Starting phenix.real_space_refine on Sat Jul 4 22:57:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m84_63701/07_2026/9m84_63701.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m84_63701/07_2026/9m84_63701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m84_63701/07_2026/9m84_63701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m84_63701/07_2026/9m84_63701.map" model { file = "/net/cci-nas-00/data/ceres_data/9m84_63701/07_2026/9m84_63701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m84_63701/07_2026/9m84_63701.cif" } resolution = 3.61 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= 0.013 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 58 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 14878 2.51 5 N 4273 2.21 5 O 4723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24018 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 13, 'TRANS': 216} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1246, 9747 Classifications: {'peptide': 1246} Link IDs: {'PTRANS': 55, 'TRANS': 1190} Chain: "F" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "G" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12649 SG CYS D 60 104.599 51.522 80.013 1.00159.99 S ATOM 12667 SG CYS D 62 105.033 49.233 76.973 1.00162.48 S ATOM 12776 SG CYS D 75 106.203 52.963 76.851 1.00162.23 S ATOM 12802 SG CYS D 78 102.842 52.451 76.621 1.00151.50 S ATOM 19201 SG CYS D 886 72.107 109.447 102.312 1.00 89.18 S ATOM 19765 SG CYS D 962 70.973 106.173 100.655 1.00 72.89 S ATOM 19813 SG CYS D 969 72.913 106.217 103.957 1.00 85.71 S ATOM 19832 SG CYS D 972 69.299 107.227 103.830 1.00 79.10 S Time building chain proxies: 4.71, per 1000 atoms: 0.20 Number of scatterers: 24018 At special positions: 0 Unit cell: (129.05, 133.5, 194.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 58 15.00 Mg 1 11.99 O 4723 8.00 N 4273 7.00 C 14878 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " Number of angles added : 12 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5394 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 37 sheets defined 38.5% alpha, 13.1% beta 14 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 4.290A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.688A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.515A pdb=" N ALA B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.713A pdb=" N THR C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.734A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 320 through 337 Processing helix chain 'C' and resid 366 through 393 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.675A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 420 Processing helix chain 'C' and resid 430 through 438 removed outlier: 3.699A pdb=" N GLY C 434 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 524 Processing helix chain 'C' and resid 587 through 597 Processing helix chain 'C' and resid 617 through 623 Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 911 removed outlier: 3.916A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 928 Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 removed outlier: 3.836A pdb=" N LEU C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1064 Processing helix chain 'C' and resid 1066 through 1076 removed outlier: 3.626A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1094 removed outlier: 3.752A pdb=" N TYR C1088 " --> pdb=" O ARG C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1116 removed outlier: 3.667A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 188 Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 192 through 228 Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.578A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.549A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN D 304 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.530A pdb=" N LEU D 324 " --> pdb=" O PRO D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 359 removed outlier: 3.522A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.893A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 491 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 589 removed outlier: 3.679A pdb=" N LEU D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 616 removed outlier: 3.526A pdb=" N ALA D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 670 removed outlier: 4.195A pdb=" N GLU D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 699 removed outlier: 3.925A pdb=" N LEU D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 721 removed outlier: 3.506A pdb=" N VAL D 704 " --> pdb=" O PRO D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 758 removed outlier: 4.194A pdb=" N LYS D 738 " --> pdb=" O PRO D 734 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU D 739 " --> pdb=" O ASP D 735 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 removed outlier: 3.578A pdb=" N PHE D 788 " --> pdb=" O MET D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.656A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 825 removed outlier: 3.538A pdb=" N ASN D 824 " --> pdb=" O ASN D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 876 removed outlier: 3.755A pdb=" N TYR D 844 " --> pdb=" O SER D 840 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 863 " --> pdb=" O ALA D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 Processing helix chain 'D' and resid 940 through 950 Processing helix chain 'D' and resid 969 through 974 removed outlier: 4.215A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.594A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1004 Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1108 Processing helix chain 'D' and resid 1110 through 1129 removed outlier: 3.639A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1145 Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1210 removed outlier: 3.797A pdb=" N ALA D1206 " --> pdb=" O SER D1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1223 Processing helix chain 'D' and resid 1230 through 1238 removed outlier: 3.510A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'F' and resid 13 through 23 removed outlier: 3.548A pdb=" N GLY F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 48 Proline residue: F 37 - end of helix removed outlier: 3.571A pdb=" N SER F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 73 removed outlier: 3.987A pdb=" N GLU F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 82 through 103 removed outlier: 4.020A pdb=" N PHE F 86 " --> pdb=" O PRO F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.994A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 removed outlier: 6.673A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 106 removed outlier: 4.136A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 13 removed outlier: 5.271A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL B 22 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 99 removed outlier: 8.016A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.256A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.061A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB4, first strand: chain 'C' and resid 165 through 166 removed outlier: 6.422A pdb=" N SER C 165 " --> pdb=" O ASN C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.903A pdb=" N ARG C 491 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.903A pdb=" N ARG C 491 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 545 through 546 Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC3, first strand: chain 'C' and resid 653 through 656 removed outlier: 5.770A pdb=" N THR C 647 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL C 636 " --> pdb=" O THR C 647 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 673 through 674 Processing sheet with id=AC5, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC6, first strand: chain 'C' and resid 870 through 871 removed outlier: 3.641A pdb=" N GLY C 879 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 734 through 746 removed outlier: 6.722A pdb=" N SER C 735 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 862 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS C 737 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 860 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU C 739 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR C 858 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS C 741 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 856 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 743 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU C 854 " --> pdb=" O VAL C 743 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C 745 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN C 852 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP C 840 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 854 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL C 838 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 856 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL C 836 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 858 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.764A pdb=" N ARG C 819 " --> pdb=" O THR C 793 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1121 through 1123 removed outlier: 3.595A pdb=" N ARG D 11 " --> pdb=" O GLU C1121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 26 through 27 removed outlier: 6.971A pdb=" N GLY D 26 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLU D 96 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 93 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.374A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 11.114A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.635A pdb=" N TYR D 134 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP D 253 " --> pdb=" O PHE D 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 328 through 330 removed outlier: 5.761A pdb=" N PHE D 335 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 509 through 512 removed outlier: 7.452A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL D 431 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 441 through 443 removed outlier: 6.311A pdb=" N CYS D 441 " --> pdb=" O GLN D 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 603 through 604 removed outlier: 3.648A pdb=" N ARG D 628 " --> pdb=" O PHE D 604 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 892 through 894 Processing sheet with id=AD8, first strand: chain 'D' and resid 924 through 925 removed outlier: 7.254A pdb=" N VAL D 924 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1070 through 1074 Processing sheet with id=AE1, first strand: chain 'D' and resid 1164 through 1165 removed outlier: 3.900A pdb=" N ARG D1147 " --> pdb=" O GLN D1189 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4483 1.33 - 1.45: 5882 1.45 - 1.57: 13909 1.57 - 1.70: 113 1.70 - 1.82: 149 Bond restraints: 24536 Sorted by residual: bond pdb=" C1' DT H 43 " pdb=" N1 DT H 43 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" C1' DC G 26 " pdb=" N1 DC G 26 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" C1' DT G 28 " pdb=" N1 DT G 28 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C1' DC H 45 " pdb=" N1 DC H 45 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" C1' DT H 19 " pdb=" N1 DT H 19 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.41e+01 ... (remaining 24531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 31846 1.68 - 3.37: 1337 3.37 - 5.05: 223 5.05 - 6.73: 25 6.73 - 8.41: 10 Bond angle restraints: 33441 Sorted by residual: angle pdb=" N ARG D 295 " pdb=" CA ARG D 295 " pdb=" C ARG D 295 " ideal model delta sigma weight residual 111.33 105.29 6.04 1.21e+00 6.83e-01 2.49e+01 angle pdb=" N3 DT H 43 " pdb=" C4 DT H 43 " pdb=" O4 DT H 43 " ideal model delta sigma weight residual 119.90 122.80 -2.90 6.00e-01 2.78e+00 2.34e+01 angle pdb=" N3 DT H 37 " pdb=" C4 DT H 37 " pdb=" O4 DT H 37 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" CA LEU D 296 " pdb=" C LEU D 296 " pdb=" O LEU D 296 " ideal model delta sigma weight residual 119.97 114.64 5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" CA ARG D 295 " pdb=" C ARG D 295 " pdb=" O ARG D 295 " ideal model delta sigma weight residual 120.63 115.74 4.89 1.08e+00 8.57e-01 2.05e+01 ... (remaining 33436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 14286 35.76 - 71.52: 565 71.52 - 107.29: 30 107.29 - 143.05: 1 143.05 - 178.81: 3 Dihedral angle restraints: 14885 sinusoidal: 6504 harmonic: 8381 Sorted by residual: dihedral pdb=" CA MET C 710 " pdb=" C MET C 710 " pdb=" N PRO C 711 " pdb=" CA PRO C 711 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLY D 63 " pdb=" C GLY D 63 " pdb=" N LYS D 64 " pdb=" CA LYS D 64 " ideal model delta harmonic sigma weight residual 180.00 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG C 985 " pdb=" C ARG C 985 " pdb=" N MET C 986 " pdb=" CA MET C 986 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 14882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2690 0.042 - 0.084: 759 0.084 - 0.127: 276 0.127 - 0.169: 69 0.169 - 0.211: 4 Chirality restraints: 3798 Sorted by residual: chirality pdb=" CG LEU C 995 " pdb=" CB LEU C 995 " pdb=" CD1 LEU C 995 " pdb=" CD2 LEU C 995 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU D 277 " pdb=" CB LEU D 277 " pdb=" CD1 LEU D 277 " pdb=" CD2 LEU D 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU C 269 " pdb=" CB LEU C 269 " pdb=" CD1 LEU C 269 " pdb=" CD2 LEU C 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 3795 not shown) Planarity restraints: 4204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 641 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO D 642 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 642 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 642 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D1034 " 0.052 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO D1035 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D1035 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D1035 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 546 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C LEU C 546 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU C 546 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL C 547 " -0.015 2.00e-02 2.50e+03 ... (remaining 4201 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 131 2.48 - 3.09: 17559 3.09 - 3.69: 38773 3.69 - 4.30: 52750 4.30 - 4.90: 85689 Nonbonded interactions: 194902 Sorted by model distance: nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D1401 " model vdw 1.876 2.170 nonbonded pdb=" NH1 ARG D1187 " pdb=" O PRO D1188 " model vdw 2.192 3.120 nonbonded pdb=" O PRO C 603 " pdb=" OG SER C 735 " model vdw 2.202 3.040 nonbonded pdb=" OG SER D 592 " pdb=" O GLN D 622 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR C 233 " pdb=" OE1 GLN C 256 " model vdw 2.212 3.040 ... (remaining 194897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 227) selection = (chain 'B' and resid 4 through 227) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 27.900 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 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 : 0.004 0.062 24544 Z= 0.260 Angle : 0.795 15.392 33453 Z= 0.480 Chirality : 0.047 0.211 3798 Planarity : 0.006 0.099 4204 Dihedral : 17.914 178.810 9491 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.57 % Favored : 92.33 % Rotamer: Outliers : 0.41 % Allowed : 16.34 % Favored : 83.26 % 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: -1.95 (0.15), residues: 2921 helix: -0.05 (0.16), residues: 1026 sheet: -1.55 (0.28), residues: 325 loop : -2.16 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D1147 TYR 0.012 0.001 TYR C 266 PHE 0.016 0.001 PHE D 131 TRP 0.027 0.002 TRP D 58 HIS 0.011 0.001 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.26 (24536) covalent geometry : angle 0.78907 / 0.48 (33441) hydrogen bonds : bond 0.13983 / 9.47 ( 977) hydrogen bonds : angle 6.51922 / 4.55 ( 2721) metal coordination : bond 0.00698 / 0.33 ( 8) metal coordination : angle 5.34084 / 2.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 320 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 PHE cc_start: 0.6371 (t80) cc_final: 0.4539 (m-10) REVERT: B 136 MET cc_start: 0.6929 (pmm) cc_final: 0.6175 (pmm) REVERT: C 287 LEU cc_start: 0.8513 (tp) cc_final: 0.8153 (tp) REVERT: C 512 ASP cc_start: 0.8049 (p0) cc_final: 0.7845 (p0) REVERT: D 327 MET cc_start: 0.7119 (ppp) cc_final: 0.6670 (tmm) REVERT: D 474 ARG cc_start: 0.8567 (tpm170) cc_final: 0.8343 (tpp-160) REVERT: D 494 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.7192 (t-90) REVERT: D 690 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: D 896 ILE cc_start: 0.7596 (tp) cc_final: 0.7308 (tp) REVERT: D 1218 ASP cc_start: 0.6807 (m-30) cc_final: 0.6498 (m-30) REVERT: F 49 ARG cc_start: 0.5012 (mpp80) cc_final: 0.4123 (mmm160) outliers start: 10 outliers final: 4 residues processed: 325 average time/residue: 0.1567 time to fit residues: 79.0996 Evaluate side-chains 281 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 275 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 906 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.0570 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 154 GLN B 61 HIS C 462 HIS ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN D 552 GLN D 808 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.196238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.156870 restraints weight = 46210.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.157376 restraints weight = 31236.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.158941 restraints weight = 26261.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.158748 restraints weight = 20439.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.159338 restraints weight = 19087.508| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24544 Z= 0.147 Angle : 0.677 13.369 33453 Z= 0.353 Chirality : 0.045 0.244 3798 Planarity : 0.005 0.066 4204 Dihedral : 15.154 175.649 3842 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 2.72 % Allowed : 16.38 % Favored : 80.91 % 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: -1.69 (0.15), residues: 2921 helix: 0.21 (0.16), residues: 1047 sheet: -1.40 (0.27), residues: 336 loop : -2.07 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1147 TYR 0.016 0.001 TYR D 241 PHE 0.029 0.002 PHE F 88 TRP 0.027 0.002 TRP C 54 HIS 0.008 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (24536) covalent geometry : angle 0.67041 / 0.35 (33441) hydrogen bonds : bond 0.05026 / 3.48 ( 977) hydrogen bonds : angle 5.32650 / 3.68 ( 2721) metal coordination : bond 0.00602 / 0.29 ( 8) metal coordination : angle 4.82979 / 2.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.6607 (pmm) cc_final: 0.6112 (pmm) REVERT: B 232 ILE cc_start: 0.5433 (OUTLIER) cc_final: 0.5083 (mt) REVERT: C 40 LEU cc_start: 0.6426 (tt) cc_final: 0.6145 (mp) REVERT: C 287 LEU cc_start: 0.8685 (tp) cc_final: 0.8308 (tp) REVERT: C 426 MET cc_start: 0.5327 (mmm) cc_final: 0.4727 (tpt) REVERT: C 512 ASP cc_start: 0.7710 (p0) cc_final: 0.7443 (p0) REVERT: C 969 GLU cc_start: 0.6392 (mp0) cc_final: 0.6132 (mp0) REVERT: C 1128 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7117 (mmp) REVERT: D 241 TYR cc_start: 0.8572 (t80) cc_final: 0.8221 (t80) REVERT: D 242 ARG cc_start: 0.9034 (mmm160) cc_final: 0.8543 (mmm160) REVERT: D 474 ARG cc_start: 0.8364 (tpm170) cc_final: 0.8164 (tpp-160) REVERT: D 784 MET cc_start: 0.6898 (tmm) cc_final: 0.6691 (tmm) REVERT: D 896 ILE cc_start: 0.7579 (tp) cc_final: 0.7293 (tp) REVERT: D 1218 ASP cc_start: 0.6947 (m-30) cc_final: 0.6740 (m-30) outliers start: 67 outliers final: 31 residues processed: 350 average time/residue: 0.1486 time to fit residues: 81.1539 Evaluate side-chains 307 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 797 MET Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 49 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 151 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 123 optimal weight: 50.0000 chunk 227 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 208 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN B 100 GLN ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 563 ASN D1210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.195736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.156507 restraints weight = 46286.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.157327 restraints weight = 30923.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.158387 restraints weight = 25190.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.158834 restraints weight = 19058.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.158984 restraints weight = 18250.220| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24544 Z= 0.141 Angle : 0.666 12.717 33453 Z= 0.343 Chirality : 0.045 0.282 3798 Planarity : 0.005 0.060 4204 Dihedral : 14.972 175.703 3827 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.47 % Allowed : 18.77 % Favored : 78.76 % 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: -1.57 (0.15), residues: 2921 helix: 0.33 (0.16), residues: 1049 sheet: -1.36 (0.27), residues: 347 loop : -2.01 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 293 TYR 0.011 0.001 TYR C 266 PHE 0.037 0.002 PHE F 88 TRP 0.020 0.002 TRP C 54 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (24536) covalent geometry : angle 0.66043 / 0.34 (33441) hydrogen bonds : bond 0.04640 / 3.23 ( 977) hydrogen bonds : angle 5.11471 / 3.55 ( 2721) metal coordination : bond 0.00542 / 0.25 ( 8) metal coordination : angle 4.77144 / 2.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 297 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.6584 (pmm) cc_final: 0.6198 (pmm) REVERT: B 232 ILE cc_start: 0.5392 (OUTLIER) cc_final: 0.5046 (mt) REVERT: C 40 LEU cc_start: 0.6470 (tt) cc_final: 0.6165 (mp) REVERT: C 426 MET cc_start: 0.5322 (mmm) cc_final: 0.4680 (tpt) REVERT: C 512 ASP cc_start: 0.7729 (p0) cc_final: 0.7503 (p0) REVERT: C 969 GLU cc_start: 0.6100 (mp0) cc_final: 0.5866 (mp0) REVERT: C 1128 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6821 (mmp) REVERT: D 223 TRP cc_start: 0.7328 (m100) cc_final: 0.7108 (m100) REVERT: D 241 TYR cc_start: 0.8549 (t80) cc_final: 0.8289 (t80) REVERT: D 242 ARG cc_start: 0.8958 (mmm160) cc_final: 0.8503 (mmm160) REVERT: D 554 GLU cc_start: 0.7112 (pt0) cc_final: 0.6871 (pt0) REVERT: D 784 MET cc_start: 0.6974 (tmm) cc_final: 0.6727 (tmm) REVERT: D 896 ILE cc_start: 0.7508 (tp) cc_final: 0.7244 (tp) REVERT: D 1218 ASP cc_start: 0.7022 (m-30) cc_final: 0.6739 (m-30) REVERT: F 49 ARG cc_start: 0.5734 (mtt90) cc_final: 0.5222 (mtt-85) outliers start: 61 outliers final: 36 residues processed: 330 average time/residue: 0.1597 time to fit residues: 83.3654 Evaluate side-chains 310 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 254 optimal weight: 0.8980 chunk 273 optimal weight: 20.0000 chunk 266 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 161 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 97 optimal weight: 0.0020 overall best weight: 1.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN C 235 GLN ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 HIS ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.193702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.154684 restraints weight = 46175.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.155985 restraints weight = 32908.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.157146 restraints weight = 28065.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.157038 restraints weight = 20382.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.157842 restraints weight = 19561.933| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24544 Z= 0.171 Angle : 0.682 12.889 33453 Z= 0.349 Chirality : 0.045 0.202 3798 Planarity : 0.005 0.059 4204 Dihedral : 15.011 175.622 3827 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.70 % Favored : 92.26 % Rotamer: Outliers : 3.16 % Allowed : 20.27 % Favored : 76.57 % 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: -1.55 (0.15), residues: 2921 helix: 0.36 (0.16), residues: 1051 sheet: -1.25 (0.27), residues: 356 loop : -2.04 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1147 TYR 0.012 0.001 TYR D 241 PHE 0.039 0.002 PHE F 88 TRP 0.021 0.002 TRP D 651 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (24536) covalent geometry : angle 0.67518 / 0.35 (33441) hydrogen bonds : bond 0.04622 / 3.19 ( 977) hydrogen bonds : angle 5.05306 / 3.51 ( 2721) metal coordination : bond 0.00600 / 0.29 ( 8) metal coordination : angle 5.00668 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 291 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.6610 (pmm) cc_final: 0.6154 (pmm) REVERT: C 40 LEU cc_start: 0.6795 (tt) cc_final: 0.6465 (mp) REVERT: C 200 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6468 (tt) REVERT: C 263 LEU cc_start: 0.8746 (mt) cc_final: 0.8403 (mt) REVERT: C 512 ASP cc_start: 0.7630 (p0) cc_final: 0.7424 (p0) REVERT: C 709 PHE cc_start: 0.4880 (OUTLIER) cc_final: 0.4058 (m-80) REVERT: C 1128 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6525 (mmp) REVERT: D 241 TYR cc_start: 0.8584 (t80) cc_final: 0.8259 (t80) REVERT: D 242 ARG cc_start: 0.8956 (mmm160) cc_final: 0.8539 (mmm160) REVERT: D 474 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.7868 (tpm170) REVERT: D 554 GLU cc_start: 0.7316 (pt0) cc_final: 0.6980 (pt0) REVERT: D 784 MET cc_start: 0.6968 (tmm) cc_final: 0.6705 (tmm) REVERT: D 896 ILE cc_start: 0.7619 (tp) cc_final: 0.7308 (tp) REVERT: D 1218 ASP cc_start: 0.7066 (m-30) cc_final: 0.6782 (m-30) REVERT: F 49 ARG cc_start: 0.5749 (mtt90) cc_final: 0.5169 (mtt-85) outliers start: 78 outliers final: 45 residues processed: 340 average time/residue: 0.1701 time to fit residues: 90.9229 Evaluate side-chains 327 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 709 PHE Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 90 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 229 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 200 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1182 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.192267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.153475 restraints weight = 46220.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.154045 restraints weight = 32366.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.155124 restraints weight = 29299.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.155125 restraints weight = 21175.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.156154 restraints weight = 19967.710| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24544 Z= 0.198 Angle : 0.715 13.547 33453 Z= 0.364 Chirality : 0.047 0.219 3798 Planarity : 0.005 0.059 4204 Dihedral : 15.052 175.744 3827 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 3.65 % Allowed : 21.04 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.64 (0.15), residues: 2921 helix: 0.25 (0.15), residues: 1058 sheet: -1.30 (0.27), residues: 354 loop : -2.08 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1147 TYR 0.014 0.002 TYR A 168 PHE 0.038 0.002 PHE F 88 TRP 0.024 0.002 TRP C 54 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (24536) covalent geometry : angle 0.70745 / 0.36 (33441) hydrogen bonds : bond 0.04771 / 3.28 ( 977) hydrogen bonds : angle 5.08712 / 3.55 ( 2721) metal coordination : bond 0.00663 / 0.33 ( 8) metal coordination : angle 5.44869 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 284 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7132 (tmm) cc_final: 0.6855 (tmm) REVERT: B 136 MET cc_start: 0.6684 (pmm) cc_final: 0.6191 (pmm) REVERT: C 200 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6458 (tt) REVERT: C 263 LEU cc_start: 0.8796 (mt) cc_final: 0.8457 (mt) REVERT: C 426 MET cc_start: 0.5491 (mmm) cc_final: 0.4832 (tpt) REVERT: C 512 ASP cc_start: 0.7632 (p0) cc_final: 0.7431 (p0) REVERT: C 709 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.4060 (m-80) REVERT: C 1128 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6410 (mmp) REVERT: D 277 LEU cc_start: 0.9047 (mm) cc_final: 0.8816 (mp) REVERT: D 474 ARG cc_start: 0.8440 (tpp-160) cc_final: 0.7917 (tpm170) REVERT: D 494 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7258 (t-90) REVERT: D 554 GLU cc_start: 0.7337 (pt0) cc_final: 0.6952 (pt0) REVERT: D 583 LEU cc_start: 0.6369 (tp) cc_final: 0.6063 (tp) REVERT: D 784 MET cc_start: 0.7058 (tmm) cc_final: 0.6732 (tmm) REVERT: D 946 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.4985 (mm) REVERT: D 1218 ASP cc_start: 0.7116 (m-30) cc_final: 0.6875 (m-30) REVERT: F 103 MET cc_start: 0.7077 (ptp) cc_final: 0.6861 (ptp) outliers start: 90 outliers final: 61 residues processed: 344 average time/residue: 0.1585 time to fit residues: 86.2868 Evaluate side-chains 341 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 709 PHE Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 90 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 167 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 253 optimal weight: 0.3980 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 295 optimal weight: 40.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 200 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.191900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.152916 restraints weight = 46568.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.152553 restraints weight = 32867.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.153686 restraints weight = 28986.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.154467 restraints weight = 21096.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.154805 restraints weight = 20218.292| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24544 Z= 0.194 Angle : 0.718 14.031 33453 Z= 0.364 Chirality : 0.046 0.237 3798 Planarity : 0.005 0.059 4204 Dihedral : 15.085 175.949 3827 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 3.97 % Allowed : 22.01 % Favored : 74.02 % 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: -1.65 (0.15), residues: 2921 helix: 0.24 (0.15), residues: 1058 sheet: -1.29 (0.27), residues: 360 loop : -2.08 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1147 TYR 0.016 0.002 TYR F 76 PHE 0.051 0.002 PHE F 88 TRP 0.026 0.002 TRP C 54 HIS 0.007 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (24536) covalent geometry : angle 0.71018 / 0.36 (33441) hydrogen bonds : bond 0.04675 / 3.20 ( 977) hydrogen bonds : angle 5.07121 / 3.53 ( 2721) metal coordination : bond 0.00610 / 0.30 ( 8) metal coordination : angle 5.67211 / 2.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 290 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7074 (tmm) cc_final: 0.6740 (tmm) REVERT: B 93 VAL cc_start: 0.3399 (OUTLIER) cc_final: 0.3089 (t) REVERT: B 136 MET cc_start: 0.6749 (pmm) cc_final: 0.6200 (pmm) REVERT: C 200 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6544 (tt) REVERT: C 263 LEU cc_start: 0.8860 (mt) cc_final: 0.8525 (mt) REVERT: C 426 MET cc_start: 0.5729 (mmm) cc_final: 0.5011 (tpt) REVERT: C 709 PHE cc_start: 0.4715 (OUTLIER) cc_final: 0.3994 (m-80) REVERT: C 1128 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6384 (mmp) REVERT: D 474 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.7927 (tpm170) REVERT: D 494 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7369 (t-90) REVERT: D 583 LEU cc_start: 0.6335 (tp) cc_final: 0.6059 (tp) REVERT: D 784 MET cc_start: 0.7062 (tmm) cc_final: 0.6764 (tmm) REVERT: D 920 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5156 (mp) REVERT: D 1218 ASP cc_start: 0.7223 (m-30) cc_final: 0.6917 (m-30) outliers start: 98 outliers final: 68 residues processed: 353 average time/residue: 0.1560 time to fit residues: 88.4864 Evaluate side-chains 350 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 709 PHE Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 90 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 219 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 67 optimal weight: 9.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 200 GLN B 36 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 ASN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.194949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.157197 restraints weight = 46238.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.157300 restraints weight = 34750.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.158537 restraints weight = 28906.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.159223 restraints weight = 20693.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.159627 restraints weight = 19971.579| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24544 Z= 0.137 Angle : 0.675 14.435 33453 Z= 0.343 Chirality : 0.045 0.243 3798 Planarity : 0.005 0.059 4204 Dihedral : 15.017 175.464 3827 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 2.96 % Allowed : 23.67 % Favored : 73.37 % 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: -1.47 (0.15), residues: 2921 helix: 0.38 (0.16), residues: 1060 sheet: -1.20 (0.27), residues: 371 loop : -1.98 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 84 TYR 0.015 0.001 TYR F 76 PHE 0.048 0.002 PHE F 88 TRP 0.037 0.003 TRP C 54 HIS 0.005 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (24536) covalent geometry : angle 0.66692 / 0.34 (33441) hydrogen bonds : bond 0.04253 / 2.92 ( 977) hydrogen bonds : angle 4.90561 / 3.43 ( 2721) metal coordination : bond 0.00577 / 0.26 ( 8) metal coordination : angle 5.66352 / 2.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 286 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7138 (tmm) cc_final: 0.6662 (tmm) REVERT: B 93 VAL cc_start: 0.3366 (OUTLIER) cc_final: 0.3043 (t) REVERT: B 136 MET cc_start: 0.6606 (pmm) cc_final: 0.6171 (pmm) REVERT: C 200 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6463 (tt) REVERT: C 263 LEU cc_start: 0.8785 (mt) cc_final: 0.8452 (mt) REVERT: C 266 TYR cc_start: 0.8279 (t80) cc_final: 0.7838 (t80) REVERT: C 390 MET cc_start: 0.5570 (ppp) cc_final: 0.5252 (ppp) REVERT: C 1128 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6242 (mmp) REVERT: D 242 ARG cc_start: 0.9116 (ptp-110) cc_final: 0.8897 (ptp90) REVERT: D 277 LEU cc_start: 0.8942 (mm) cc_final: 0.8736 (mp) REVERT: D 474 ARG cc_start: 0.8280 (tpp-160) cc_final: 0.7873 (tpm170) REVERT: D 494 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7363 (t-90) REVERT: D 583 LEU cc_start: 0.6022 (tp) cc_final: 0.5801 (tp) REVERT: D 784 MET cc_start: 0.7081 (tmm) cc_final: 0.6753 (tmm) REVERT: D 920 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5110 (mp) REVERT: D 946 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5026 (mm) REVERT: D 1218 ASP cc_start: 0.7215 (m-30) cc_final: 0.6854 (m-30) REVERT: F 103 MET cc_start: 0.7221 (ptp) cc_final: 0.6765 (ptp) outliers start: 73 outliers final: 51 residues processed: 330 average time/residue: 0.1510 time to fit residues: 79.1697 Evaluate side-chains 325 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 100 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 200 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.189612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.150043 restraints weight = 46362.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.149389 restraints weight = 32633.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.150784 restraints weight = 31063.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.150812 restraints weight = 22586.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.151729 restraints weight = 21190.381| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24544 Z= 0.245 Angle : 0.777 17.377 33453 Z= 0.391 Chirality : 0.048 0.247 3798 Planarity : 0.006 0.078 4204 Dihedral : 15.130 175.858 3827 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.87 % Favored : 91.10 % Rotamer: Outliers : 3.45 % Allowed : 23.71 % Favored : 72.84 % 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: -1.69 (0.15), residues: 2921 helix: 0.19 (0.16), residues: 1058 sheet: -1.27 (0.28), residues: 344 loop : -2.11 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1147 TYR 0.016 0.002 TYR D 116 PHE 0.050 0.002 PHE F 88 TRP 0.041 0.003 TRP D 58 HIS 0.006 0.001 HIS C 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (24536) covalent geometry : angle 0.76933 / 0.39 (33441) hydrogen bonds : bond 0.04938 / 3.36 ( 977) hydrogen bonds : angle 5.13485 / 3.58 ( 2721) metal coordination : bond 0.00770 / 0.40 ( 8) metal coordination : angle 5.92182 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 279 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6885 (tmm) cc_final: 0.6566 (tmm) REVERT: B 93 VAL cc_start: 0.3412 (OUTLIER) cc_final: 0.3099 (t) REVERT: B 136 MET cc_start: 0.6831 (pmm) cc_final: 0.6192 (pmm) REVERT: C 200 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6508 (tt) REVERT: C 263 LEU cc_start: 0.8879 (mt) cc_final: 0.8534 (mt) REVERT: C 266 TYR cc_start: 0.8310 (t80) cc_final: 0.7932 (t80) REVERT: C 390 MET cc_start: 0.6025 (ppp) cc_final: 0.5771 (ppp) REVERT: C 709 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.4237 (m-80) REVERT: C 1093 LYS cc_start: 0.7770 (pptt) cc_final: 0.7404 (tmtt) REVERT: C 1128 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6349 (mmp) REVERT: D 277 LEU cc_start: 0.9061 (mm) cc_final: 0.8836 (mp) REVERT: D 474 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.8061 (tpm170) REVERT: D 554 GLU cc_start: 0.7367 (pt0) cc_final: 0.6989 (pt0) REVERT: D 583 LEU cc_start: 0.6372 (tp) cc_final: 0.6146 (tp) REVERT: D 784 MET cc_start: 0.7151 (tmm) cc_final: 0.6814 (tmm) REVERT: D 946 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5235 (mm) REVERT: D 1218 ASP cc_start: 0.7255 (m-30) cc_final: 0.6885 (m-30) REVERT: F 103 MET cc_start: 0.7418 (ptp) cc_final: 0.7208 (ptp) outliers start: 85 outliers final: 64 residues processed: 337 average time/residue: 0.1537 time to fit residues: 83.3382 Evaluate side-chains 342 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 709 PHE Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1009 SER Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 90 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 224 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 295 optimal weight: 40.0000 chunk 44 optimal weight: 0.0370 chunk 11 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 144 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 255 optimal weight: 0.0970 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 200 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.195082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.157365 restraints weight = 46409.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.157983 restraints weight = 34156.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.159561 restraints weight = 27977.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.159184 restraints weight = 20890.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.160084 restraints weight = 19875.296| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24544 Z= 0.132 Angle : 0.696 15.744 33453 Z= 0.349 Chirality : 0.046 0.380 3798 Planarity : 0.005 0.059 4204 Dihedral : 15.041 175.789 3827 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 2.59 % Allowed : 24.56 % Favored : 72.84 % 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: -1.40 (0.15), residues: 2921 helix: 0.46 (0.16), residues: 1054 sheet: -1.03 (0.28), residues: 340 loop : -1.97 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1147 TYR 0.016 0.001 TYR D 973 PHE 0.051 0.001 PHE F 88 TRP 0.040 0.002 TRP C 54 HIS 0.004 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (24536) covalent geometry : angle 0.68729 / 0.35 (33441) hydrogen bonds : bond 0.04130 / 2.83 ( 977) hydrogen bonds : angle 4.86355 / 3.40 ( 2721) metal coordination : bond 0.00582 / 0.26 ( 8) metal coordination : angle 5.71406 / 2.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7052 (tmm) cc_final: 0.6584 (tmm) REVERT: B 93 VAL cc_start: 0.3316 (OUTLIER) cc_final: 0.3044 (t) REVERT: B 136 MET cc_start: 0.6652 (pmm) cc_final: 0.6117 (pmm) REVERT: C 200 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6552 (tt) REVERT: C 263 LEU cc_start: 0.8765 (mt) cc_final: 0.8425 (mt) REVERT: C 266 TYR cc_start: 0.8271 (t80) cc_final: 0.7945 (t80) REVERT: C 287 LEU cc_start: 0.8718 (tp) cc_final: 0.8364 (tp) REVERT: C 390 MET cc_start: 0.5908 (ppp) cc_final: 0.5385 (ppp) REVERT: C 426 MET cc_start: 0.5827 (mmm) cc_final: 0.5291 (tpt) REVERT: C 1128 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6324 (mmp) REVERT: D 474 ARG cc_start: 0.8235 (tpp-160) cc_final: 0.7894 (tpm170) REVERT: D 494 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7366 (t-90) REVERT: D 554 GLU cc_start: 0.6926 (pt0) cc_final: 0.6624 (pt0) REVERT: D 583 LEU cc_start: 0.6006 (tp) cc_final: 0.5800 (tp) REVERT: D 637 ARG cc_start: 0.7206 (mmm160) cc_final: 0.6786 (mmm160) REVERT: D 784 MET cc_start: 0.7085 (tmm) cc_final: 0.6708 (tmm) REVERT: D 920 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5200 (mp) REVERT: D 946 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5112 (mm) REVERT: D 1218 ASP cc_start: 0.7222 (m-30) cc_final: 0.6864 (m-30) outliers start: 64 outliers final: 48 residues processed: 322 average time/residue: 0.1585 time to fit residues: 81.0998 Evaluate side-chains 325 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 271 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 100 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 192 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 292 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN C 462 HIS ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 811 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.194931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.156743 restraints weight = 46588.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.156527 restraints weight = 34946.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.157935 restraints weight = 28875.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.158413 restraints weight = 20978.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.158689 restraints weight = 20117.495| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.261 24544 Z= 0.173 Angle : 0.815 59.199 33453 Z= 0.433 Chirality : 0.046 0.374 3798 Planarity : 0.005 0.059 4204 Dihedral : 15.038 175.803 3827 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.94 % Rotamer: Outliers : 2.47 % Allowed : 24.73 % Favored : 72.80 % Cbeta Deviations : 0.04 % 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 (0.15), residues: 2921 helix: 0.46 (0.16), residues: 1054 sheet: -1.02 (0.28), residues: 340 loop : -1.96 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1147 TYR 0.012 0.001 TYR D 973 PHE 0.048 0.002 PHE F 88 TRP 0.033 0.003 TRP C 54 HIS 0.005 0.001 HIS D 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (24536) covalent geometry : angle 0.80766 / 0.43 (33441) hydrogen bonds : bond 0.04142 / 2.84 ( 977) hydrogen bonds : angle 4.88069 / 3.42 ( 2721) metal coordination : bond 0.00575 / 0.26 ( 8) metal coordination : angle 5.71240 / 2.53 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7021 (tmm) cc_final: 0.6552 (tmm) REVERT: A 154 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: B 93 VAL cc_start: 0.3303 (OUTLIER) cc_final: 0.3034 (t) REVERT: B 136 MET cc_start: 0.6672 (pmm) cc_final: 0.6192 (pmm) REVERT: C 81 ILE cc_start: 0.6460 (OUTLIER) cc_final: 0.6239 (mt) REVERT: C 200 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6535 (tt) REVERT: C 263 LEU cc_start: 0.8772 (mt) cc_final: 0.8433 (mt) REVERT: C 266 TYR cc_start: 0.8277 (t80) cc_final: 0.7950 (t80) REVERT: C 287 LEU cc_start: 0.8683 (tp) cc_final: 0.8373 (tp) REVERT: C 390 MET cc_start: 0.5953 (ppp) cc_final: 0.5460 (ppp) REVERT: C 426 MET cc_start: 0.5871 (mmm) cc_final: 0.5304 (tpt) REVERT: C 1128 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6347 (mmp) REVERT: D 474 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.7900 (tpm170) REVERT: D 494 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7383 (t-90) REVERT: D 583 LEU cc_start: 0.6055 (tp) cc_final: 0.5838 (tp) REVERT: D 637 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6790 (mmm160) REVERT: D 784 MET cc_start: 0.7090 (tmm) cc_final: 0.6703 (tmm) REVERT: D 920 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5204 (mp) REVERT: D 946 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5101 (mm) REVERT: D 1218 ASP cc_start: 0.7235 (m-30) cc_final: 0.6868 (m-30) outliers start: 61 outliers final: 48 residues processed: 306 average time/residue: 0.1631 time to fit residues: 80.3873 Evaluate side-chains 329 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 273 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 90 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 295 optimal weight: 40.0000 chunk 85 optimal weight: 0.6980 chunk 28 optimal weight: 0.0030 chunk 123 optimal weight: 40.0000 chunk 236 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 811 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.194904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.156214 restraints weight = 46138.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.156115 restraints weight = 32012.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.157827 restraints weight = 27907.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.157632 restraints weight = 20907.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.157973 restraints weight = 19847.263| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.261 24544 Z= 0.173 Angle : 0.815 59.200 33453 Z= 0.433 Chirality : 0.046 0.374 3798 Planarity : 0.005 0.059 4204 Dihedral : 15.038 175.803 3827 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.94 % Rotamer: Outliers : 2.27 % Allowed : 24.89 % Favored : 72.84 % Cbeta Deviations : 0.04 % 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 (0.15), residues: 2921 helix: 0.46 (0.16), residues: 1054 sheet: -1.02 (0.28), residues: 340 loop : -1.96 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1147 TYR 0.012 0.001 TYR D 973 PHE 0.048 0.002 PHE F 88 TRP 0.033 0.003 TRP C 54 HIS 0.005 0.001 HIS D 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (24536) covalent geometry : angle 0.80766 / 0.43 (33441) hydrogen bonds : bond 0.04142 / 2.84 ( 977) hydrogen bonds : angle 4.88069 / 3.42 ( 2721) metal coordination : bond 0.00575 / 0.26 ( 8) metal coordination : angle 5.71240 / 2.53 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4263.68 seconds wall clock time: 74 minutes 32.36 seconds (4472.36 seconds total)