Starting phenix.real_space_refine on Thu Aug 6 17:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_17605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_17605.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_17605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_17605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_17605.map" model { file = "/net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_17605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pd8_17605/08_2026/8pd8_17605.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'RNAv2': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B Time building chain proxies: 8.31, per 1000 atoms: 0.52 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: 1.01 Conformation dependent library (CDL) restraints added in 671.6 milliseconds 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: 0.55 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: 3.36 Time building geometry restraints manager: 1.43 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: 21514 2.06 - 4.12: 670 4.12 - 6.18: 81 6.18 - 8.23: 21 8.23 - 10.29: 18 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: 9584 29.58 - 59.17: 194 59.17 - 88.75: 24 88.75 - 118.34: 0 118.34 - 147.92: 4 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 - 0.050: 2005 0.050 - 0.101: 587 0.101 - 0.151: 77 0.151 - 0.201: 13 0.201 - 0.252: 2 Chirality restraints: 2684 Sorted by residual: chirality pdb=" C2' CMP B1401 " pdb=" C1' CMP B1401 " pdb=" C3' CMP B1401 " pdb=" O2' CMP B1401 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2' CMP A1401 " pdb=" C1' CMP A1401 " pdb=" C3' CMP A1401 " pdb=" O2' CMP A1401 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.55e+00 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 ... (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: 0.04 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.670 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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= 0.274 Angle : 0.863 10.292 22304 Z= 0.480 Chirality : 0.047 0.252 2684 Planarity : 0.005 0.050 2738 Dihedral : 12.796 147.921 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.001 ARG B1169 TYR 0.034 0.003 TYR B 984 PHE 0.021 0.002 PHE B 625 TRP 0.032 0.003 TRP B 643 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.27 (16438) covalent geometry : angle 0.86291 / 0.48 (22304) hydrogen bonds : bond 0.12976 / 9.06 ( 1162) hydrogen bonds : angle 5.55026 / 4.02 ( 3414) *********************** 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 : 0.602 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: 0.7240 (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: 0.1272 time to fit residues: 100.4262 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 : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS A 421 ASN A 691 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 691 ASN B 900 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.176738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145981 restraints weight = 23614.798| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.29 r_work: 0.3593 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16438 Z= 0.145 Angle : 0.622 8.293 22304 Z= 0.317 Chirality : 0.042 0.157 2684 Planarity : 0.004 0.049 2738 Dihedral : 7.176 132.382 2194 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.77 % Allowed : 10.96 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2012 helix: 1.27 (0.13), residues: 1464 sheet: 0.03 (0.58), residues: 82 loop : 0.23 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 812 TYR 0.026 0.001 TYR A 309 PHE 0.016 0.001 PHE A 268 TRP 0.033 0.002 TRP A 962 HIS 0.010 0.001 HIS B 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (16438) covalent geometry : angle 0.62214 / 0.32 (22304) hydrogen bonds : bond 0.05265 / 3.57 ( 1162) hydrogen bonds : angle 4.28770 / 3.09 ( 3414) *********************** 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 476 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 445 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6787 (mmm) cc_final: 0.6154 (mmm) REVERT: A 134 ASP cc_start: 0.7539 (m-30) cc_final: 0.6945 (t0) REVERT: A 149 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 155 ASP cc_start: 0.7498 (t70) cc_final: 0.7095 (t70) REVERT: A 164 SER cc_start: 0.8748 (m) cc_final: 0.8459 (t) REVERT: A 289 PHE cc_start: 0.8472 (m-80) cc_final: 0.8224 (m-80) REVERT: A 380 VAL cc_start: 0.8710 (t) cc_final: 0.8346 (m) REVERT: A 522 ASP cc_start: 0.8184 (t0) cc_final: 0.7817 (t0) REVERT: A 525 ILE cc_start: 0.9018 (mm) cc_final: 0.8441 (mt) REVERT: A 527 THR cc_start: 0.8790 (t) cc_final: 0.8584 (p) REVERT: A 584 LEU cc_start: 0.8855 (mt) cc_final: 0.8514 (mt) REVERT: A 591 LYS cc_start: 0.8934 (mttp) cc_final: 0.8713 (mtpp) REVERT: A 602 MET cc_start: 0.5838 (mmp) cc_final: 0.5586 (mmm) REVERT: A 606 GLU cc_start: 0.7875 (pm20) cc_final: 0.7563 (pm20) REVERT: A 634 SER cc_start: 0.7843 (m) cc_final: 0.7623 (p) REVERT: A 645 LYS cc_start: 0.8152 (tttt) cc_final: 0.7533 (tttp) REVERT: A 647 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7648 (mmtt) REVERT: A 828 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7957 (mmtt) REVERT: A 887 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7943 (mmm-85) REVERT: A 947 SER cc_start: 0.8268 (t) cc_final: 0.7748 (p) REVERT: A 991 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6492 (mm-30) REVERT: A 998 LEU cc_start: 0.8020 (mp) cc_final: 0.7812 (mp) REVERT: A 1007 LYS cc_start: 0.7979 (tttt) cc_final: 0.7468 (tttp) REVERT: A 1068 ILE cc_start: 0.7791 (mp) cc_final: 0.7555 (tt) REVERT: A 1122 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6904 (tp30) REVERT: B 133 MET cc_start: 0.6582 (mmm) cc_final: 0.6137 (mmm) REVERT: B 155 ASP cc_start: 0.7649 (t70) cc_final: 0.7239 (t70) REVERT: B 164 SER cc_start: 0.8729 (m) cc_final: 0.8472 (t) REVERT: B 171 LEU cc_start: 0.8242 (mm) cc_final: 0.8038 (mm) REVERT: B 380 VAL cc_start: 0.8726 (t) cc_final: 0.8443 (m) REVERT: B 522 ASP cc_start: 0.8119 (t0) cc_final: 0.7771 (t0) REVERT: B 525 ILE cc_start: 0.8991 (mm) cc_final: 0.8283 (mt) REVERT: B 534 ASP cc_start: 0.7457 (p0) cc_final: 0.7243 (p0) REVERT: B 586 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7489 (ttp) REVERT: B 588 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7776 (ttmt) REVERT: B 596 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8632 (ttmt) REVERT: B 613 GLN cc_start: 0.7854 (tt0) cc_final: 0.7572 (tm-30) REVERT: B 623 ASP cc_start: 0.7911 (t0) cc_final: 0.7576 (t0) REVERT: B 634 SER cc_start: 0.8017 (m) cc_final: 0.7766 (p) REVERT: B 645 LYS cc_start: 0.8510 (tttt) cc_final: 0.7839 (tptt) REVERT: B 828 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7903 (mmmm) REVERT: B 863 ILE cc_start: 0.7039 (mm) cc_final: 0.6207 (tp) REVERT: B 981 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6807 (t-90) REVERT: B 991 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6768 (mm-30) REVERT: B 1073 MET cc_start: 0.6006 (mmm) cc_final: 0.5790 (tmm) REVERT: B 1122 GLU cc_start: 0.7433 (tp30) cc_final: 0.6966 (tp30) outliers start: 31 outliers final: 14 residues processed: 459 average time/residue: 0.1142 time to fit residues: 78.0423 Evaluate side-chains 437 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 421 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 401 MET Chi-restraints excluded: chain A residue 419 TRP 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 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 586 MET 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 144 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 ASN B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148628 restraints weight = 23730.523| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.21 r_work: 0.3577 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2476 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= 0.150 Angle : 0.598 8.460 22304 Z= 0.300 Chirality : 0.041 0.152 2684 Planarity : 0.004 0.041 2738 Dihedral : 7.024 132.426 2194 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.63 % Allowed : 12.56 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2012 helix: 1.46 (0.13), residues: 1466 sheet: 0.03 (0.59), residues: 82 loop : 0.25 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 812 TYR 0.024 0.001 TYR A 309 PHE 0.024 0.001 PHE B 982 TRP 0.036 0.002 TRP A 962 HIS 0.009 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16438) covalent geometry : angle 0.59754 / 0.30 (22304) hydrogen bonds : bond 0.04822 / 3.25 ( 1162) hydrogen bonds : angle 4.07919 / 2.93 ( 3414) *********************** 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 485 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 439 time to evaluate : 0.613 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: 0.6865 (mmm) cc_final: 0.6272 (mmm) REVERT: A 134 ASP cc_start: 0.7505 (m-30) cc_final: 0.6928 (t0) REVERT: A 149 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 155 ASP cc_start: 0.7449 (t70) cc_final: 0.6964 (t70) REVERT: A 164 SER cc_start: 0.8688 (m) cc_final: 0.8336 (t) REVERT: A 500 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7516 (ttp80) REVERT: A 522 ASP cc_start: 0.8131 (t0) cc_final: 0.7853 (t0) REVERT: A 525 ILE cc_start: 0.8969 (mm) cc_final: 0.8461 (mt) REVERT: A 527 THR cc_start: 0.8728 (t) cc_final: 0.8490 (p) REVERT: A 531 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 591 LYS cc_start: 0.8934 (mttp) cc_final: 0.8705 (mtpp) REVERT: A 596 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8449 (ttpp) REVERT: A 602 MET cc_start: 0.5909 (mmp) cc_final: 0.5648 (mmm) REVERT: A 606 GLU cc_start: 0.7841 (pm20) cc_final: 0.7529 (pm20) REVERT: A 647 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7609 (mmtt) REVERT: A 828 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7846 (mmtt) REVERT: A 863 ILE cc_start: 0.6986 (mm) cc_final: 0.6650 (mm) REVERT: A 887 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7820 (mmm-85) REVERT: A 938 MET cc_start: 0.8639 (tpp) cc_final: 0.8301 (ttt) REVERT: A 947 SER cc_start: 0.8300 (t) cc_final: 0.7771 (p) REVERT: A 958 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8433 (mttm) REVERT: A 982 PHE cc_start: 0.7223 (m-80) cc_final: 0.6996 (m-80) REVERT: A 1007 LYS cc_start: 0.8078 (tttt) cc_final: 0.7628 (tttp) REVERT: A 1068 ILE cc_start: 0.7731 (mp) cc_final: 0.7400 (tt) REVERT: A 1122 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6876 (tp30) REVERT: B 133 MET cc_start: 0.6618 (mmm) cc_final: 0.6237 (mmm) REVERT: B 155 ASP cc_start: 0.7579 (t70) cc_final: 0.7127 (t70) REVERT: B 164 SER cc_start: 0.8655 (m) cc_final: 0.8367 (t) REVERT: B 171 LEU cc_start: 0.8213 (mm) cc_final: 0.8001 (mm) REVERT: B 218 LYS cc_start: 0.8406 (mttt) cc_final: 0.8054 (ttmm) REVERT: B 380 VAL cc_start: 0.8763 (t) cc_final: 0.8430 (m) REVERT: B 398 ILE cc_start: 0.8653 (mm) cc_final: 0.8421 (mt) REVERT: B 522 ASP cc_start: 0.8031 (t0) cc_final: 0.7738 (t0) REVERT: B 525 ILE cc_start: 0.8945 (mm) cc_final: 0.8340 (mt) REVERT: B 534 ASP cc_start: 0.7565 (p0) cc_final: 0.7313 (p0) REVERT: B 588 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7996 (ttmt) REVERT: B 623 ASP cc_start: 0.7887 (t0) cc_final: 0.7495 (t0) REVERT: B 634 SER cc_start: 0.8076 (m) cc_final: 0.7721 (p) REVERT: B 645 LYS cc_start: 0.8522 (tttt) cc_final: 0.7845 (tttt) REVERT: B 828 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8008 (mmtt) REVERT: B 832 GLN cc_start: 0.8099 (tp40) cc_final: 0.7857 (tp40) REVERT: B 938 MET cc_start: 0.8542 (tpp) cc_final: 0.8199 (ttt) REVERT: B 947 SER cc_start: 0.8373 (t) cc_final: 0.7736 (p) REVERT: B 991 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6579 (mm-30) REVERT: B 1007 LYS cc_start: 0.7839 (tttt) cc_final: 0.7380 (ttmm) REVERT: B 1122 GLU cc_start: 0.7446 (tp30) cc_final: 0.6984 (tp30) outliers start: 46 outliers final: 26 residues processed: 462 average time/residue: 0.1168 time to fit residues: 81.4222 Evaluate side-chains 438 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 411 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 500 ARG 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 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 200 MET 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 512 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1058 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 20 optimal weight: 0.0770 chunk 181 optimal weight: 0.7980 chunk 168 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN B1064 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150913 restraints weight = 23280.481| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.24 r_work: 0.3586 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2813 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= 0.136 Angle : 0.579 8.338 22304 Z= 0.288 Chirality : 0.040 0.147 2684 Planarity : 0.004 0.041 2738 Dihedral : 6.939 133.112 2194 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.63 % Allowed : 13.24 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2012 helix: 1.65 (0.13), residues: 1466 sheet: 0.38 (0.68), residues: 64 loop : 0.17 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 812 TYR 0.020 0.001 TYR A 309 PHE 0.016 0.001 PHE B 982 TRP 0.041 0.002 TRP A 962 HIS 0.008 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (16438) covalent geometry : angle 0.57875 / 0.29 (22304) hydrogen bonds : bond 0.04482 / 3.03 ( 1162) hydrogen bonds : angle 3.95684 / 2.84 ( 3414) *********************** 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 466 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 420 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.6996 (m-80) cc_final: 0.6479 (m-80) REVERT: A 133 MET cc_start: 0.6813 (mmm) cc_final: 0.6413 (mmm) REVERT: A 134 ASP cc_start: 0.7387 (m-30) cc_final: 0.6802 (t0) REVERT: A 149 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 154 MET cc_start: 0.8315 (ttm) cc_final: 0.8013 (ttm) REVERT: A 155 ASP cc_start: 0.7363 (t70) cc_final: 0.6897 (t70) REVERT: A 164 SER cc_start: 0.8673 (m) cc_final: 0.8339 (t) REVERT: A 525 ILE cc_start: 0.8922 (mm) cc_final: 0.8667 (mt) REVERT: A 527 THR cc_start: 0.8728 (t) cc_final: 0.8466 (p) REVERT: A 531 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 536 TYR cc_start: 0.8343 (m-10) cc_final: 0.8141 (m-10) REVERT: A 591 LYS cc_start: 0.8912 (mttp) cc_final: 0.8699 (mtpp) REVERT: A 596 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8468 (ttpp) REVERT: A 602 MET cc_start: 0.6046 (mmp) cc_final: 0.5829 (mmm) REVERT: A 606 GLU cc_start: 0.7834 (pm20) cc_final: 0.7565 (pm20) REVERT: A 610 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8813 (tp) REVERT: A 647 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7613 (mmtt) REVERT: A 828 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7882 (mmtt) REVERT: A 863 ILE cc_start: 0.7104 (mm) cc_final: 0.6235 (tp) REVERT: A 887 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7774 (mmm-85) REVERT: A 935 GLU cc_start: 0.8089 (tp30) cc_final: 0.7787 (tp30) REVERT: A 938 MET cc_start: 0.8633 (tpp) cc_final: 0.8259 (ttt) REVERT: A 947 SER cc_start: 0.8300 (t) cc_final: 0.7772 (p) REVERT: A 982 PHE cc_start: 0.7224 (m-80) cc_final: 0.7003 (m-80) REVERT: A 986 GLU cc_start: 0.7356 (tp30) cc_final: 0.7063 (tp30) REVERT: A 1007 LYS cc_start: 0.8125 (tttt) cc_final: 0.7670 (tttp) REVERT: A 1068 ILE cc_start: 0.7670 (mp) cc_final: 0.7363 (tt) REVERT: A 1122 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6866 (tp30) REVERT: B 133 MET cc_start: 0.6563 (mmm) cc_final: 0.6231 (mmm) REVERT: B 149 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 155 ASP cc_start: 0.7524 (t70) cc_final: 0.7076 (t70) REVERT: B 164 SER cc_start: 0.8627 (m) cc_final: 0.8332 (t) REVERT: B 218 LYS cc_start: 0.8359 (mttt) cc_final: 0.7995 (ttmm) REVERT: B 484 SER cc_start: 0.8682 (p) cc_final: 0.8382 (t) REVERT: B 522 ASP cc_start: 0.8007 (t0) cc_final: 0.7743 (t0) REVERT: B 525 ILE cc_start: 0.8866 (mm) cc_final: 0.8304 (mt) REVERT: B 588 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7968 (ttmt) REVERT: B 610 LEU cc_start: 0.9054 (tp) cc_final: 0.8784 (tt) REVERT: B 623 ASP cc_start: 0.7938 (t0) cc_final: 0.7522 (t0) REVERT: B 634 SER cc_start: 0.8067 (m) cc_final: 0.7756 (p) REVERT: B 644 LEU cc_start: 0.8323 (mm) cc_final: 0.8078 (mm) REVERT: B 676 HIS cc_start: 0.4429 (OUTLIER) cc_final: 0.3368 (m90) REVERT: B 828 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7818 (mmmm) REVERT: B 852 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8665 (mtpp) REVERT: B 876 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 931 GLU cc_start: 0.7870 (tt0) cc_final: 0.7629 (mt-10) REVERT: B 947 SER cc_start: 0.8314 (t) cc_final: 0.7687 (p) REVERT: B 986 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6699 (mt-10) REVERT: B 991 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6491 (mm-30) REVERT: B 1003 SER cc_start: 0.8148 (t) cc_final: 0.7933 (m) REVERT: B 1007 LYS cc_start: 0.7907 (tttt) cc_final: 0.7390 (ttmm) REVERT: B 1089 ARG cc_start: 0.6880 (mtp85) cc_final: 0.6639 (mtp85) REVERT: B 1122 GLU cc_start: 0.7480 (tp30) cc_final: 0.7036 (tp30) outliers start: 46 outliers final: 23 residues processed: 439 average time/residue: 0.1149 time to fit residues: 75.1748 Evaluate side-chains 432 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 406 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 610 LEU 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 B residue 84 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 257 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 676 HIS Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 876 LEU 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 1119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 187 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 860 ASN A1054 ASN A1064 GLN B 192 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 614 HIS B 900 GLN B1054 ASN B1064 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.182452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151791 restraints weight = 23314.569| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.24 r_work: 0.3561 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16438 Z= 0.169 Angle : 0.589 8.381 22304 Z= 0.294 Chirality : 0.041 0.157 2684 Planarity : 0.004 0.043 2738 Dihedral : 6.933 133.667 2194 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.03 % Allowed : 14.33 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2012 helix: 1.67 (0.13), residues: 1468 sheet: -0.04 (0.65), residues: 74 loop : 0.14 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 887 TYR 0.022 0.001 TYR B 309 PHE 0.018 0.001 PHE B 982 TRP 0.049 0.002 TRP A 962 HIS 0.014 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (16438) covalent geometry : angle 0.58902 / 0.29 (22304) hydrogen bonds : bond 0.04651 / 3.14 ( 1162) hydrogen bonds : angle 3.95527 / 2.85 ( 3414) *********************** 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 465 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 412 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6841 (mmm) cc_final: 0.6467 (mmm) REVERT: A 134 ASP cc_start: 0.7439 (m-30) cc_final: 0.6982 (t0) REVERT: A 149 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7553 (tm-30) REVERT: A 155 ASP cc_start: 0.7390 (t70) cc_final: 0.6936 (t70) REVERT: A 164 SER cc_start: 0.8650 (m) cc_final: 0.8342 (t) REVERT: A 494 MET cc_start: 0.8799 (tpp) cc_final: 0.8591 (tpp) REVERT: A 500 ARG cc_start: 0.7841 (tpp80) cc_final: 0.7524 (ttp80) REVERT: A 525 ILE cc_start: 0.8971 (mm) cc_final: 0.8717 (mt) REVERT: A 527 THR cc_start: 0.8754 (t) cc_final: 0.8493 (p) REVERT: A 531 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 591 LYS cc_start: 0.8934 (mttp) cc_final: 0.8725 (mtpp) REVERT: A 596 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8468 (ttpp) REVERT: A 606 GLU cc_start: 0.7870 (pm20) cc_final: 0.7638 (pm20) REVERT: A 647 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7571 (mmtt) REVERT: A 828 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7852 (mmtt) REVERT: A 854 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8688 (tp) REVERT: A 887 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: A 935 GLU cc_start: 0.8079 (tp30) cc_final: 0.7796 (tp30) REVERT: A 938 MET cc_start: 0.8617 (tpp) cc_final: 0.8235 (ttt) REVERT: A 947 SER cc_start: 0.8362 (t) cc_final: 0.7804 (p) REVERT: A 986 GLU cc_start: 0.7414 (tp30) cc_final: 0.7128 (tp30) REVERT: A 1007 LYS cc_start: 0.8087 (tttt) cc_final: 0.7636 (tttp) REVERT: A 1068 ILE cc_start: 0.7671 (mp) cc_final: 0.7331 (tt) REVERT: A 1122 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6877 (tp30) REVERT: B 133 MET cc_start: 0.6569 (mmm) cc_final: 0.6226 (mmm) REVERT: B 149 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 155 ASP cc_start: 0.7578 (t70) cc_final: 0.7140 (t70) REVERT: B 164 SER cc_start: 0.8617 (m) cc_final: 0.8300 (t) REVERT: B 218 LYS cc_start: 0.8440 (mttt) cc_final: 0.8038 (ttmm) REVERT: B 390 ILE cc_start: 0.8480 (mm) cc_final: 0.8171 (mt) REVERT: B 484 SER cc_start: 0.8652 (p) cc_final: 0.8349 (t) REVERT: B 522 ASP cc_start: 0.8032 (t0) cc_final: 0.7746 (t0) REVERT: B 525 ILE cc_start: 0.8893 (mm) cc_final: 0.8353 (mt) REVERT: B 534 ASP cc_start: 0.7752 (p0) cc_final: 0.7497 (p0) REVERT: B 588 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7941 (ttmt) REVERT: B 610 LEU cc_start: 0.9079 (tp) cc_final: 0.8800 (tt) REVERT: B 623 ASP cc_start: 0.7973 (t0) cc_final: 0.7544 (t0) REVERT: B 644 LEU cc_start: 0.8351 (mm) cc_final: 0.8031 (mm) REVERT: B 828 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7983 (mmtt) REVERT: B 852 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8705 (mtpp) REVERT: B 876 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 931 GLU cc_start: 0.7910 (tt0) cc_final: 0.7668 (mt-10) REVERT: B 938 MET cc_start: 0.8542 (tpp) cc_final: 0.8261 (ttt) REVERT: B 947 SER cc_start: 0.8375 (t) cc_final: 0.7722 (p) REVERT: B 986 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6667 (mt-10) REVERT: B 991 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6517 (mm-30) REVERT: B 1007 LYS cc_start: 0.7964 (tttt) cc_final: 0.7426 (ttmm) REVERT: B 1122 GLU cc_start: 0.7495 (tp30) cc_final: 0.7139 (tp30) outliers start: 53 outliers final: 30 residues processed: 432 average time/residue: 0.1137 time to fit residues: 73.4497 Evaluate side-chains 431 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 399 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 339 THR 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 854 ILE Chi-restraints excluded: chain A residue 900 GLN 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 A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 257 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 613 GLN Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 837 TYR 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 935 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 60 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1054 ASN A1177 GLN B 192 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN B 900 GLN B1054 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146307 restraints weight = 23170.718| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.16 r_work: 0.3572 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3116 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= 0.156 Angle : 0.592 8.392 22304 Z= 0.294 Chirality : 0.040 0.200 2684 Planarity : 0.004 0.043 2738 Dihedral : 6.943 134.768 2194 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.68 % Allowed : 15.13 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 2012 helix: 1.75 (0.13), residues: 1466 sheet: 0.04 (0.65), residues: 74 loop : 0.11 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 887 TYR 0.022 0.001 TYR B 309 PHE 0.018 0.001 PHE B 982 TRP 0.056 0.001 TRP A 962 HIS 0.004 0.001 HIS B 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (16438) covalent geometry : angle 0.59175 / 0.29 (22304) hydrogen bonds : bond 0.04536 / 3.06 ( 1162) hydrogen bonds : angle 3.91450 / 2.82 ( 3414) *********************** 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 450 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 403 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6848 (mmm) cc_final: 0.6482 (mmm) REVERT: A 134 ASP cc_start: 0.7469 (m-30) cc_final: 0.6971 (t0) REVERT: A 149 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 155 ASP cc_start: 0.7367 (t70) cc_final: 0.6906 (t70) REVERT: A 164 SER cc_start: 0.8648 (m) cc_final: 0.8355 (t) REVERT: A 525 ILE cc_start: 0.8954 (mm) cc_final: 0.8697 (mt) REVERT: A 527 THR cc_start: 0.8759 (t) cc_final: 0.8497 (p) REVERT: A 531 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 596 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8486 (ttpp) REVERT: A 606 GLU cc_start: 0.7848 (pm20) cc_final: 0.7605 (pm20) REVERT: A 647 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7570 (mmtt) REVERT: A 828 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7846 (mmtt) REVERT: A 887 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7903 (mmm-85) REVERT: A 935 GLU cc_start: 0.8079 (tp30) cc_final: 0.7808 (tp30) REVERT: A 938 MET cc_start: 0.8622 (tpp) cc_final: 0.8209 (ttt) REVERT: A 947 SER cc_start: 0.8333 (t) cc_final: 0.7753 (p) REVERT: A 958 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8381 (mtmm) REVERT: A 986 GLU cc_start: 0.7455 (tp30) cc_final: 0.7172 (tp30) REVERT: A 1007 LYS cc_start: 0.8112 (tttt) cc_final: 0.7670 (tttp) REVERT: A 1122 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6876 (tp30) REVERT: B 133 MET cc_start: 0.6572 (mmm) cc_final: 0.6220 (mmm) REVERT: B 149 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 155 ASP cc_start: 0.7557 (t70) cc_final: 0.7106 (t70) REVERT: B 160 MET cc_start: 0.8126 (mmt) cc_final: 0.7817 (mmm) REVERT: B 164 SER cc_start: 0.8610 (m) cc_final: 0.8293 (t) REVERT: B 218 LYS cc_start: 0.8441 (mttt) cc_final: 0.8035 (ttmm) REVERT: B 390 ILE cc_start: 0.8473 (mm) cc_final: 0.8177 (mt) REVERT: B 484 SER cc_start: 0.8519 (p) cc_final: 0.8231 (t) REVERT: B 525 ILE cc_start: 0.8870 (mm) cc_final: 0.8519 (mt) REVERT: B 534 ASP cc_start: 0.7788 (p0) cc_final: 0.7521 (p0) REVERT: B 588 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7968 (ttmt) REVERT: B 623 ASP cc_start: 0.8009 (t0) cc_final: 0.7566 (t0) REVERT: B 644 LEU cc_start: 0.8362 (mm) cc_final: 0.8070 (mm) REVERT: B 828 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7998 (mmtt) REVERT: B 852 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8683 (mtpp) REVERT: B 876 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 931 GLU cc_start: 0.7855 (tt0) cc_final: 0.7617 (mt-10) REVERT: B 938 MET cc_start: 0.8552 (tpp) cc_final: 0.8257 (ttt) REVERT: B 947 SER cc_start: 0.8386 (t) cc_final: 0.7744 (p) REVERT: B 986 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6702 (mt-10) REVERT: B 991 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6492 (mm-30) REVERT: B 1007 LYS cc_start: 0.8001 (tttt) cc_final: 0.7471 (ttmm) REVERT: B 1073 MET cc_start: 0.6473 (tmm) cc_final: 0.6235 (mmm) REVERT: B 1122 GLU cc_start: 0.7494 (tp30) cc_final: 0.7128 (tp30) outliers start: 47 outliers final: 30 residues processed: 419 average time/residue: 0.1330 time to fit residues: 83.1597 Evaluate side-chains 421 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 390 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 900 GLN 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 A residue 1073 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 154 MET 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 876 LEU 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 1119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 158 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1054 ASN B 510 ASN B 900 GLN B1054 ASN B1177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.177189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145473 restraints weight = 22989.049| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.21 r_work: 0.3544 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16438 Z= 0.220 Angle : 0.629 8.579 22304 Z= 0.317 Chirality : 0.042 0.244 2684 Planarity : 0.004 0.044 2738 Dihedral : 7.045 136.046 2194 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.08 % Allowed : 15.64 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 2012 helix: 1.65 (0.13), residues: 1464 sheet: 0.03 (0.66), residues: 74 loop : -0.04 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1089 TYR 0.027 0.002 TYR B 309 PHE 0.037 0.002 PHE A 982 TRP 0.057 0.002 TRP A 962 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (16438) covalent geometry : angle 0.62856 / 0.32 (22304) hydrogen bonds : bond 0.04993 / 3.36 ( 1162) hydrogen bonds : angle 4.02610 / 2.91 ( 3414) *********************** 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 477 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 423 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6889 (mmm) cc_final: 0.6617 (mmm) REVERT: A 134 ASP cc_start: 0.7543 (m-30) cc_final: 0.7292 (m-30) REVERT: A 149 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 155 ASP cc_start: 0.7419 (t70) cc_final: 0.6959 (t70) REVERT: A 164 SER cc_start: 0.8659 (m) cc_final: 0.8376 (t) REVERT: A 209 ASP cc_start: 0.8023 (t0) cc_final: 0.7553 (t70) REVERT: A 525 ILE cc_start: 0.9009 (mm) cc_final: 0.8790 (mt) REVERT: A 527 THR cc_start: 0.8763 (t) cc_final: 0.8480 (p) REVERT: A 531 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 596 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8570 (ttpp) REVERT: A 606 GLU cc_start: 0.7884 (pm20) cc_final: 0.7632 (pm20) REVERT: A 647 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7556 (mmtt) REVERT: A 678 MET cc_start: 0.2115 (ppp) cc_final: 0.1132 (ppp) REVERT: A 828 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7840 (mmtt) REVERT: A 852 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8459 (mtpp) REVERT: A 877 GLN cc_start: 0.8158 (mt0) cc_final: 0.7944 (tt0) REVERT: A 935 GLU cc_start: 0.8174 (tp30) cc_final: 0.7918 (tp30) REVERT: A 938 MET cc_start: 0.8655 (tpp) cc_final: 0.8246 (ttt) REVERT: A 947 SER cc_start: 0.8464 (t) cc_final: 0.7896 (p) REVERT: A 986 GLU cc_start: 0.7439 (tp30) cc_final: 0.7106 (tp30) REVERT: A 1007 LYS cc_start: 0.8145 (tttt) cc_final: 0.7699 (tttp) REVERT: A 1122 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6921 (tp30) REVERT: B 133 MET cc_start: 0.6670 (mmm) cc_final: 0.6289 (mmm) REVERT: B 149 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 155 ASP cc_start: 0.7603 (t70) cc_final: 0.7169 (t70) REVERT: B 160 MET cc_start: 0.8221 (mmt) cc_final: 0.7920 (mmm) REVERT: B 164 SER cc_start: 0.8624 (m) cc_final: 0.8336 (t) REVERT: B 218 LYS cc_start: 0.8453 (mttt) cc_final: 0.8048 (mtpp) REVERT: B 390 ILE cc_start: 0.8478 (mm) cc_final: 0.8201 (mt) REVERT: B 484 SER cc_start: 0.8536 (p) cc_final: 0.8199 (t) REVERT: B 525 ILE cc_start: 0.8860 (mm) cc_final: 0.8634 (mt) REVERT: B 534 ASP cc_start: 0.7873 (p0) cc_final: 0.7646 (p0) REVERT: B 586 MET cc_start: 0.7787 (ttm) cc_final: 0.7565 (ttp) REVERT: B 588 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7989 (ttmt) REVERT: B 606 GLU cc_start: 0.7700 (pm20) cc_final: 0.7358 (pm20) REVERT: B 623 ASP cc_start: 0.8089 (t0) cc_final: 0.7653 (t0) REVERT: B 828 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8016 (mmtt) REVERT: B 852 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8714 (mtpp) REVERT: B 876 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8448 (mp) REVERT: B 938 MET cc_start: 0.8571 (tpp) cc_final: 0.8278 (ttt) REVERT: B 947 SER cc_start: 0.8452 (t) cc_final: 0.7841 (p) REVERT: B 986 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6661 (mt-10) REVERT: B 991 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6532 (mm-30) REVERT: B 1007 LYS cc_start: 0.8013 (tttt) cc_final: 0.7478 (ttmm) REVERT: B 1054 ASN cc_start: 0.7977 (t0) cc_final: 0.7731 (t0) REVERT: B 1073 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6236 (mmm) REVERT: B 1122 GLU cc_start: 0.7552 (tp30) cc_final: 0.7185 (tp30) outliers start: 54 outliers final: 32 residues processed: 442 average time/residue: 0.1341 time to fit residues: 88.2526 Evaluate side-chains 444 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 410 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ARG 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 339 THR 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 443 GLU Chi-restraints excluded: chain A residue 610 LEU 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 988 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1098 ILE 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 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 876 LEU 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 1068 ILE Chi-restraints excluded: chain B residue 1073 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 20 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN B1064 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.177375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145890 restraints weight = 23109.388| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.17 r_work: 0.3563 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16438 Z= 0.168 Angle : 0.624 9.379 22304 Z= 0.308 Chirality : 0.041 0.263 2684 Planarity : 0.004 0.048 2738 Dihedral : 7.030 136.276 2194 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.68 % Allowed : 16.95 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.19), residues: 2012 helix: 1.72 (0.13), residues: 1464 sheet: 0.05 (0.66), residues: 74 loop : -0.11 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1089 TYR 0.024 0.001 TYR B 309 PHE 0.029 0.001 PHE B 982 TRP 0.055 0.002 TRP A 962 HIS 0.003 0.000 HIS B 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16438) covalent geometry : angle 0.62394 / 0.31 (22304) hydrogen bonds : bond 0.04627 / 3.12 ( 1162) hydrogen bonds : angle 3.95931 / 2.86 ( 3414) *********************** 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 458 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 411 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6897 (mmm) cc_final: 0.6641 (mmm) REVERT: A 134 ASP cc_start: 0.7487 (m-30) cc_final: 0.7249 (m-30) REVERT: A 149 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 155 ASP cc_start: 0.7345 (t70) cc_final: 0.6877 (t70) REVERT: A 164 SER cc_start: 0.8684 (m) cc_final: 0.8370 (t) REVERT: A 525 ILE cc_start: 0.8981 (mm) cc_final: 0.8762 (mt) REVERT: A 527 THR cc_start: 0.8759 (t) cc_final: 0.8478 (p) REVERT: A 531 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 596 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8547 (ttpp) REVERT: A 606 GLU cc_start: 0.7805 (pm20) cc_final: 0.7564 (pm20) REVERT: A 647 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7584 (mmtt) REVERT: A 678 MET cc_start: 0.2120 (ppp) cc_final: 0.1170 (ppp) REVERT: A 828 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7803 (mmtt) REVERT: A 852 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8402 (mtpp) REVERT: A 877 GLN cc_start: 0.8136 (mt0) cc_final: 0.7917 (tt0) REVERT: A 926 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 935 GLU cc_start: 0.8173 (tp30) cc_final: 0.7900 (tp30) REVERT: A 938 MET cc_start: 0.8647 (tpp) cc_final: 0.8210 (ttt) REVERT: A 947 SER cc_start: 0.8376 (t) cc_final: 0.7771 (p) REVERT: A 986 GLU cc_start: 0.7386 (tp30) cc_final: 0.7093 (tp30) REVERT: A 1007 LYS cc_start: 0.8137 (tttt) cc_final: 0.7711 (tttp) REVERT: A 1045 MET cc_start: 0.7572 (pmm) cc_final: 0.6672 (pmm) REVERT: A 1073 MET cc_start: 0.6596 (tmm) cc_final: 0.6279 (tmm) REVERT: A 1122 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6910 (tp30) REVERT: B 133 MET cc_start: 0.6675 (mmm) cc_final: 0.6271 (mmm) REVERT: B 149 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 155 ASP cc_start: 0.7553 (t70) cc_final: 0.7116 (t70) REVERT: B 160 MET cc_start: 0.8215 (mmt) cc_final: 0.7921 (mmm) REVERT: B 164 SER cc_start: 0.8626 (m) cc_final: 0.8322 (t) REVERT: B 218 LYS cc_start: 0.8437 (mttt) cc_final: 0.8009 (ttmm) REVERT: B 390 ILE cc_start: 0.8396 (mm) cc_final: 0.8116 (mt) REVERT: B 525 ILE cc_start: 0.8876 (mm) cc_final: 0.8610 (mt) REVERT: B 534 ASP cc_start: 0.7864 (p0) cc_final: 0.7637 (p0) REVERT: B 536 TYR cc_start: 0.8298 (m-10) cc_final: 0.8087 (m-10) REVERT: B 586 MET cc_start: 0.7791 (ttm) cc_final: 0.7553 (ttp) REVERT: B 588 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7891 (ttmt) REVERT: B 606 GLU cc_start: 0.7615 (pm20) cc_final: 0.7303 (pm20) REVERT: B 644 LEU cc_start: 0.8375 (mm) cc_final: 0.8104 (mm) REVERT: B 645 LYS cc_start: 0.8511 (tttt) cc_final: 0.8016 (tttt) REVERT: B 676 HIS cc_start: 0.4491 (OUTLIER) cc_final: 0.3842 (m90) REVERT: B 828 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7955 (mmtt) REVERT: B 852 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8647 (mtpp) REVERT: B 876 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8488 (mp) REVERT: B 938 MET cc_start: 0.8551 (tpp) cc_final: 0.8247 (ttt) REVERT: B 947 SER cc_start: 0.8405 (t) cc_final: 0.7828 (p) REVERT: B 986 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6666 (mt-10) REVERT: B 991 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6492 (mm-30) REVERT: B 1007 LYS cc_start: 0.7986 (tttt) cc_final: 0.7448 (ttmm) REVERT: B 1045 MET cc_start: 0.7705 (pmm) cc_final: 0.6907 (pmm) REVERT: B 1073 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.6155 (mmm) REVERT: B 1122 GLU cc_start: 0.7514 (tp30) cc_final: 0.7151 (tp30) outliers start: 47 outliers final: 31 residues processed: 430 average time/residue: 0.1324 time to fit residues: 85.1423 Evaluate side-chains 431 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 397 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 443 GLU Chi-restraints excluded: chain A residue 610 LEU 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 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 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 468 VAL 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 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 1068 ILE Chi-restraints excluded: chain B residue 1073 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 57 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 0.0010 chunk 195 optimal weight: 0.9990 chunk 2 optimal weight: 0.0050 chunk 168 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 200 optimal weight: 0.0980 chunk 63 optimal weight: 8.9990 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 GLN B 192 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN B 613 GLN B1054 ASN B1064 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.179935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148901 restraints weight = 23101.260| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.15 r_work: 0.3605 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16438 Z= 0.118 Angle : 0.601 11.020 22304 Z= 0.292 Chirality : 0.040 0.219 2684 Planarity : 0.004 0.043 2738 Dihedral : 6.950 135.978 2194 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.28 % Allowed : 17.75 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 2012 helix: 1.98 (0.13), residues: 1454 sheet: 0.47 (0.68), residues: 68 loop : -0.12 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1089 TYR 0.022 0.001 TYR B 309 PHE 0.021 0.001 PHE A 982 TRP 0.051 0.001 TRP A 962 HIS 0.004 0.000 HIS B 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (16438) covalent geometry : angle 0.60137 / 0.29 (22304) hydrogen bonds : bond 0.04041 / 2.73 ( 1162) hydrogen bonds : angle 3.84907 / 2.76 ( 3414) *********************** 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 457 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 417 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8269 (t) cc_final: 0.7809 (p) REVERT: A 133 MET cc_start: 0.6811 (mmm) cc_final: 0.6461 (mmm) REVERT: A 134 ASP cc_start: 0.7396 (m-30) cc_final: 0.6868 (t0) REVERT: A 149 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 154 MET cc_start: 0.8265 (ttm) cc_final: 0.8004 (ttp) REVERT: A 155 ASP cc_start: 0.7224 (t70) cc_final: 0.6739 (t70) REVERT: A 164 SER cc_start: 0.8658 (m) cc_final: 0.8355 (t) REVERT: A 525 ILE cc_start: 0.8919 (mm) cc_final: 0.8672 (mt) REVERT: A 527 THR cc_start: 0.8769 (t) cc_final: 0.8509 (p) REVERT: A 531 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 606 GLU cc_start: 0.7729 (pm20) cc_final: 0.7478 (pm20) REVERT: A 644 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 647 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7616 (mmtt) REVERT: A 678 MET cc_start: 0.2292 (ppp) cc_final: 0.1362 (ppp) REVERT: A 823 LEU cc_start: 0.8346 (mm) cc_final: 0.8100 (mp) REVERT: A 828 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7810 (mmtt) REVERT: A 877 GLN cc_start: 0.8102 (mt0) cc_final: 0.7875 (tt0) REVERT: A 935 GLU cc_start: 0.8130 (tp30) cc_final: 0.7853 (tp30) REVERT: A 938 MET cc_start: 0.8617 (tpp) cc_final: 0.8200 (ttt) REVERT: A 947 SER cc_start: 0.8244 (t) cc_final: 0.7634 (p) REVERT: A 986 GLU cc_start: 0.7348 (tp30) cc_final: 0.7043 (tp30) REVERT: A 1007 LYS cc_start: 0.8113 (tttt) cc_final: 0.7722 (tttp) REVERT: A 1045 MET cc_start: 0.7370 (pmm) cc_final: 0.6653 (pmm) REVERT: A 1073 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6287 (tmm) REVERT: A 1122 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6865 (tp30) REVERT: B 133 MET cc_start: 0.6581 (mmm) cc_final: 0.6224 (mmm) REVERT: B 149 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 155 ASP cc_start: 0.7499 (t70) cc_final: 0.7038 (t70) REVERT: B 164 SER cc_start: 0.8604 (m) cc_final: 0.8322 (t) REVERT: B 171 LEU cc_start: 0.8161 (mm) cc_final: 0.7891 (mm) REVERT: B 199 MET cc_start: 0.8237 (mmm) cc_final: 0.7870 (mmm) REVERT: B 218 LYS cc_start: 0.8401 (mttt) cc_final: 0.7996 (ttmm) REVERT: B 525 ILE cc_start: 0.8773 (mm) cc_final: 0.8477 (mt) REVERT: B 586 MET cc_start: 0.7729 (ttm) cc_final: 0.7504 (ttp) REVERT: B 588 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7667 (ttmt) REVERT: B 590 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 606 GLU cc_start: 0.7513 (pm20) cc_final: 0.7212 (pm20) REVERT: B 644 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8052 (mm) REVERT: B 645 LYS cc_start: 0.8484 (tttt) cc_final: 0.7972 (tttt) REVERT: B 676 HIS cc_start: 0.4451 (OUTLIER) cc_final: 0.3795 (m90) REVERT: B 828 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7912 (mmtt) REVERT: B 852 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8474 (mtpp) REVERT: B 876 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 938 MET cc_start: 0.8502 (tpp) cc_final: 0.8130 (ttt) REVERT: B 947 SER cc_start: 0.8385 (t) cc_final: 0.7736 (p) REVERT: B 986 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6686 (mt-10) REVERT: B 991 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6434 (mm-30) REVERT: B 1007 LYS cc_start: 0.7969 (tttt) cc_final: 0.7441 (ttmm) REVERT: B 1045 MET cc_start: 0.7500 (pmm) cc_final: 0.6843 (pmm) REVERT: B 1073 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.6134 (mmm) REVERT: B 1122 GLU cc_start: 0.7449 (tp30) cc_final: 0.7113 (tp30) REVERT: B 1144 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6802 (t0) outliers start: 40 outliers final: 27 residues processed: 434 average time/residue: 0.1242 time to fit residues: 80.7281 Evaluate side-chains 434 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 400 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 443 GLU Chi-restraints excluded: chain A residue 644 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 1058 THR Chi-restraints excluded: chain A residue 1073 MET 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 613 GLN 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 1068 ILE 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 159 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 104 optimal weight: 0.0770 chunk 157 optimal weight: 0.4980 chunk 200 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN B1054 ASN B1064 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151690 restraints weight = 23313.034| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.27 r_work: 0.3591 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16438 Z= 0.132 Angle : 0.628 11.044 22304 Z= 0.304 Chirality : 0.041 0.232 2684 Planarity : 0.004 0.045 2738 Dihedral : 6.971 136.884 2194 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.05 % Allowed : 18.95 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.19), residues: 2012 helix: 1.96 (0.13), residues: 1454 sheet: 0.56 (0.69), residues: 68 loop : -0.15 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1089 TYR 0.026 0.001 TYR B 191 PHE 0.025 0.001 PHE B 982 TRP 0.051 0.001 TRP A 962 HIS 0.008 0.000 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16438) covalent geometry : angle 0.62807 / 0.30 (22304) hydrogen bonds : bond 0.04177 / 2.81 ( 1162) hydrogen bonds : angle 3.88553 / 2.79 ( 3414) ********************** 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 446 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 410 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8290 (t) cc_final: 0.7823 (p) REVERT: A 133 MET cc_start: 0.6891 (mmm) cc_final: 0.6546 (mmm) REVERT: A 134 ASP cc_start: 0.7581 (m-30) cc_final: 0.7014 (t0) REVERT: A 149 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7532 (tm-30) REVERT: A 154 MET cc_start: 0.8285 (ttm) cc_final: 0.8015 (ttp) REVERT: A 155 ASP cc_start: 0.7275 (t70) cc_final: 0.6735 (t70) REVERT: A 164 SER cc_start: 0.8669 (m) cc_final: 0.8417 (t) REVERT: A 525 ILE cc_start: 0.8952 (mm) cc_final: 0.8717 (mt) REVERT: A 527 THR cc_start: 0.8857 (t) cc_final: 0.8605 (p) REVERT: A 531 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 606 GLU cc_start: 0.7722 (pm20) cc_final: 0.7412 (pm20) REVERT: A 644 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7793 (mm) REVERT: A 647 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7640 (mmtt) REVERT: A 678 MET cc_start: 0.2290 (ppp) cc_final: 0.1370 (ppp) REVERT: A 823 LEU cc_start: 0.8403 (mm) cc_final: 0.8154 (mp) REVERT: A 828 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7851 (mmtt) REVERT: A 852 LYS cc_start: 0.8685 (mttt) cc_final: 0.8383 (mtmm) REVERT: A 935 GLU cc_start: 0.8139 (tp30) cc_final: 0.7847 (tp30) REVERT: A 938 MET cc_start: 0.8511 (tpp) cc_final: 0.8062 (ttt) REVERT: A 947 SER cc_start: 0.8275 (t) cc_final: 0.7664 (p) REVERT: A 986 GLU cc_start: 0.7395 (tp30) cc_final: 0.7047 (tp30) REVERT: A 1007 LYS cc_start: 0.8083 (tttt) cc_final: 0.7677 (tttp) REVERT: A 1045 MET cc_start: 0.7457 (pmm) cc_final: 0.6691 (pmm) REVERT: A 1073 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6388 (tmm) REVERT: A 1122 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6989 (tp30) REVERT: B 133 MET cc_start: 0.6585 (mmm) cc_final: 0.6232 (mmm) REVERT: B 149 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 155 ASP cc_start: 0.7518 (t70) cc_final: 0.7087 (t70) REVERT: B 164 SER cc_start: 0.8628 (m) cc_final: 0.8356 (t) REVERT: B 199 MET cc_start: 0.8261 (mmm) cc_final: 0.7878 (mmm) REVERT: B 390 ILE cc_start: 0.8468 (mm) cc_final: 0.8176 (mt) REVERT: B 418 THR cc_start: 0.8304 (m) cc_final: 0.7857 (p) REVERT: B 525 ILE cc_start: 0.8795 (mm) cc_final: 0.8502 (mt) REVERT: B 586 MET cc_start: 0.7685 (ttm) cc_final: 0.7466 (ttp) REVERT: B 588 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7733 (ttmt) REVERT: B 590 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8024 (mt-10) REVERT: B 606 GLU cc_start: 0.7592 (pm20) cc_final: 0.7290 (pm20) REVERT: B 644 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8062 (mm) REVERT: B 645 LYS cc_start: 0.8488 (tttt) cc_final: 0.7982 (tttt) REVERT: B 676 HIS cc_start: 0.4520 (OUTLIER) cc_final: 0.3858 (m90) REVERT: B 828 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7930 (mmtt) REVERT: B 852 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8504 (mtpp) REVERT: B 876 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8493 (mp) REVERT: B 938 MET cc_start: 0.8348 (tpp) cc_final: 0.8046 (ttt) REVERT: B 947 SER cc_start: 0.8362 (t) cc_final: 0.7751 (p) REVERT: B 986 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6797 (mt-10) REVERT: B 1007 LYS cc_start: 0.7973 (tttt) cc_final: 0.7515 (tttp) REVERT: B 1045 MET cc_start: 0.7676 (pmm) cc_final: 0.6952 (pmm) REVERT: B 1073 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6259 (mmm) REVERT: B 1122 GLU cc_start: 0.7487 (tp30) cc_final: 0.7155 (tp30) outliers start: 36 outliers final: 25 residues processed: 423 average time/residue: 0.1238 time to fit residues: 78.1938 Evaluate side-chains 429 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 398 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 443 GLU Chi-restraints excluded: chain A residue 644 LEU 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 1073 MET 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 500 ARG 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 1068 ILE Chi-restraints excluded: chain B residue 1073 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN B1054 ASN B1064 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.182785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151658 restraints weight = 23241.255| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.30 r_work: 0.3582 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16438 Z= 0.157 Angle : 0.647 11.166 22304 Z= 0.314 Chirality : 0.042 0.251 2684 Planarity : 0.004 0.046 2738 Dihedral : 6.991 137.379 2194 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.83 % Allowed : 19.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2012 helix: 1.91 (0.13), residues: 1456 sheet: 0.52 (0.68), residues: 68 loop : -0.11 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1089 TYR 0.023 0.001 TYR B 309 PHE 0.032 0.001 PHE B 982 TRP 0.057 0.002 TRP A 962 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16438) covalent geometry : angle 0.64722 / 0.31 (22304) hydrogen bonds : bond 0.04414 / 2.97 ( 1162) hydrogen bonds : angle 3.92924 / 2.82 ( 3414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4731.21 seconds wall clock time: 81 minutes 27.07 seconds (4887.07 seconds total)