Starting phenix.real_space_refine on Mon Aug 25 00:35:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m84_63701/08_2025/9m84_63701.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m84_63701/08_2025/9m84_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_63701/08_2025/9m84_63701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m84_63701/08_2025/9m84_63701.map" model { file = "/net/cci-nas-00/data/ceres_data/9m84_63701/08_2025/9m84_63701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m84_63701/08_2025/9m84_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-2.0-5787/lib/python3.9/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: 4.52, per 1000 atoms: 0.19 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: 1.95 Conformation dependent library (CDL) restraints added in 980.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.89 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: 4.75 Time building geometry restraints manager: 2.59 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=" C ARG D 295 " pdb=" O ARG D 295 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.18e-02 7.18e+03 8.77e+00 bond pdb=" N GLN C 861 " pdb=" CA GLN C 861 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.52e+00 bond pdb=" N VAL C 547 " pdb=" CA VAL C 547 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 5.96e+00 bond pdb=" N ASP C 587 " pdb=" CA ASP C 587 " ideal model delta sigma weight residual 1.454 1.482 -0.029 1.18e-02 7.18e+03 5.89e+00 bond pdb=" N VAL B 51 " pdb=" CA VAL B 51 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.68e+00 ... (remaining 24531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 31937 1.68 - 3.37: 1250 3.37 - 5.05: 220 5.05 - 6.73: 24 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=" 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 angle pdb=" N SER D 255 " pdb=" CA SER D 255 " pdb=" C SER D 255 " ideal model delta sigma weight residual 107.73 112.79 -5.06 1.34e+00 5.57e-01 1.42e+01 angle pdb=" N ILE C 675 " pdb=" CA ILE C 675 " pdb=" C ILE C 675 " ideal model delta sigma weight residual 113.71 110.13 3.58 9.50e-01 1.11e+00 1.42e+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: 2717 0.042 - 0.084: 779 0.084 - 0.127: 260 0.127 - 0.169: 38 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 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 0.050 24544 Z= 0.202 Angle : 0.780 15.392 33453 Z= 0.441 Chirality : 0.045 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 aren 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 covalent geometry : bond 0.00406 (24536) covalent geometry : angle 0.77332 (33441) hydrogen bonds : bond 0.13983 ( 977) hydrogen bonds : angle 6.51922 ( 2721) metal coordination : bond 0.00698 ( 8) metal coordination : angle 5.34084 ( 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 : 0.869 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: 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: 0.7846 (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: 0.1560 time to fit residues: 78.6009 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 : 0.578 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4818 r_free = 0.4818 target = 0.196392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.157273 restraints weight = 46215.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.157249 restraints weight = 30507.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.158391 restraints weight = 26615.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.158945 restraints weight = 20110.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.159112 restraints weight = 19181.490| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24544 Z= 0.139 Angle : 0.653 13.154 33453 Z= 0.337 Chirality : 0.045 0.176 3798 Planarity : 0.005 0.063 4204 Dihedral : 15.101 177.901 3842 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 2.51 % Allowed : 16.54 % Favored : 80.95 % 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 aren not related in a simple way. whole: -1.55 (0.15), residues: 2921 helix: 0.36 (0.16), residues: 1048 sheet: -1.32 (0.28), residues: 334 loop : -2.01 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 819 TYR 0.022 0.001 TYR D 241 PHE 0.038 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 covalent geometry : bond 0.00316 (24536) covalent geometry : angle 0.64700 (33441) hydrogen bonds : bond 0.04501 ( 977) hydrogen bonds : angle 5.12562 ( 2721) metal coordination : bond 0.00497 ( 8) metal coordination : angle 4.71391 ( 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 379 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 0.881 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: 0.6620 (pmm) cc_final: 0.6155 (pmm) REVERT: B 232 ILE cc_start: 0.5399 (OUTLIER) cc_final: 0.5058 (mt) REVERT: C 40 LEU cc_start: 0.6410 (tt) cc_final: 0.6123 (mp) REVERT: C 287 LEU cc_start: 0.8677 (tp) cc_final: 0.8288 (tp) REVERT: C 426 MET cc_start: 0.5449 (mmm) cc_final: 0.4856 (tpt) REVERT: C 512 ASP cc_start: 0.7741 (p0) cc_final: 0.7501 (p0) REVERT: C 1128 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6688 (mmp) REVERT: D 242 ARG cc_start: 0.8967 (mmm160) cc_final: 0.8488 (mmm160) REVERT: D 458 LYS cc_start: 0.6141 (mttt) cc_final: 0.5922 (mmtt) REVERT: D 693 ASN cc_start: 0.7200 (t0) cc_final: 0.6965 (t0) REVERT: D 896 ILE cc_start: 0.7553 (tp) cc_final: 0.7236 (tp) REVERT: D 1218 ASP cc_start: 0.6965 (m-30) cc_final: 0.6641 (m-30) outliers start: 62 outliers final: 28 residues processed: 350 average time/residue: 0.1528 time to fit residues: 83.0429 Evaluate side-chains 302 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 116 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 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 1128 MET Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 125 LEU 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 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 1164 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: 10.0000 chunk 167 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 123 optimal weight: 50.0000 chunk 227 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 208 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 100 GLN ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 HIS C1027 HIS D1210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.190971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.151630 restraints weight = 46673.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.153095 restraints weight = 32481.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.153797 restraints weight = 28777.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.153645 restraints weight = 20716.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.154236 restraints weight = 19509.749| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24544 Z= 0.216 Angle : 0.728 13.937 33453 Z= 0.370 Chirality : 0.047 0.208 3798 Planarity : 0.006 0.060 4204 Dihedral : 15.032 178.535 3827 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.18 % Favored : 91.78 % Rotamer: Outliers : 3.53 % Allowed : 19.34 % Favored : 77.14 % 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 aren not related in a simple way. whole: -1.73 (0.15), residues: 2921 helix: 0.15 (0.15), residues: 1053 sheet: -1.38 (0.27), residues: 344 loop : -2.09 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1147 TYR 0.020 0.002 TYR D 116 PHE 0.036 0.002 PHE F 88 TRP 0.032 0.003 TRP D 58 HIS 0.007 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00507 (24536) covalent geometry : angle 0.72114 (33441) hydrogen bonds : bond 0.04973 ( 977) hydrogen bonds : angle 5.16331 ( 2721) metal coordination : bond 0.00652 ( 8) metal coordination : angle 5.41521 ( 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 376 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 289 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 LEU cc_start: 0.7627 (tt) cc_final: 0.7397 (tt) REVERT: B 136 MET cc_start: 0.6639 (pmm) cc_final: 0.6073 (pmm) REVERT: B 177 LYS cc_start: 0.6652 (mmtt) cc_final: 0.6358 (mmmt) REVERT: C 38 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7146 (mp) REVERT: C 426 MET cc_start: 0.5743 (mmm) cc_final: 0.5408 (mmm) REVERT: C 512 ASP cc_start: 0.7754 (p0) cc_final: 0.7528 (p0) REVERT: C 616 MET cc_start: 0.7874 (mpp) cc_final: 0.7623 (mpp) REVERT: C 709 PHE cc_start: 0.4865 (OUTLIER) cc_final: 0.4065 (m-80) REVERT: C 1128 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6472 (mmp) REVERT: D 223 TRP cc_start: 0.7366 (m100) cc_final: 0.7135 (m100) REVERT: D 583 LEU cc_start: 0.6389 (tp) cc_final: 0.6055 (tp) REVERT: D 1218 ASP cc_start: 0.7110 (m-30) cc_final: 0.6852 (m-30) outliers start: 87 outliers final: 53 residues processed: 343 average time/residue: 0.1428 time to fit residues: 76.7583 Evaluate side-chains 330 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 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 480 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 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 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 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 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 558 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 732 VAL 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 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1217 THR 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: 0.9990 chunk 273 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 161 optimal weight: 0.1980 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 36 ASN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 563 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.194738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.155807 restraints weight = 46226.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.157063 restraints weight = 31812.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.158297 restraints weight = 26462.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.158140 restraints weight = 19491.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.159068 restraints weight = 18594.972| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24544 Z= 0.138 Angle : 0.661 15.339 33453 Z= 0.334 Chirality : 0.044 0.191 3798 Planarity : 0.005 0.060 4204 Dihedral : 14.964 179.255 3827 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 3.08 % Allowed : 21.32 % Favored : 75.60 % 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 aren not related in a simple way. whole: -1.47 (0.15), residues: 2921 helix: 0.39 (0.16), residues: 1059 sheet: -1.16 (0.28), residues: 344 loop : -1.99 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 474 TYR 0.010 0.001 TYR A 168 PHE 0.038 0.001 PHE F 88 TRP 0.031 0.002 TRP D 651 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00318 (24536) covalent geometry : angle 0.65229 (33441) hydrogen bonds : bond 0.04219 ( 977) hydrogen bonds : angle 4.89387 ( 2721) metal coordination : bond 0.00489 ( 8) metal coordination : angle 5.76519 ( 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 376 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 300 time to evaluate : 0.885 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 200 GLN cc_start: 0.7213 (mt0) cc_final: 0.6947 (mt0) REVERT: B 136 MET cc_start: 0.6647 (pmm) cc_final: 0.6215 (pmm) REVERT: C 263 LEU cc_start: 0.8839 (mt) cc_final: 0.8500 (mt) REVERT: C 287 LEU cc_start: 0.8738 (tp) cc_final: 0.8328 (tp) REVERT: C 319 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5570 (pt) REVERT: C 426 MET cc_start: 0.5609 (mmm) cc_final: 0.5315 (mmm) REVERT: C 512 ASP cc_start: 0.7667 (p0) cc_final: 0.7456 (p0) REVERT: C 1128 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6358 (mmp) REVERT: D 242 ARG cc_start: 0.9017 (mmm160) cc_final: 0.8727 (mmm160) REVERT: D 256 MET cc_start: 0.7139 (mmm) cc_final: 0.6871 (mmm) REVERT: D 314 LEU cc_start: 0.7258 (mt) cc_final: 0.7023 (mt) REVERT: D 474 ARG cc_start: 0.8305 (tpm170) cc_final: 0.7916 (tpm170) REVERT: D 494 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7103 (t-90) REVERT: D 583 LEU cc_start: 0.6018 (tp) cc_final: 0.5725 (tp) REVERT: D 896 ILE cc_start: 0.7598 (tp) cc_final: 0.7338 (tp) REVERT: D 920 LEU cc_start: 0.5435 (OUTLIER) cc_final: 0.5094 (mp) REVERT: D 1170 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7177 (tp30) REVERT: D 1218 ASP cc_start: 0.7160 (m-30) cc_final: 0.6850 (m-30) outliers start: 76 outliers final: 45 residues processed: 352 average time/residue: 0.1448 time to fit residues: 81.1081 Evaluate side-chains 323 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 128 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR 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 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 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 125 LEU Chi-restraints excluded: chain D residue 379 ASP 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 552 GLN Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 797 MET 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 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1208 SER 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: 3.9990 chunk 149 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 198 optimal weight: 0.0370 chunk 87 optimal weight: 3.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 36 ASN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 HIS D1182 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.189271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.149845 restraints weight = 46461.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.150383 restraints weight = 32684.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.151608 restraints weight = 28789.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.151411 restraints weight = 21637.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.152259 restraints weight = 20467.977| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24544 Z= 0.242 Angle : 0.763 14.593 33453 Z= 0.385 Chirality : 0.047 0.179 3798 Planarity : 0.006 0.059 4204 Dihedral : 15.082 179.729 3827 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.59 % Favored : 91.37 % Rotamer: Outliers : 4.22 % Allowed : 22.29 % Favored : 73.49 % 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 aren not related in a simple way. whole: -1.69 (0.15), residues: 2921 helix: 0.18 (0.16), residues: 1056 sheet: -1.33 (0.28), residues: 347 loop : -2.08 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1029 TYR 0.015 0.002 TYR D 116 PHE 0.045 0.002 PHE F 88 TRP 0.025 0.003 TRP C 54 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00568 (24536) covalent geometry : angle 0.75512 (33441) hydrogen bonds : bond 0.04997 ( 977) hydrogen bonds : angle 5.18152 ( 2721) metal coordination : bond 0.00650 ( 8) metal coordination : angle 5.96339 ( 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 393 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 289 time to evaluate : 0.926 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: 0.7015 (tmm) cc_final: 0.6599 (tmm) REVERT: B 95 MET cc_start: 0.6024 (tmm) cc_final: 0.5268 (tmm) REVERT: B 136 MET cc_start: 0.6745 (pmm) cc_final: 0.6145 (pmm) REVERT: C 40 LEU cc_start: 0.7225 (tt) cc_final: 0.6433 (mp) REVERT: C 200 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6511 (tt) REVERT: C 263 LEU cc_start: 0.8847 (mt) cc_final: 0.8502 (mt) REVERT: C 266 TYR cc_start: 0.8309 (t80) cc_final: 0.8001 (t80) REVERT: C 426 MET cc_start: 0.6056 (mmm) cc_final: 0.5731 (mmm) REVERT: C 616 MET cc_start: 0.7925 (mpp) cc_final: 0.7618 (mpp) REVERT: C 709 PHE cc_start: 0.4700 (OUTLIER) cc_final: 0.4051 (m-10) REVERT: C 1128 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6380 (mmp) REVERT: D 256 MET cc_start: 0.7322 (mmm) cc_final: 0.7004 (mmm) REVERT: D 314 LEU cc_start: 0.7228 (mt) cc_final: 0.6999 (mt) REVERT: D 474 ARG cc_start: 0.8334 (tpm170) cc_final: 0.8097 (tpm170) REVERT: D 946 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5421 (mm) REVERT: D 1218 ASP cc_start: 0.7329 (m-30) cc_final: 0.6940 (m-30) REVERT: F 103 MET cc_start: 0.6901 (ptp) cc_final: 0.6695 (ptp) outliers start: 104 outliers final: 69 residues processed: 357 average time/residue: 0.1438 time to fit residues: 81.4676 Evaluate side-chains 346 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 658 THR Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 797 MET 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 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 1208 SER Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1245 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 167 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 226 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 295 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 200 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 ASN D 552 GLN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.194682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.155682 restraints weight = 46434.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.155200 restraints weight = 31597.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.156540 restraints weight = 27535.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.156975 restraints weight = 20828.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.157102 restraints weight = 19780.175| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24544 Z= 0.132 Angle : 0.665 14.477 33453 Z= 0.333 Chirality : 0.044 0.197 3798 Planarity : 0.005 0.059 4204 Dihedral : 14.949 179.049 3827 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 3.61 % Allowed : 23.75 % Favored : 72.64 % 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 aren not related in a simple way. whole: -1.39 (0.15), residues: 2921 helix: 0.48 (0.16), residues: 1059 sheet: -1.12 (0.28), residues: 351 loop : -1.96 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 242 TYR 0.015 0.001 TYR D 973 PHE 0.044 0.001 PHE F 88 TRP 0.032 0.002 TRP C 54 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00305 (24536) covalent geometry : angle 0.65650 (33441) hydrogen bonds : bond 0.04058 ( 977) hydrogen bonds : angle 4.83832 ( 2721) metal coordination : bond 0.00452 ( 8) metal coordination : angle 5.71154 ( 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 382 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 293 time to evaluate : 0.728 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: 0.6977 (tmm) cc_final: 0.6409 (tmm) REVERT: B 95 MET cc_start: 0.5785 (tmm) cc_final: 0.5192 (tmm) REVERT: B 136 MET cc_start: 0.6608 (pmm) cc_final: 0.6065 (pmm) REVERT: C 200 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6742 (tt) REVERT: C 209 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6848 (mmp) REVERT: C 263 LEU cc_start: 0.8804 (mt) cc_final: 0.8464 (mt) REVERT: C 266 TYR cc_start: 0.8270 (t80) cc_final: 0.7893 (t80) REVERT: C 390 MET cc_start: 0.5467 (ppp) cc_final: 0.4978 (ppp) REVERT: C 426 MET cc_start: 0.5814 (mmm) cc_final: 0.5490 (mmm) REVERT: C 616 MET cc_start: 0.7912 (mpp) cc_final: 0.7694 (mpp) REVERT: C 709 PHE cc_start: 0.4665 (OUTLIER) cc_final: 0.3864 (m-80) REVERT: C 1128 MET cc_start: 0.6615 (mmp) cc_final: 0.6291 (mmp) REVERT: D 256 MET cc_start: 0.7285 (mmm) cc_final: 0.6981 (mmm) REVERT: D 314 LEU cc_start: 0.7020 (mt) cc_final: 0.6771 (mt) REVERT: D 494 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7327 (t-90) REVERT: D 896 ILE cc_start: 0.7748 (tp) cc_final: 0.7420 (tp) REVERT: D 920 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5221 (mp) REVERT: D 946 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5075 (mm) REVERT: D 1170 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7122 (tp30) REVERT: D 1218 ASP cc_start: 0.7222 (m-30) cc_final: 0.6880 (m-30) outliers start: 89 outliers final: 54 residues processed: 357 average time/residue: 0.1493 time to fit residues: 83.8664 Evaluate side-chains 333 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 273 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 153 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 425 PHE Chi-restraints excluded: chain C residue 572 MET 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 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 1076 ILE Chi-restraints excluded: chain C residue 1116 LEU 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 129 ILE 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 509 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain D residue 797 MET 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 1208 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 219 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 154 GLN C 235 GLN C 424 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** 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 = 0.4801 r_free = 0.4801 target = 0.194959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.155702 restraints weight = 46223.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.155037 restraints weight = 31117.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.156505 restraints weight = 26382.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.156805 restraints weight = 20707.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.156978 restraints weight = 19673.303| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24544 Z= 0.131 Angle : 0.671 15.500 33453 Z= 0.333 Chirality : 0.044 0.198 3798 Planarity : 0.005 0.060 4204 Dihedral : 14.909 178.374 3827 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 3.53 % Allowed : 24.32 % Favored : 72.15 % 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 aren not related in a simple way. whole: -1.27 (0.15), residues: 2921 helix: 0.59 (0.16), residues: 1058 sheet: -1.05 (0.27), residues: 356 loop : -1.90 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 242 TYR 0.014 0.001 TYR D 973 PHE 0.047 0.001 PHE F 88 TRP 0.034 0.002 TRP C 54 HIS 0.005 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00306 (24536) covalent geometry : angle 0.66301 (33441) hydrogen bonds : bond 0.03953 ( 977) hydrogen bonds : angle 4.77071 ( 2721) metal coordination : bond 0.00465 ( 8) metal coordination : angle 5.52977 ( 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 373 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 286 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5999 (tt) REVERT: A 95 MET cc_start: 0.6836 (tmm) cc_final: 0.6346 (tmm) REVERT: B 95 MET cc_start: 0.5773 (tmm) cc_final: 0.5143 (tmm) REVERT: B 136 MET cc_start: 0.6559 (pmm) cc_final: 0.5880 (pmm) REVERT: C 81 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.6114 (mt) REVERT: C 200 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6358 (tt) REVERT: C 209 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6856 (mmp) REVERT: C 263 LEU cc_start: 0.8893 (mt) cc_final: 0.8554 (mt) REVERT: C 266 TYR cc_start: 0.8288 (t80) cc_final: 0.7954 (t80) REVERT: C 390 MET cc_start: 0.5830 (ppp) cc_final: 0.5525 (ppp) REVERT: C 616 MET cc_start: 0.7850 (mpp) cc_final: 0.7579 (mpp) REVERT: C 709 PHE cc_start: 0.4544 (OUTLIER) cc_final: 0.3745 (m-80) REVERT: C 1128 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6352 (mmp) REVERT: D 256 MET cc_start: 0.7210 (mmm) cc_final: 0.6880 (mmm) REVERT: D 314 LEU cc_start: 0.7101 (mt) cc_final: 0.6872 (mt) REVERT: D 458 LYS cc_start: 0.5908 (mttt) cc_final: 0.5695 (mttm) REVERT: D 494 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7327 (t-90) REVERT: D 896 ILE cc_start: 0.7633 (tp) cc_final: 0.7354 (tp) REVERT: D 920 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5192 (mp) REVERT: D 946 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.4858 (mm) REVERT: D 1218 ASP cc_start: 0.7219 (m-30) cc_final: 0.6802 (m-30) outliers start: 87 outliers final: 58 residues processed: 344 average time/residue: 0.1442 time to fit residues: 78.8585 Evaluate side-chains 341 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 274 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 13 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 138 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 153 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 413 ILE 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 483 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 884 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 946 ILE 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 129 ILE 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 509 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 780 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 1208 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 154 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** 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 = 0.4727 r_free = 0.4727 target = 0.187983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.148657 restraints weight = 46540.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.148984 restraints weight = 34108.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.150411 restraints weight = 29519.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.149999 restraints weight = 22402.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.150897 restraints weight = 21082.814| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 24544 Z= 0.280 Angle : 0.829 15.311 33453 Z= 0.415 Chirality : 0.049 0.200 3798 Planarity : 0.006 0.066 4204 Dihedral : 15.133 179.934 3827 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.01 % Allowed : 24.93 % Favored : 71.06 % 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 aren not related in a simple way. whole: -1.74 (0.15), residues: 2921 helix: 0.20 (0.16), residues: 1044 sheet: -1.22 (0.28), residues: 353 loop : -2.17 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 242 TYR 0.016 0.002 TYR A 168 PHE 0.044 0.002 PHE F 88 TRP 0.034 0.003 TRP C 54 HIS 0.007 0.001 HIS C 465 Details of bonding type rmsd covalent geometry : bond 0.00656 (24536) covalent geometry : angle 0.82056 (33441) hydrogen bonds : bond 0.05212 ( 977) hydrogen bonds : angle 5.26725 ( 2721) metal coordination : bond 0.00799 ( 8) metal coordination : angle 6.28179 ( 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 376 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 277 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.6276 (mt) cc_final: 0.5966 (tt) REVERT: A 95 MET cc_start: 0.6699 (tmm) cc_final: 0.6418 (tmm) REVERT: B 95 MET cc_start: 0.6084 (tmm) cc_final: 0.5364 (tmm) REVERT: B 128 LEU cc_start: 0.8477 (mp) cc_final: 0.8230 (mt) REVERT: B 136 MET cc_start: 0.6783 (pmm) cc_final: 0.6014 (pmm) REVERT: C 81 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6284 (mt) REVERT: C 200 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6535 (tt) REVERT: C 263 LEU cc_start: 0.8863 (mt) cc_final: 0.8518 (mt) REVERT: C 266 TYR cc_start: 0.8315 (t80) cc_final: 0.8100 (t80) REVERT: C 426 MET cc_start: 0.6132 (mmm) cc_final: 0.5339 (tpt) REVERT: C 709 PHE cc_start: 0.4951 (OUTLIER) cc_final: 0.4371 (m-10) REVERT: C 1128 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6350 (mmp) REVERT: D 256 MET cc_start: 0.7381 (mmm) cc_final: 0.7028 (mmm) REVERT: D 314 LEU cc_start: 0.7078 (mt) cc_final: 0.6841 (mt) REVERT: D 373 MET cc_start: 0.6888 (mmp) cc_final: 0.5953 (ttm) REVERT: D 494 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7546 (t-90) REVERT: D 920 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5183 (mp) REVERT: D 946 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5428 (mm) REVERT: D 1218 ASP cc_start: 0.7458 (m-30) cc_final: 0.6958 (m-30) REVERT: F 95 VAL cc_start: 0.8090 (t) cc_final: 0.7877 (t) outliers start: 99 outliers final: 73 residues processed: 344 average time/residue: 0.1440 time to fit residues: 79.2437 Evaluate side-chains 349 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 269 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 123 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 149 THR Chi-restraints excluded: chain C residue 153 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 425 PHE Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 495 PHE 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 719 ASP 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 922 LEU 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 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 129 ILE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 349 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 432 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 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 724 VAL Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 879 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 1193 ILE Chi-restraints excluded: chain D residue 1208 SER Chi-restraints excluded: chain D residue 1229 ILE Chi-restraints excluded: chain D residue 1245 THR Chi-restraints excluded: chain F residue 61 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: 0.9980 chunk 55 optimal weight: 0.2980 chunk 295 optimal weight: 10.0000 chunk 44 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 91 optimal weight: 0.0040 chunk 285 optimal weight: 20.0000 chunk 144 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 154 GLN A 200 GLN B 36 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.196444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.157573 restraints weight = 46346.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.158156 restraints weight = 29832.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.159311 restraints weight = 26123.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.159224 restraints weight = 19965.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.159496 restraints weight = 18443.260| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24544 Z= 0.127 Angle : 0.696 15.734 33453 Z= 0.347 Chirality : 0.045 0.300 3798 Planarity : 0.005 0.061 4204 Dihedral : 14.959 179.186 3827 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.55 % Allowed : 26.47 % Favored : 70.98 % 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 aren not related in a simple way. whole: -1.26 (0.15), residues: 2921 helix: 0.56 (0.16), residues: 1060 sheet: -0.97 (0.28), residues: 349 loop : -1.89 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 242 TYR 0.013 0.001 TYR D 106 PHE 0.046 0.001 PHE F 88 TRP 0.040 0.003 TRP C 54 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00290 (24536) covalent geometry : angle 0.68707 (33441) hydrogen bonds : bond 0.03889 ( 977) hydrogen bonds : angle 4.81448 ( 2721) metal coordination : bond 0.00526 ( 8) metal coordination : angle 5.88521 ( 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 356 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5936 (tt) REVERT: A 41 THR cc_start: 0.7145 (t) cc_final: 0.6816 (t) REVERT: A 61 HIS cc_start: 0.7934 (p90) cc_final: 0.7673 (p-80) REVERT: A 95 MET cc_start: 0.6945 (tmm) cc_final: 0.6458 (tmm) REVERT: B 128 LEU cc_start: 0.8439 (mp) cc_final: 0.8208 (mt) REVERT: B 136 MET cc_start: 0.6558 (pmm) cc_final: 0.5872 (pmm) REVERT: B 177 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6409 (mmmt) REVERT: C 81 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6091 (mt) REVERT: C 200 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6456 (tt) REVERT: C 263 LEU cc_start: 0.8868 (mt) cc_final: 0.8525 (mt) REVERT: C 266 TYR cc_start: 0.8234 (t80) cc_final: 0.7997 (t80) REVERT: C 287 LEU cc_start: 0.8720 (tp) cc_final: 0.8371 (tp) REVERT: C 426 MET cc_start: 0.5504 (mmm) cc_final: 0.4802 (tpt) REVERT: C 616 MET cc_start: 0.7829 (mpp) cc_final: 0.7561 (mpp) REVERT: C 709 PHE cc_start: 0.4606 (OUTLIER) cc_final: 0.3855 (m-80) REVERT: C 1128 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6340 (mmp) REVERT: D 256 MET cc_start: 0.7437 (mmm) cc_final: 0.7137 (mmm) REVERT: D 373 MET cc_start: 0.6604 (mmp) cc_final: 0.5802 (ttm) REVERT: D 474 ARG cc_start: 0.8504 (tpm170) cc_final: 0.8151 (tpm170) REVERT: D 494 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7434 (t-90) REVERT: D 637 ARG cc_start: 0.7225 (mmm160) cc_final: 0.7010 (mmm160) REVERT: D 896 ILE cc_start: 0.7647 (tp) cc_final: 0.7388 (tp) REVERT: D 920 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5452 (mp) REVERT: D 946 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5126 (mm) REVERT: D 1218 ASP cc_start: 0.7336 (m-30) cc_final: 0.6990 (m-30) outliers start: 63 outliers final: 45 residues processed: 335 average time/residue: 0.1563 time to fit residues: 82.4490 Evaluate side-chains 330 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 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 13 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 177 LYS 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 153 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 425 PHE 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 825 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 946 ILE 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 125 LEU Chi-restraints excluded: chain D residue 338 SER 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 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 1148 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1208 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 192 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 219 optimal weight: 0.3980 chunk 247 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN B 36 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** 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 = 0.4759 r_free = 0.4759 target = 0.190885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.152271 restraints weight = 46782.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.151461 restraints weight = 35820.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.152698 restraints weight = 31516.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.153486 restraints weight = 22937.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.153744 restraints weight = 21654.934| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2658 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= 0.210 Angle : 0.763 14.513 33453 Z= 0.380 Chirality : 0.047 0.323 3798 Planarity : 0.006 0.097 4204 Dihedral : 15.036 178.828 3827 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.77 % Favored : 92.19 % Rotamer: Outliers : 2.51 % Allowed : 26.35 % Favored : 71.14 % 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 aren not related in a simple way. whole: -1.45 (0.15), residues: 2921 helix: 0.40 (0.16), residues: 1059 sheet: -1.09 (0.27), residues: 355 loop : -1.98 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 242 TYR 0.012 0.002 TYR A 168 PHE 0.051 0.002 PHE F 88 TRP 0.037 0.003 TRP C 54 HIS 0.007 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00498 (24536) covalent geometry : angle 0.75557 (33441) hydrogen bonds : bond 0.04489 ( 977) hydrogen bonds : angle 4.99006 ( 2721) metal coordination : bond 0.00654 ( 8) metal coordination : angle 5.70626 ( 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 340 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 0.581 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 76 LEU cc_start: 0.6438 (mt) cc_final: 0.6213 (tt) REVERT: A 95 MET cc_start: 0.6791 (tmm) cc_final: 0.6229 (tmm) REVERT: B 136 MET cc_start: 0.6568 (pmm) cc_final: 0.5897 (pmm) REVERT: B 177 LYS cc_start: 0.6617 (mmtt) cc_final: 0.6303 (mmmt) REVERT: C 81 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6367 (mt) REVERT: C 142 MET cc_start: 0.6272 (mmm) cc_final: 0.5690 (mpp) REVERT: C 200 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6556 (tt) REVERT: C 263 LEU cc_start: 0.8762 (mt) cc_final: 0.8415 (mt) REVERT: C 426 MET cc_start: 0.5915 (mmm) cc_final: 0.5084 (tpt) REVERT: C 616 MET cc_start: 0.7961 (mpp) cc_final: 0.7716 (mpp) REVERT: C 709 PHE cc_start: 0.4714 (OUTLIER) cc_final: 0.4084 (m-80) REVERT: C 1128 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6322 (mmp) REVERT: D 256 MET cc_start: 0.7331 (mmm) cc_final: 0.7004 (mmm) REVERT: D 314 LEU cc_start: 0.6924 (mt) cc_final: 0.6585 (mt) REVERT: D 373 MET cc_start: 0.6786 (mmp) cc_final: 0.5919 (ttm) REVERT: D 474 ARG cc_start: 0.8382 (tpm170) cc_final: 0.8173 (tpm170) REVERT: D 494 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7525 (t-90) REVERT: D 920 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5269 (mp) REVERT: D 946 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5327 (mm) REVERT: F 103 MET cc_start: 0.7999 (pmm) cc_final: 0.7780 (pmm) outliers start: 62 outliers final: 52 residues processed: 320 average time/residue: 0.1474 time to fit residues: 75.1425 Evaluate side-chains 328 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 269 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 208 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 123 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 153 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 413 ILE Chi-restraints excluded: chain C residue 419 THR 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 825 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 1061 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 125 LEU Chi-restraints excluded: chain D residue 338 SER 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 558 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL 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 946 LEU Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 1208 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 295 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 28 optimal weight: 0.0050 chunk 123 optimal weight: 50.0000 chunk 236 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 269 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 200 GLN B 36 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN ** D1133 HIS ** 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 = 0.4811 r_free = 0.4811 target = 0.195749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.156775 restraints weight = 46085.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.156999 restraints weight = 31772.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.158481 restraints weight = 25629.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.158755 restraints weight = 19389.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.159070 restraints weight = 18877.770| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24544 Z= 0.129 Angle : 0.701 14.220 33453 Z= 0.348 Chirality : 0.045 0.321 3798 Planarity : 0.005 0.061 4204 Dihedral : 14.986 178.779 3827 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 2.27 % Allowed : 26.83 % Favored : 70.90 % 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 aren not related in a simple way. whole: -1.19 (0.15), residues: 2921 helix: 0.59 (0.16), residues: 1060 sheet: -0.92 (0.28), residues: 349 loop : -1.81 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 242 TYR 0.023 0.001 TYR C 266 PHE 0.053 0.001 PHE F 88 TRP 0.038 0.002 TRP C 54 HIS 0.005 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00300 (24536) covalent geometry : angle 0.69278 (33441) hydrogen bonds : bond 0.03877 ( 977) hydrogen bonds : angle 4.77536 ( 2721) metal coordination : bond 0.00536 ( 8) metal coordination : angle 5.66876 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4064.51 seconds wall clock time: 70 minutes 53.81 seconds (4253.81 seconds total)