (t70) REVERT: B 160 MET cc_start: 0.8130 (mmt) cc_final: 0.7839 (mmm) REVERT: B 164 SER cc_start: 0.8676 (m) cc_final: 0.8358 (t) REVERT: B 218 LYS cc_start: 0.8452 (mttt) cc_final: 0.8087 (ttmm) REVERT: B 367 MET cc_start: 0.8115 (mtm) cc_final: 0.7906 (mtm) REVERT: B 380 VAL cc_start: 0.8758 (t) cc_final: 0.8400 (m) REVERT: B 398 ILE cc_start: 0.8510 (mm) cc_final: 0.8302 (mt) REVERT: B 500 ARG cc_start: 0.8331 (tpp80) cc_final: 0.7975 (tpp80) REVERT: B 522 ASP cc_start: 0.8088 (t0) cc_final: 0.7759 (t0) REVERT: B 525 ILE cc_start: 0.8984 (mm) cc_final: 0.8369 (mt) REVERT: B 588 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8031 (ttmt) REVERT: B 606 GLU cc_start: 0.7617 (pm20) cc_final: 0.7359 (pm20) REVERT: B 623 ASP cc_start: 0.7944 (t0) cc_final: 0.7547 (t0) REVERT: B 645 LYS cc_start: 0.8525 (tttt) cc_final: 0.7959 (tttt) REVERT: B 828 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8086 (mmtt) REVERT: B 847 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7979 (mm-30) REVERT: B 866 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 938 MET cc_start: 0.8567 (tpp) cc_final: 0.8195 (ttt) REVERT: B 947 SER cc_start: 0.8406 (t) cc_final: 0.7781 (p) REVERT: B 991 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6630 (mm-30) REVERT: B 1007 LYS cc_start: 0.7907 (tttt) cc_final: 0.7297 (ttmm) REVERT: B 1068 ILE cc_start: 0.7897 (mp) cc_final: 0.7625 (tt) REVERT: B 1104 MET cc_start: 0.7308 (mmm) cc_final: 0.6683 (tpt) REVERT: B 1122 GLU cc_start: 0.7492 (tp30) cc_final: 0.7018 (tp30) outliers start: 49 outliers final: 32 residues processed: 456 average time/residue: 0.2807 time to fit residues: 188.7173 Evaluate side-chains 455 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 423 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 75 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS A1054 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN B1064 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.172273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141114 restraints weight = 23385.529| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.20 r_work: 0.3586 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16438 Z= 0.138 Angle : 0.566 9.105 22304 Z= 0.291 Chirality : 0.040 0.147 2684 Planarity : 0.004 0.042 2738 Dihedral : 8.364 145.354 2194 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.85 % Allowed : 14.21 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.68 (0.18), residues: 2012 helix: 1.54 (0.13), residues: 1464 sheet: 0.14 (0.65), residues: 64 loop : 0.10 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 962 HIS 0.016 0.001 HIS A 676 PHE 0.016 0.001 PHE B 254 TYR 0.032 0.001 TYR B 594 ARG 0.005 0.000 ARG B 812 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 1162) hydrogen bonds : angle 4.00449 ( 3414) covalent geometry : bond 0.00297 (16438) covalent geometry : angle 0.56602 (22304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 413 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.6928 (m-80) cc_final: 0.6389 (m-80) REVERT: A 133 MET cc_start: 0.6870 (mmm) cc_final: 0.6311 (mmm) REVERT: A 134 ASP cc_start: 0.7435 (m-30) cc_final: 0.6976 (t0) REVERT: A 149 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 155 ASP cc_start: 0.7343 (t70) cc_final: 0.6884 (t70) REVERT: A 164 SER cc_start: 0.8670 (m) cc_final: 0.8324 (t) REVERT: A 254 PHE cc_start: 0.8468 (m-80) cc_final: 0.8111 (m-10) REVERT: A 380 VAL cc_start: 0.8720 (t) cc_final: 0.8385 (m) REVERT: A 522 ASP cc_start: 0.8048 (t0) cc_final: 0.7716 (t0) REVERT: A 531 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 536 TYR cc_start: 0.8391 (m-10) cc_final: 0.8126 (m-10) REVERT: A 591 LYS cc_start: 0.8903 (mttp) cc_final: 0.8696 (mtpp) REVERT: A 602 MET cc_start: 0.5915 (mmp) cc_final: 0.5676 (mmm) REVERT: A 606 GLU cc_start: 0.7805 (pm20) cc_final: 0.7438 (pm20) REVERT: A 647 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7614 (mmtt) REVERT: A 678 MET cc_start: 0.1916 (ppp) cc_final: 0.0805 (ppp) REVERT: A 828 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7866 (mmtt) REVERT: A 863 ILE cc_start: 0.7124 (mm) cc_final: 0.6290 (tp) REVERT: A 887 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7775 (mmm-85) REVERT: A 925 MET cc_start: 0.7271 (tmm) cc_final: 0.6810 (tmm) REVERT: A 938 MET cc_start: 0.8554 (tpp) cc_final: 0.8282 (ttt) REVERT: A 947 SER cc_start: 0.8308 (t) cc_final: 0.7756 (p) REVERT: A 986 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6589 (mt-10) REVERT: A 1007 LYS cc_start: 0.8064 (tttt) cc_final: 0.7627 (tttp) REVERT: A 1068 ILE cc_start: 0.7685 (mp) cc_final: 0.7346 (tt) REVERT: A 1122 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6889 (tp30) REVERT: B 133 MET cc_start: 0.6663 (mmm) cc_final: 0.6236 (mmm) REVERT: B 155 ASP cc_start: 0.7546 (t70) cc_final: 0.7102 (t70) REVERT: B 164 SER cc_start: 0.8660 (m) cc_final: 0.8350 (t) REVERT: B 218 LYS cc_start: 0.8408 (mttt) cc_final: 0.8032 (ttmm) REVERT: B 380 VAL cc_start: 0.8729 (t) cc_final: 0.8373 (m) REVERT: B 525 ILE cc_start: 0.8916 (mm) cc_final: 0.8686 (mt) REVERT: B 534 ASP cc_start: 0.7711 (p0) cc_final: 0.7461 (p0) REVERT: B 588 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7940 (ttmt) REVERT: B 606 GLU cc_start: 0.7599 (pm20) cc_final: 0.7340 (pm20) REVERT: B 610 LEU cc_start: 0.9025 (tp) cc_final: 0.8758 (tt) REVERT: B 623 ASP cc_start: 0.7939 (t0) cc_final: 0.7513 (t0) REVERT: B 644 LEU cc_start: 0.8361 (mm) cc_final: 0.8122 (mm) REVERT: B 828 LYS cc_start: 0.8273 (mmtt) cc_final: 0.8030 (mmtt) REVERT: B 852 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8575 (mtpp) REVERT: B 853 ILE cc_start: 0.9092 (mt) cc_final: 0.8859 (tp) REVERT: B 876 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8562 (mp) REVERT: B 938 MET cc_start: 0.8572 (tpp) cc_final: 0.8240 (ttt) REVERT: B 947 SER cc_start: 0.8304 (t) cc_final: 0.7664 (p) REVERT: B 986 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 991 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6465 (mm-30) REVERT: B 1007 LYS cc_start: 0.7873 (tttt) cc_final: 0.7357 (ttmm) REVERT: B 1104 MET cc_start: 0.7107 (mmm) cc_final: 0.6889 (tpt) REVERT: B 1122 GLU cc_start: 0.7464 (tp30) cc_final: 0.6999 (tp30) outliers start: 50 outliers final: 27 residues processed: 436 average time/residue: 0.2845 time to fit residues: 181.0284 Evaluate side-chains 427 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 399 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 860 ASN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 125 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A 860 ASN A1054 ASN B 192 ASN B 614 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143458 restraints weight = 23334.994| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.28 r_work: 0.3559 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16438 Z= 0.171 Angle : 0.580 9.782 22304 Z= 0.298 Chirality : 0.041 0.173 2684 Planarity : 0.004 0.043 2738 Dihedral : 8.325 145.651 2194 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.08 % Allowed : 14.61 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.73 (0.19), residues: 2012 helix: 1.61 (0.13), residues: 1468 sheet: -0.18 (0.62), residues: 74 loop : 0.06 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 962 HIS 0.007 0.001 HIS A 614 PHE 0.019 0.001 PHE B 982 TYR 0.021 0.001 TYR A 309 ARG 0.007 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 1162) hydrogen bonds : angle 4.00428 ( 3414) covalent geometry : bond 0.00379 (16438) covalent geometry : angle 0.58049 (22304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 404 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8308 (t) cc_final: 0.7871 (p) REVERT: A 133 MET cc_start: 0.6852 (mmm) cc_final: 0.6441 (mmm) REVERT: A 134 ASP cc_start: 0.7518 (m-30) cc_final: 0.7000 (t0) REVERT: A 149 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 155 ASP cc_start: 0.7393 (t70) cc_final: 0.6917 (t70) REVERT: A 164 SER cc_start: 0.8669 (m) cc_final: 0.8346 (t) REVERT: A 319 LEU cc_start: 0.8865 (mt) cc_final: 0.8665 (mp) REVERT: A 380 VAL cc_start: 0.8760 (t) cc_final: 0.8409 (m) REVERT: A 483 MET cc_start: 0.8703 (mtp) cc_final: 0.8488 (mtm) REVERT: A 484 SER cc_start: 0.8562 (p) cc_final: 0.8350 (p) REVERT: A 531 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 534 ASP cc_start: 0.7955 (p0) cc_final: 0.7745 (p0) REVERT: A 591 LYS cc_start: 0.8938 (mttp) cc_final: 0.8727 (mtpp) REVERT: A 606 GLU cc_start: 0.7880 (pm20) cc_final: 0.7468 (pm20) REVERT: A 608 LEU cc_start: 0.8612 (tp) cc_final: 0.8389 (tt) REVERT: A 647 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7550 (mmtt) REVERT: A 828 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7835 (mmtt) REVERT: A 887 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7900 (mmm-85) REVERT: A 938 MET cc_start: 0.8611 (tpp) cc_final: 0.8200 (ttt) REVERT: A 947 SER cc_start: 0.8342 (t) cc_final: 0.7757 (p) REVERT: A 986 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6614 (mt-10) REVERT: A 1007 LYS cc_start: 0.8062 (tttt) cc_final: 0.7599 (tttp) REVERT: A 1068 ILE cc_start: 0.7680 (mp) cc_final: 0.7312 (tt) REVERT: A 1122 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6914 (tp30) REVERT: B 133 MET cc_start: 0.6636 (mmm) cc_final: 0.6223 (mmm) REVERT: B 149 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 155 ASP cc_start: 0.7579 (t70) cc_final: 0.7115 (t70) REVERT: B 164 SER cc_start: 0.8644 (m) cc_final: 0.8350 (t) REVERT: B 218 LYS cc_start: 0.8479 (mttt) cc_final: 0.8063 (mtpp) REVERT: B 380 VAL cc_start: 0.8735 (t) cc_final: 0.8417 (m) REVERT: B 383 MET cc_start: 0.7807 (mmm) cc_final: 0.7596 (mmt) REVERT: B 390 ILE cc_start: 0.8437 (mm) cc_final: 0.8123 (mt) REVERT: B 484 SER cc_start: 0.8528 (p) cc_final: 0.8328 (t) REVERT: B 525 ILE cc_start: 0.8924 (mm) cc_final: 0.8558 (mt) REVERT: B 534 ASP cc_start: 0.7788 (p0) cc_final: 0.7584 (p0) REVERT: B 588 LYS cc_start: 0.8318 (ttmt) cc_final: 0.7923 (ttmt) REVERT: B 610 LEU cc_start: 0.9014 (tp) cc_final: 0.8753 (tt) REVERT: B 623 ASP cc_start: 0.8042 (t0) cc_final: 0.7606 (t0) REVERT: B 828 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8030 (mmtt) REVERT: B 852 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8613 (mtpp) REVERT: B 876 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 887 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7965 (mmm-85) REVERT: B 947 SER cc_start: 0.8361 (t) cc_final: 0.7735 (p) REVERT: B 986 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6659 (mt-10) REVERT: B 991 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6504 (mm-30) REVERT: B 1007 LYS cc_start: 0.7950 (tttt) cc_final: 0.7409 (ttmm) REVERT: B 1104 MET cc_start: 0.7259 (mmm) cc_final: 0.6984 (tpt) REVERT: B 1122 GLU cc_start: 0.7528 (tp30) cc_final: 0.7057 (tp30) outliers start: 54 outliers final: 33 residues processed: 422 average time/residue: 0.2850 time to fit residues: 175.7589 Evaluate side-chains 426 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 392 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 ASN A1177 GLN B 192 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN B 877 GLN B1177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148906 restraints weight = 23149.075| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.26 r_work: 0.3567 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16438 Z= 0.163 Angle : 0.576 10.662 22304 Z= 0.294 Chirality : 0.040 0.209 2684 Planarity : 0.004 0.044 2738 Dihedral : 8.325 146.237 2194 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.03 % Allowed : 15.75 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.82 (0.19), residues: 2012 helix: 1.68 (0.13), residues: 1468 sheet: -0.03 (0.64), residues: 74 loop : 0.08 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 962 HIS 0.004 0.000 HIS B 928 PHE 0.018 0.001 PHE B 982 TYR 0.020 0.001 TYR A 309 ARG 0.006 0.000 ARG A1089 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 1162) hydrogen bonds : angle 3.95914 ( 3414) covalent geometry : bond 0.00360 (16438) covalent geometry : angle 0.57553 (22304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 404 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8288 (t) cc_final: 0.7844 (p) REVERT: A 133 MET cc_start: 0.6860 (mmm) cc_final: 0.6468 (mmm) REVERT: A 134 ASP cc_start: 0.7481 (m-30) cc_final: 0.6920 (t70) REVERT: A 149 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 154 MET cc_start: 0.8286 (ttm) cc_final: 0.7997 (ttp) REVERT: A 155 ASP cc_start: 0.7349 (t70) cc_final: 0.6873 (t70) REVERT: A 164 SER cc_start: 0.8669 (m) cc_final: 0.8326 (t) REVERT: A 380 VAL cc_start: 0.8756 (t) cc_final: 0.8411 (m) REVERT: A 531 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 591 LYS cc_start: 0.8925 (mttp) cc_final: 0.8723 (mtpp) REVERT: A 606 GLU cc_start: 0.7857 (pm20) cc_final: 0.7445 (pm20) REVERT: A 608 LEU cc_start: 0.8562 (tp) cc_final: 0.8337 (tt) REVERT: A 647 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7566 (mmtt) REVERT: A 678 MET cc_start: 0.2028 (ppp) cc_final: 0.1036 (ppp) REVERT: A 828 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7824 (mmtt) REVERT: A 887 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7913 (mmm-85) REVERT: A 938 MET cc_start: 0.8537 (tpp) cc_final: 0.8308 (ttt) REVERT: A 947 SER cc_start: 0.8333 (t) cc_final: 0.7755 (p) REVERT: A 958 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8396 (mtmm) REVERT: A 986 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6615 (mt-10) REVERT: A 1007 LYS cc_start: 0.8125 (tttt) cc_final: 0.7687 (tttp) REVERT: A 1122 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6900 (tp30) REVERT: B 133 MET cc_start: 0.6632 (mmm) cc_final: 0.6272 (mmm) REVERT: B 149 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 155 ASP cc_start: 0.7581 (t70) cc_final: 0.7142 (t70) REVERT: B 164 SER cc_start: 0.8654 (m) cc_final: 0.8365 (t) REVERT: B 218 LYS cc_start: 0.8428 (mttt) cc_final: 0.8014 (ttmm) REVERT: B 380 VAL cc_start: 0.8728 (t) cc_final: 0.8418 (m) REVERT: B 390 ILE cc_start: 0.8487 (mm) cc_final: 0.8166 (mt) REVERT: B 525 ILE cc_start: 0.8857 (mm) cc_final: 0.8574 (mt) REVERT: B 534 ASP cc_start: 0.7808 (p0) cc_final: 0.7564 (p0) REVERT: B 588 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7889 (ttmt) REVERT: B 623 ASP cc_start: 0.8092 (t0) cc_final: 0.7657 (t0) REVERT: B 644 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 645 LYS cc_start: 0.8497 (tttt) cc_final: 0.8010 (tttt) REVERT: B 676 HIS cc_start: 0.4287 (OUTLIER) cc_final: 0.3489 (m90) REVERT: B 828 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8023 (mmtt) REVERT: B 852 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8605 (mtpp) REVERT: B 876 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8534 (mp) REVERT: B 925 MET cc_start: 0.7074 (tmm) cc_final: 0.6868 (tmm) REVERT: B 938 MET cc_start: 0.8560 (tpp) cc_final: 0.8287 (ttt) REVERT: B 947 SER cc_start: 0.8362 (t) cc_final: 0.7745 (p) REVERT: B 986 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6706 (mt-10) REVERT: B 991 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6485 (mm-30) REVERT: B 1007 LYS cc_start: 0.8014 (tttt) cc_final: 0.7480 (ttmm) REVERT: B 1073 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.6106 (tmm) REVERT: B 1104 MET cc_start: 0.7206 (mmm) cc_final: 0.6995 (tpt) REVERT: B 1122 GLU cc_start: 0.7502 (tp30) cc_final: 0.7135 (tp30) outliers start: 53 outliers final: 30 residues processed: 426 average time/residue: 0.2855 time to fit residues: 177.2537 Evaluate side-chains 429 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 395 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1073 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 156 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 179 optimal weight: 0.2980 chunk 193 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.179800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148424 restraints weight = 23181.625| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.17 r_work: 0.3574 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16438 Z= 0.145 Angle : 0.580 10.723 22304 Z= 0.293 Chirality : 0.040 0.248 2684 Planarity : 0.004 0.044 2738 Dihedral : 8.332 146.898 2194 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.63 % Allowed : 16.38 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.97 (0.19), residues: 2012 helix: 1.84 (0.13), residues: 1456 sheet: 0.07 (0.65), residues: 74 loop : -0.02 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 962 HIS 0.004 0.000 HIS B 928 PHE 0.025 0.001 PHE B 982 TYR 0.020 0.001 TYR A 309 ARG 0.005 0.000 ARG A1089 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 1162) hydrogen bonds : angle 3.89842 ( 3414) covalent geometry : bond 0.00319 (16438) covalent geometry : angle 0.57981 (22304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 405 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8228 (t) cc_final: 0.7788 (p) REVERT: A 133 MET cc_start: 0.6851 (mmm) cc_final: 0.6475 (mmm) REVERT: A 134 ASP cc_start: 0.7461 (m-30) cc_final: 0.6880 (t70) REVERT: A 149 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 155 ASP cc_start: 0.7306 (t70) cc_final: 0.6845 (t70) REVERT: A 164 SER cc_start: 0.8685 (m) cc_final: 0.8350 (t) REVERT: A 380 VAL cc_start: 0.8760 (t) cc_final: 0.8413 (m) REVERT: A 531 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 591 LYS cc_start: 0.8923 (mttp) cc_final: 0.8717 (mtpp) REVERT: A 606 GLU cc_start: 0.7840 (pm20) cc_final: 0.7578 (pm20) REVERT: A 608 LEU cc_start: 0.8547 (tp) cc_final: 0.8345 (tt) REVERT: A 647 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7608 (mmtt) REVERT: A 678 MET cc_start: 0.2095 (ppp) cc_final: 0.1169 (ppp) REVERT: A 828 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7822 (mmtt) REVERT: A 935 GLU cc_start: 0.8262 (tp30) cc_final: 0.7895 (tp30) REVERT: A 938 MET cc_start: 0.8579 (tpp) cc_final: 0.8188 (ttt) REVERT: A 947 SER cc_start: 0.8343 (t) cc_final: 0.7744 (p) REVERT: A 986 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6589 (mt-10) REVERT: A 1007 LYS cc_start: 0.8134 (tttt) cc_final: 0.7697 (tttp) REVERT: A 1122 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6909 (tp30) REVERT: B 133 MET cc_start: 0.6650 (mmm) cc_final: 0.6299 (mmm) REVERT: B 149 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7660 (tm-30) REVERT: B 155 ASP cc_start: 0.7538 (t70) cc_final: 0.7108 (t70) REVERT: B 164 SER cc_start: 0.8615 (m) cc_final: 0.8295 (t) REVERT: B 218 LYS cc_start: 0.8443 (mttt) cc_final: 0.8026 (ttmm) REVERT: B 380 VAL cc_start: 0.8751 (t) cc_final: 0.8452 (m) REVERT: B 390 ILE cc_start: 0.8452 (mm) cc_final: 0.8143 (mt) REVERT: B 525 ILE cc_start: 0.8832 (mm) cc_final: 0.8596 (mt) REVERT: B 534 ASP cc_start: 0.7813 (p0) cc_final: 0.7574 (p0) REVERT: B 588 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7860 (ttmt) REVERT: B 623 ASP cc_start: 0.8108 (t0) cc_final: 0.7672 (t0) REVERT: B 644 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8087 (mm) REVERT: B 645 LYS cc_start: 0.8466 (tttt) cc_final: 0.7991 (tttt) REVERT: B 828 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7962 (mmtt) REVERT: B 852 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8570 (mtpp) REVERT: B 876 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8543 (mp) REVERT: B 938 MET cc_start: 0.8565 (tpp) cc_final: 0.8266 (ttt) REVERT: B 947 SER cc_start: 0.8369 (t) cc_final: 0.7786 (p) REVERT: B 986 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6681 (mt-10) REVERT: B 991 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6485 (mm-30) REVERT: B 1007 LYS cc_start: 0.8006 (tttt) cc_final: 0.7469 (ttmm) REVERT: B 1073 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5995 (tmm) REVERT: B 1104 MET cc_start: 0.7219 (mmm) cc_final: 0.6976 (tpt) REVERT: B 1122 GLU cc_start: 0.7504 (tp30) cc_final: 0.7148 (tp30) REVERT: B 1144 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6972 (t0) outliers start: 46 outliers final: 29 residues processed: 424 average time/residue: 0.2839 time to fit residues: 175.6460 Evaluate side-chains 421 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 388 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 93 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 99 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN A1054 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150200 restraints weight = 22975.074| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.28 r_work: 0.3580 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16438 Z= 0.131 Angle : 0.581 11.392 22304 Z= 0.292 Chirality : 0.040 0.266 2684 Planarity : 0.004 0.047 2738 Dihedral : 8.368 148.627 2194 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.45 % Allowed : 17.35 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.05 (0.19), residues: 2012 helix: 1.92 (0.13), residues: 1454 sheet: -0.07 (0.64), residues: 78 loop : -0.02 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP A 962 HIS 0.004 0.000 HIS B 928 PHE 0.024 0.001 PHE B 982 TYR 0.023 0.001 TYR B 309 ARG 0.007 0.000 ARG A1089 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 1162) hydrogen bonds : angle 3.86788 ( 3414) covalent geometry : bond 0.00286 (16438) covalent geometry : angle 0.58090 (22304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 395 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8206 (t) cc_final: 0.7761 (p) REVERT: A 133 MET cc_start: 0.6855 (mmm) cc_final: 0.6483 (mmm) REVERT: A 134 ASP cc_start: 0.7470 (m-30) cc_final: 0.6937 (t0) REVERT: A 149 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 155 ASP cc_start: 0.7260 (t70) cc_final: 0.6741 (t70) REVERT: A 164 SER cc_start: 0.8650 (m) cc_final: 0.8323 (t) REVERT: A 278 TRP cc_start: 0.8773 (t-100) cc_final: 0.8439 (t-100) REVERT: A 380 VAL cc_start: 0.8771 (t) cc_final: 0.8420 (m) REVERT: A 531 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 606 GLU cc_start: 0.7817 (pm20) cc_final: 0.7574 (pm20) REVERT: A 608 LEU cc_start: 0.8553 (tp) cc_final: 0.8335 (tt) REVERT: A 644 LEU cc_start: 0.8210 (mm) cc_final: 0.7931 (mm) REVERT: A 647 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7626 (mmtt) REVERT: A 678 MET cc_start: 0.2037 (ppp) cc_final: 0.1137 (ppp) REVERT: A 828 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7797 (mmtt) REVERT: A 938 MET cc_start: 0.8607 (tpp) cc_final: 0.8187 (ttt) REVERT: A 947 SER cc_start: 0.8329 (t) cc_final: 0.7731 (p) REVERT: A 958 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8308 (mtmm) REVERT: A 986 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6557 (mt-10) REVERT: A 1007 LYS cc_start: 0.8103 (tttt) cc_final: 0.7655 (tttp) REVERT: A 1045 MET cc_start: 0.7513 (pmm) cc_final: 0.6728 (pmm) REVERT: A 1122 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6914 (tp30) REVERT: B 133 MET cc_start: 0.6620 (mmm) cc_final: 0.6247 (mmm) REVERT: B 149 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 155 ASP cc_start: 0.7557 (t70) cc_final: 0.7105 (t70) REVERT: B 164 SER cc_start: 0.8601 (m) cc_final: 0.8289 (t) REVERT: B 199 MET cc_start: 0.8282 (mmm) cc_final: 0.7790 (mmm) REVERT: B 380 VAL cc_start: 0.8745 (t) cc_final: 0.8430 (m) REVERT: B 390 ILE cc_start: 0.8437 (mm) cc_final: 0.8133 (mt) REVERT: B 525 ILE cc_start: 0.8826 (mm) cc_final: 0.8583 (mt) REVERT: B 534 ASP cc_start: 0.7817 (p0) cc_final: 0.7565 (p0) REVERT: B 588 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7719 (ttmt) REVERT: B 590 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8070 (mt-10) REVERT: B 644 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8060 (mm) REVERT: B 645 LYS cc_start: 0.8487 (tttt) cc_final: 0.7971 (tttt) REVERT: B 676 HIS cc_start: 0.4408 (OUTLIER) cc_final: 0.3719 (m90) REVERT: B 828 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7943 (mmtt) REVERT: B 832 GLN cc_start: 0.8128 (tp40) cc_final: 0.7921 (tp40) REVERT: B 852 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8572 (mtpp) REVERT: B 876 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8528 (mp) REVERT: B 938 MET cc_start: 0.8582 (tpp) cc_final: 0.8227 (ttt) REVERT: B 947 SER cc_start: 0.8411 (t) cc_final: 0.7775 (p) REVERT: B 986 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6704 (mt-10) REVERT: B 991 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6476 (mm-30) REVERT: B 1007 LYS cc_start: 0.7978 (tttt) cc_final: 0.7438 (ttmm) REVERT: B 1045 MET cc_start: 0.7546 (pmm) cc_final: 0.6726 (pmm) REVERT: B 1073 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.6007 (tmm) REVERT: B 1104 MET cc_start: 0.7202 (mmm) cc_final: 0.6953 (tpt) REVERT: B 1122 GLU cc_start: 0.7505 (tp30) cc_final: 0.7137 (tp30) REVERT: B 1144 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6989 (t0) outliers start: 43 outliers final: 26 residues processed: 413 average time/residue: 0.2887 time to fit residues: 174.0491 Evaluate side-chains 416 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 385 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 195 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 109 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 ASN A1064 GLN B 192 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN B1064 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.181640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150326 restraints weight = 23140.921| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.26 r_work: 0.3585 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16438 Z= 0.137 Angle : 0.598 11.150 22304 Z= 0.297 Chirality : 0.040 0.290 2684 Planarity : 0.004 0.044 2738 Dihedral : 8.384 149.940 2194 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.11 % Allowed : 18.15 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.09 (0.19), residues: 2012 helix: 1.95 (0.13), residues: 1454 sheet: 0.02 (0.64), residues: 78 loop : -0.03 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A 962 HIS 0.004 0.000 HIS B 928 PHE 0.044 0.001 PHE A 982 TYR 0.022 0.001 TYR B 309 ARG 0.006 0.000 ARG A1089 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 1162) hydrogen bonds : angle 3.87317 ( 3414) covalent geometry : bond 0.00303 (16438) covalent geometry : angle 0.59799 (22304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 409 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8239 (t) cc_final: 0.7787 (p) REVERT: A 133 MET cc_start: 0.6850 (mmm) cc_final: 0.6495 (mmm) REVERT: A 134 ASP cc_start: 0.7494 (m-30) cc_final: 0.6900 (t70) REVERT: A 149 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 155 ASP cc_start: 0.7279 (t70) cc_final: 0.6816 (t70) REVERT: A 164 SER cc_start: 0.8650 (m) cc_final: 0.8344 (t) REVERT: A 380 VAL cc_start: 0.8767 (t) cc_final: 0.8412 (m) REVERT: A 531 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 597 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: A 606 GLU cc_start: 0.7737 (pm20) cc_final: 0.7502 (pm20) REVERT: A 608 LEU cc_start: 0.8520 (tp) cc_final: 0.8307 (tt) REVERT: A 644 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7925 (mm) REVERT: A 647 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7663 (mmtt) REVERT: A 828 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7859 (mmtt) REVERT: A 938 MET cc_start: 0.8602 (tpp) cc_final: 0.8197 (ttt) REVERT: A 947 SER cc_start: 0.8284 (t) cc_final: 0.7674 (p) REVERT: A 958 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8302 (mtmm) REVERT: A 986 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6637 (mt-10) REVERT: A 1007 LYS cc_start: 0.8117 (tttt) cc_final: 0.7693 (tttp) REVERT: A 1045 MET cc_start: 0.7539 (pmm) cc_final: 0.6793 (pmm) REVERT: A 1122 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6934 (tp30) REVERT: B 133 MET cc_start: 0.6631 (mmm) cc_final: 0.6277 (mmm) REVERT: B 149 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 155 ASP cc_start: 0.7518 (t70) cc_final: 0.7087 (t70) REVERT: B 164 SER cc_start: 0.8613 (m) cc_final: 0.8296 (t) REVERT: B 199 MET cc_start: 0.8278 (mmm) cc_final: 0.7900 (mmm) REVERT: B 380 VAL cc_start: 0.8722 (t) cc_final: 0.8414 (m) REVERT: B 390 ILE cc_start: 0.8457 (mm) cc_final: 0.8150 (mt) REVERT: B 525 ILE cc_start: 0.8839 (mm) cc_final: 0.8599 (mt) REVERT: B 534 ASP cc_start: 0.7853 (p0) cc_final: 0.7597 (p0) REVERT: B 588 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7749 (ttmt) REVERT: B 590 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 606 GLU cc_start: 0.7606 (pm20) cc_final: 0.7226 (pm20) REVERT: B 644 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8045 (mm) REVERT: B 645 LYS cc_start: 0.8484 (tttt) cc_final: 0.7973 (tttt) REVERT: B 676 HIS cc_start: 0.4374 (OUTLIER) cc_final: 0.3688 (m90) REVERT: B 828 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7958 (mmtt) REVERT: B 852 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8560 (mtpp) REVERT: B 876 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 938 MET cc_start: 0.8558 (tpp) cc_final: 0.8250 (ttt) REVERT: B 947 SER cc_start: 0.8404 (t) cc_final: 0.7780 (p) REVERT: B 986 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6723 (mt-10) REVERT: B 991 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6482 (mm-30) REVERT: B 1007 LYS cc_start: 0.8003 (tttt) cc_final: 0.7476 (ttmm) REVERT: B 1045 MET cc_start: 0.7607 (pmm) cc_final: 0.6931 (pmm) REVERT: B 1073 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.6003 (tmm) REVERT: B 1104 MET cc_start: 0.7161 (mmm) cc_final: 0.6960 (tpt) REVERT: B 1122 GLU cc_start: 0.7495 (tp30) cc_final: 0.7130 (tp30) REVERT: B 1144 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6983 (t0) outliers start: 37 outliers final: 24 residues processed: 424 average time/residue: 0.2884 time to fit residues: 177.6379 Evaluate side-chains 431 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 400 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 113 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 chunk 177 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.0070 chunk 167 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN A 877 GLN A1054 ASN A1064 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 ASN B1064 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.184018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152304 restraints weight = 23398.765| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.48 r_work: 0.3590 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16438 Z= 0.126 Angle : 0.609 11.124 22304 Z= 0.298 Chirality : 0.040 0.280 2684 Planarity : 0.004 0.043 2738 Dihedral : 8.396 150.513 2194 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.94 % Allowed : 19.01 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.18 (0.19), residues: 2012 helix: 1.97 (0.13), residues: 1464 sheet: 0.55 (0.67), residues: 68 loop : 0.02 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 962 HIS 0.005 0.000 HIS A 614 PHE 0.039 0.001 PHE A 982 TYR 0.025 0.001 TYR B 309 ARG 0.007 0.000 ARG B1089 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1162) hydrogen bonds : angle 3.85889 ( 3414) covalent geometry : bond 0.00274 (16438) covalent geometry : angle 0.60853 (22304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 394 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6937 (mmm) cc_final: 0.6606 (mmm) REVERT: A 134 ASP cc_start: 0.7579 (m-30) cc_final: 0.7051 (t0) REVERT: A 149 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 155 ASP cc_start: 0.7294 (t70) cc_final: 0.6793 (t70) REVERT: A 164 SER cc_start: 0.8696 (m) cc_final: 0.8430 (t) REVERT: A 380 VAL cc_start: 0.8736 (t) cc_final: 0.8379 (m) REVERT: A 531 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 644 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7883 (mm) REVERT: A 647 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7697 (mmtt) REVERT: A 678 MET cc_start: 0.2280 (ppp) cc_final: 0.1382 (ppp) REVERT: A 828 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7879 (mmtt) REVERT: A 938 MET cc_start: 0.8480 (tpp) cc_final: 0.8056 (ttt) REVERT: A 947 SER cc_start: 0.8257 (t) cc_final: 0.7663 (p) REVERT: A 958 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8386 (mtmm) REVERT: A 986 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6683 (mt-10) REVERT: A 1007 LYS cc_start: 0.8101 (tttt) cc_final: 0.7688 (tttp) REVERT: A 1045 MET cc_start: 0.7518 (pmm) cc_final: 0.6742 (pmm) REVERT: A 1122 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6967 (tp30) REVERT: B 133 MET cc_start: 0.6607 (mmm) cc_final: 0.6273 (mmm) REVERT: B 149 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 155 ASP cc_start: 0.7565 (t70) cc_final: 0.7161 (t70) REVERT: B 164 SER cc_start: 0.8660 (m) cc_final: 0.8381 (t) REVERT: B 199 MET cc_start: 0.8266 (mmm) cc_final: 0.7890 (mmm) REVERT: B 380 VAL cc_start: 0.8727 (t) cc_final: 0.8415 (m) REVERT: B 390 ILE cc_start: 0.8482 (mm) cc_final: 0.8183 (mt) REVERT: B 525 ILE cc_start: 0.8911 (mm) cc_final: 0.8680 (mt) REVERT: B 534 ASP cc_start: 0.7908 (p0) cc_final: 0.7647 (p0) REVERT: B 588 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7677 (ttmt) REVERT: B 590 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 644 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8062 (mm) REVERT: B 645 LYS cc_start: 0.8434 (tttt) cc_final: 0.7945 (tttt) REVERT: B 676 HIS cc_start: 0.4405 (OUTLIER) cc_final: 0.3713 (m90) REVERT: B 828 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7950 (mmtt) REVERT: B 852 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8477 (mtpp) REVERT: B 876 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 938 MET cc_start: 0.8331 (tpp) cc_final: 0.8043 (ttt) REVERT: B 947 SER cc_start: 0.8327 (t) cc_final: 0.7735 (p) REVERT: B 986 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6834 (mt-10) REVERT: B 991 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6621 (mm-30) REVERT: B 1007 LYS cc_start: 0.8009 (tttt) cc_final: 0.7476 (ttmm) REVERT: B 1045 MET cc_start: 0.7622 (pmm) cc_final: 0.6912 (pmm) REVERT: B 1073 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.6095 (tmm) REVERT: B 1122 GLU cc_start: 0.7486 (tp30) cc_final: 0.7152 (tp30) REVERT: B 1144 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7026 (t0) outliers start: 34 outliers final: 23 residues processed: 408 average time/residue: 0.2850 time to fit residues: 169.8755 Evaluate side-chains 417 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 388 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 196 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 157 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 ASN A1064 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.183510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152737 restraints weight = 23299.890| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.20 r_work: 0.3600 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16438 Z= 0.132 Angle : 0.613 10.949 22304 Z= 0.302 Chirality : 0.040 0.231 2684 Planarity : 0.004 0.043 2738 Dihedral : 8.409 151.470 2194 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.71 % Allowed : 19.52 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.18 (0.19), residues: 2012 helix: 1.97 (0.13), residues: 1464 sheet: 0.55 (0.67), residues: 68 loop : 0.03 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP A 962 HIS 0.004 0.000 HIS A 614 PHE 0.032 0.001 PHE A 982 TYR 0.025 0.001 TYR A 309 ARG 0.006 0.000 ARG B1089 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 1162) hydrogen bonds : angle 3.87082 ( 3414) covalent geometry : bond 0.00294 (16438) covalent geometry : angle 0.61260 (22304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10104.40 seconds wall clock time: 174 minutes 54.98 seconds (10494.98 seconds total)