Starting phenix.real_space_refine on Fri Jun 20 19:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m84_63701/06_2025/9m84_63701.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m84_63701/06_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_63701/06_2025/9m84_63701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m84_63701/06_2025/9m84_63701.map" model { file = "/net/cci-nas-00/data/ceres_data/9m84_63701/06_2025/9m84_63701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m84_63701/06_2025/9m84_63701.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.44, per 1000 atoms: 0.56 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: 8.02 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " Number of angles added : 12 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5394 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 37 sheets defined 38.5% alpha, 13.1% beta 14 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 8.49 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: 10.32 Time building geometry restraints manager: 9.11 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: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 68.690 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (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 TRP 0.027 0.002 TRP D 58 HIS 0.011 0.001 HIS F 93 PHE 0.016 0.001 PHE D 131 TYR 0.012 0.001 TYR C 266 ARG 0.018 0.001 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.13983 ( 977) hydrogen bonds : angle 6.51922 ( 2721) metal coordination : bond 0.00698 ( 8) metal coordination : angle 5.34084 ( 12) covalent geometry : bond 0.00406 (24536) covalent geometry : angle 0.77332 (33441) *********************** 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 : 2.500 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: 0.4112 time to fit residues: 207.0788 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 : 3.366 ------------------------------------------------------------------------------- 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 249 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 50.0000 chunk 76 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 424 GLN ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 ASN C1027 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.192223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.152483 restraints weight = 46359.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.152121 restraints weight = 31801.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.153367 restraints weight = 27679.188| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24544 Z= 0.197 Angle : 0.711 13.702 33453 Z= 0.367 Chirality : 0.047 0.190 3798 Planarity : 0.006 0.064 4204 Dihedral : 15.205 178.976 3842 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.98 % Favored : 91.99 % Rotamer: Outliers : 2.88 % Allowed : 17.35 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 2921 helix: 0.11 (0.16), residues: 1049 sheet: -1.51 (0.28), residues: 321 loop : -2.13 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 54 HIS 0.009 0.001 HIS D 849 PHE 0.040 0.002 PHE F 88 TYR 0.018 0.002 TYR D 241 ARG 0.008 0.001 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 977) hydrogen bonds : angle 5.31877 ( 2721) metal coordination : bond 0.00599 ( 8) metal coordination : angle 5.01952 ( 12) covalent geometry : bond 0.00460 (24536) covalent geometry : angle 0.70485 (33441) *********************** 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 383 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 312 time to evaluate : 2.871 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: 0.6712 (pmm) cc_final: 0.6116 (pmm) REVERT: C 38 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7033 (mp) REVERT: C 266 TYR cc_start: 0.8324 (t80) cc_final: 0.7741 (t80) REVERT: C 426 MET cc_start: 0.5642 (mmm) cc_final: 0.4962 (tpt) REVERT: C 512 ASP cc_start: 0.7856 (p0) cc_final: 0.7604 (p0) REVERT: C 709 PHE cc_start: 0.4824 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: C 1128 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6767 (mmp) REVERT: D 242 ARG cc_start: 0.9019 (mmm160) cc_final: 0.8550 (mmm160) REVERT: D 458 LYS cc_start: 0.6252 (mttt) cc_final: 0.5935 (mmtt) REVERT: D 784 MET cc_start: 0.7003 (tmm) cc_final: 0.6794 (tmm) REVERT: D 1218 ASP cc_start: 0.7064 (m-30) cc_final: 0.6789 (m-30) outliers start: 71 outliers final: 39 residues processed: 353 average time/residue: 0.3722 time to fit residues: 204.0332 Evaluate side-chains 321 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 38 LEU 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 462 HIS Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 709 PHE Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 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 1016 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 313 VAL 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 558 LEU 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 238 optimal weight: 0.0040 chunk 104 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN D 563 ASN D 808 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.195311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.156381 restraints weight = 45799.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.157294 restraints weight = 30931.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.158703 restraints weight = 26190.181| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24544 Z= 0.133 Angle : 0.656 13.972 33453 Z= 0.333 Chirality : 0.044 0.202 3798 Planarity : 0.005 0.060 4204 Dihedral : 14.954 179.870 3827 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 2.80 % Allowed : 19.74 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2921 helix: 0.34 (0.16), residues: 1056 sheet: -1.27 (0.28), residues: 326 loop : -2.01 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 651 HIS 0.006 0.001 HIS D 849 PHE 0.037 0.002 PHE F 88 TYR 0.011 0.001 TYR C 266 ARG 0.006 0.000 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 977) hydrogen bonds : angle 4.97665 ( 2721) metal coordination : bond 0.00511 ( 8) metal coordination : angle 5.23019 ( 12) covalent geometry : bond 0.00302 (24536) covalent geometry : angle 0.64844 (33441) *********************** 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 362 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 LEU cc_start: 0.7591 (tt) cc_final: 0.7377 (tt) REVERT: B 136 MET cc_start: 0.6582 (pmm) cc_final: 0.6126 (pmm) REVERT: C 40 LEU cc_start: 0.6508 (tt) cc_final: 0.5871 (mp) REVERT: C 212 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7473 (m) REVERT: C 287 LEU cc_start: 0.8730 (tp) cc_final: 0.8326 (tp) REVERT: C 426 MET cc_start: 0.5418 (mmm) cc_final: 0.5181 (mmm) REVERT: C 512 ASP cc_start: 0.7717 (p0) cc_final: 0.7493 (p0) REVERT: C 1128 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6433 (mmp) REVERT: D 223 TRP cc_start: 0.7404 (m100) cc_final: 0.7152 (m100) REVERT: D 277 LEU cc_start: 0.9054 (mm) cc_final: 0.8848 (mp) REVERT: D 474 ARG cc_start: 0.8453 (tpp-160) cc_final: 0.7944 (tpm170) REVERT: D 494 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.6937 (t-90) REVERT: D 784 MET cc_start: 0.6979 (tmm) cc_final: 0.6739 (tmm) REVERT: D 896 ILE cc_start: 0.7500 (tp) cc_final: 0.7227 (tp) REVERT: D 920 LEU cc_start: 0.5427 (OUTLIER) cc_final: 0.5034 (mp) REVERT: D 1218 ASP cc_start: 0.7115 (m-30) cc_final: 0.6846 (m-30) outliers start: 69 outliers final: 33 residues processed: 338 average time/residue: 0.4287 time to fit residues: 231.9245 Evaluate side-chains 306 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 3.209 ------------------------------------------------------------------------------- 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 C residue 116 THR 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 425 PHE Chi-restraints excluded: chain C residue 462 HIS 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 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 1128 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 797 MET Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 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 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 265 optimal weight: 0.3980 chunk 187 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 195 optimal weight: 0.0770 chunk 231 optimal weight: 10.0000 chunk 286 optimal weight: 40.0000 chunk 128 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D1210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.195143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.156245 restraints weight = 46475.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.157596 restraints weight = 31887.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.158624 restraints weight = 27192.172| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.1789 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= 0.133 Angle : 0.653 17.183 33453 Z= 0.328 Chirality : 0.044 0.186 3798 Planarity : 0.005 0.060 4204 Dihedral : 14.915 178.249 3827 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.28 % Allowed : 20.43 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 2921 helix: 0.52 (0.16), residues: 1059 sheet: -1.13 (0.28), residues: 347 loop : -1.92 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 54 HIS 0.006 0.001 HIS D 849 PHE 0.039 0.001 PHE F 88 TYR 0.012 0.001 TYR C 288 ARG 0.007 0.000 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 977) hydrogen bonds : angle 4.82779 ( 2721) metal coordination : bond 0.00614 ( 8) metal coordination : angle 6.29222 ( 12) covalent geometry : bond 0.00300 (24536) covalent geometry : angle 0.64260 (33441) *********************** 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 380 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 299 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6959 (tmm) cc_final: 0.6433 (tmm) REVERT: A 200 GLN cc_start: 0.7223 (mt0) cc_final: 0.7014 (mt0) REVERT: B 95 MET cc_start: 0.5599 (tmm) cc_final: 0.4986 (tmm) REVERT: B 136 MET cc_start: 0.6586 (pmm) cc_final: 0.6049 (pmm) REVERT: C 200 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6465 (tt) REVERT: C 401 GLN cc_start: 0.8431 (mt0) cc_final: 0.8137 (mm110) REVERT: C 512 ASP cc_start: 0.7669 (p0) cc_final: 0.7464 (p0) REVERT: C 616 MET cc_start: 0.7848 (mpp) cc_final: 0.7643 (mpp) REVERT: C 1128 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6419 (mmp) REVERT: D 241 TYR cc_start: 0.8745 (t80) cc_final: 0.8216 (t80) REVERT: D 242 ARG cc_start: 0.8955 (mmm160) cc_final: 0.8595 (mmm160) REVERT: D 314 LEU cc_start: 0.7247 (mt) cc_final: 0.7020 (mt) REVERT: D 474 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.8017 (tpm170) REVERT: D 583 LEU cc_start: 0.6014 (tp) cc_final: 0.5729 (tp) REVERT: D 784 MET cc_start: 0.7009 (tmm) cc_final: 0.6615 (tmm) REVERT: D 920 LEU cc_start: 0.5476 (OUTLIER) cc_final: 0.5117 (mp) REVERT: D 1218 ASP cc_start: 0.7156 (m-30) cc_final: 0.6846 (m-30) outliers start: 81 outliers final: 47 residues processed: 356 average time/residue: 0.3643 time to fit residues: 203.9931 Evaluate side-chains 329 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 128 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 200 LEU 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 425 PHE Chi-restraints excluded: chain C residue 462 HIS 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 857 VAL 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 1128 MET 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 351 ASN 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 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 590 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 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 184 optimal weight: 5.9990 chunk 280 optimal weight: 0.2980 chunk 266 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 154 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN C 41 GLN ** 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 = 0.4811 r_free = 0.4811 target = 0.195739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.156147 restraints weight = 46350.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.156866 restraints weight = 30130.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.158117 restraints weight = 24723.050| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24544 Z= 0.132 Angle : 0.641 15.833 33453 Z= 0.322 Chirality : 0.044 0.165 3798 Planarity : 0.005 0.059 4204 Dihedral : 14.885 177.832 3827 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.32 % Allowed : 21.89 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 2921 helix: 0.60 (0.16), residues: 1062 sheet: -1.11 (0.27), residues: 353 loop : -1.87 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 54 HIS 0.005 0.001 HIS D 849 PHE 0.043 0.001 PHE F 88 TYR 0.010 0.001 TYR D 134 ARG 0.008 0.000 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 977) hydrogen bonds : angle 4.73538 ( 2721) metal coordination : bond 0.00542 ( 8) metal coordination : angle 5.85467 ( 12) covalent geometry : bond 0.00305 (24536) covalent geometry : angle 0.63161 (33441) *********************** 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 376 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 294 time to evaluate : 2.944 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 61 HIS cc_start: 0.7916 (p90) cc_final: 0.7653 (p-80) REVERT: A 95 MET cc_start: 0.6788 (tmm) cc_final: 0.6322 (tmm) REVERT: B 95 MET cc_start: 0.5748 (tmm) cc_final: 0.5129 (tmm) REVERT: B 136 MET cc_start: 0.6609 (pmm) cc_final: 0.6135 (pmm) REVERT: B 232 ILE cc_start: 0.5284 (OUTLIER) cc_final: 0.4945 (mt) REVERT: C 263 LEU cc_start: 0.8867 (mt) cc_final: 0.8530 (mt) REVERT: C 266 TYR cc_start: 0.8296 (t80) cc_final: 0.7924 (t80) REVERT: C 287 LEU cc_start: 0.8721 (tp) cc_final: 0.8369 (tp) REVERT: C 426 MET cc_start: 0.5340 (mmm) cc_final: 0.5063 (mmm) REVERT: C 616 MET cc_start: 0.7849 (mpp) cc_final: 0.7585 (mpp) REVERT: C 709 PHE cc_start: 0.4606 (OUTLIER) cc_final: 0.3781 (m-80) REVERT: C 1128 MET cc_start: 0.6557 (mmp) cc_final: 0.6258 (mmp) REVERT: D 256 MET cc_start: 0.6847 (mmm) cc_final: 0.6362 (mmm) REVERT: D 277 LEU cc_start: 0.9044 (mm) cc_final: 0.8814 (mp) REVERT: D 314 LEU cc_start: 0.7247 (mt) cc_final: 0.7036 (mt) REVERT: D 458 LYS cc_start: 0.6052 (mttm) cc_final: 0.5825 (mttm) REVERT: D 474 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.8077 (tpm170) REVERT: D 637 ARG cc_start: 0.7323 (mmm160) cc_final: 0.7029 (mmm160) REVERT: D 784 MET cc_start: 0.7022 (tmm) cc_final: 0.6631 (tmm) REVERT: D 920 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5054 (mp) REVERT: D 946 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4883 (mm) REVERT: D 1218 ASP cc_start: 0.7276 (m-30) cc_final: 0.6903 (m-30) outliers start: 82 outliers final: 51 residues processed: 354 average time/residue: 0.4461 time to fit residues: 254.3644 Evaluate side-chains 327 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 4.560 ------------------------------------------------------------------------------- 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 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 14 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 148 MET 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 462 HIS Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 709 PHE 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 949 ASP 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 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 351 ASN 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 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 229 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 41 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.193168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.153828 restraints weight = 46278.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.154170 restraints weight = 31326.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.155507 restraints weight = 28312.927| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24544 Z= 0.168 Angle : 0.676 16.639 33453 Z= 0.339 Chirality : 0.045 0.191 3798 Planarity : 0.005 0.058 4204 Dihedral : 14.918 178.210 3827 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 3.45 % Allowed : 23.10 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2921 helix: 0.57 (0.16), residues: 1063 sheet: -1.10 (0.28), residues: 354 loop : -1.93 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 54 HIS 0.005 0.001 HIS D 849 PHE 0.043 0.002 PHE F 88 TYR 0.011 0.001 TYR B 168 ARG 0.008 0.000 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 977) hydrogen bonds : angle 4.79375 ( 2721) metal coordination : bond 0.00535 ( 8) metal coordination : angle 6.12478 ( 12) covalent geometry : bond 0.00393 (24536) covalent geometry : angle 0.66567 (33441) *********************** 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 371 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 286 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6712 (tmm) cc_final: 0.6212 (tmm) REVERT: B 95 MET cc_start: 0.6021 (tmm) cc_final: 0.5392 (tmm) REVERT: B 136 MET cc_start: 0.6623 (pmm) cc_final: 0.6114 (pmm) REVERT: C 81 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6343 (mt) REVERT: C 263 LEU cc_start: 0.8876 (mt) cc_final: 0.8539 (mt) REVERT: C 266 TYR cc_start: 0.8270 (t80) cc_final: 0.7946 (t80) REVERT: C 287 LEU cc_start: 0.8769 (tp) cc_final: 0.8387 (tp) REVERT: C 390 MET cc_start: 0.5472 (ppp) cc_final: 0.4984 (ppp) REVERT: C 616 MET cc_start: 0.7924 (mpp) cc_final: 0.7650 (mpp) REVERT: C 709 PHE cc_start: 0.4758 (OUTLIER) cc_final: 0.3960 (m-80) REVERT: C 1128 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6354 (mmp) REVERT: D 314 LEU cc_start: 0.7089 (mt) cc_final: 0.6868 (mt) REVERT: D 458 LYS cc_start: 0.6187 (mttm) cc_final: 0.5906 (mttm) REVERT: D 474 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8075 (tpm170) REVERT: D 494 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7428 (t-90) REVERT: D 637 ARG cc_start: 0.7343 (mmm160) cc_final: 0.7058 (mmm160) REVERT: D 784 MET cc_start: 0.7092 (tmm) cc_final: 0.6667 (tmm) REVERT: D 920 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.5117 (mp) REVERT: D 946 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.4934 (mm) REVERT: D 1006 MET cc_start: 0.3484 (OUTLIER) cc_final: 0.3171 (tmm) REVERT: D 1218 ASP cc_start: 0.7296 (m-30) cc_final: 0.6861 (m-30) REVERT: F 116 MET cc_start: 0.5092 (pmm) cc_final: 0.4885 (pmm) outliers start: 85 outliers final: 60 residues processed: 344 average time/residue: 0.5659 time to fit residues: 317.1611 Evaluate side-chains 339 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 272 time to evaluate : 3.941 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 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 419 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 709 PHE 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 949 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 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 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 954 VAL Chi-restraints excluded: chain D residue 1006 MET 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 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 73 optimal weight: 0.5980 chunk 213 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 48 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 288 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 ASN ** D 552 GLN ** 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 = 0.4819 r_free = 0.4819 target = 0.196538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.157365 restraints weight = 46146.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.158636 restraints weight = 30241.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.159423 restraints weight = 25772.077| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2290 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= 0.120 Angle : 0.650 17.250 33453 Z= 0.323 Chirality : 0.044 0.218 3798 Planarity : 0.005 0.058 4204 Dihedral : 14.858 177.946 3827 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.12 % Allowed : 24.00 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 2921 helix: 0.65 (0.16), residues: 1067 sheet: -0.99 (0.28), residues: 355 loop : -1.79 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 54 HIS 0.005 0.001 HIS D 849 PHE 0.046 0.001 PHE F 88 TYR 0.014 0.001 TYR D 134 ARG 0.011 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 977) hydrogen bonds : angle 4.64420 ( 2721) metal coordination : bond 0.00586 ( 8) metal coordination : angle 6.68160 ( 12) covalent geometry : bond 0.00273 (24536) covalent geometry : angle 0.63807 (33441) *********************** 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 363 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 286 time to evaluate : 2.640 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 41 THR cc_start: 0.7227 (t) cc_final: 0.6922 (t) REVERT: A 61 HIS cc_start: 0.7869 (p90) cc_final: 0.7614 (p-80) REVERT: A 95 MET cc_start: 0.6718 (tmm) cc_final: 0.6259 (tmm) REVERT: B 95 MET cc_start: 0.5856 (tmm) cc_final: 0.5363 (tmm) REVERT: B 128 LEU cc_start: 0.8386 (mp) cc_final: 0.8184 (mt) REVERT: B 136 MET cc_start: 0.6604 (pmm) cc_final: 0.6204 (pmm) REVERT: C 263 LEU cc_start: 0.8854 (mt) cc_final: 0.8516 (mt) REVERT: C 266 TYR cc_start: 0.8234 (t80) cc_final: 0.7944 (t80) REVERT: C 287 LEU cc_start: 0.8719 (tp) cc_final: 0.8371 (tp) REVERT: C 390 MET cc_start: 0.5725 (ppp) cc_final: 0.5439 (ppp) REVERT: C 469 MET cc_start: 0.7432 (tpt) cc_final: 0.7151 (tpt) REVERT: C 616 MET cc_start: 0.7828 (mpp) cc_final: 0.7587 (mpp) REVERT: C 1128 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6259 (mmp) REVERT: D 277 LEU cc_start: 0.9021 (mm) cc_final: 0.8811 (mp) REVERT: D 314 LEU cc_start: 0.7143 (mt) cc_final: 0.6926 (mt) REVERT: D 373 MET cc_start: 0.6572 (mmp) cc_final: 0.5711 (ttm) REVERT: D 474 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8130 (tpm170) REVERT: D 494 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7306 (t-90) REVERT: D 637 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7200 (mmm160) REVERT: D 784 MET cc_start: 0.7004 (tmm) cc_final: 0.6641 (tmm) REVERT: D 920 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5168 (mp) REVERT: D 946 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.4958 (mm) REVERT: D 1006 MET cc_start: 0.3413 (OUTLIER) cc_final: 0.3116 (tmm) REVERT: D 1218 ASP cc_start: 0.7231 (m-30) cc_final: 0.6840 (m-30) outliers start: 77 outliers final: 52 residues processed: 338 average time/residue: 0.3578 time to fit residues: 193.4602 Evaluate side-chains 329 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 45 SER 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 208 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 209 MET 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 462 HIS 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 857 VAL 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 1128 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 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 954 VAL Chi-restraints excluded: chain D residue 1006 MET 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 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 127 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 215 optimal weight: 0.0570 chunk 211 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- 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 ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.188915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.150225 restraints weight = 46724.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.149944 restraints weight = 36191.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.150981 restraints weight = 31193.825| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 24544 Z= 0.281 Angle : 0.804 17.530 33453 Z= 0.405 Chirality : 0.049 0.199 3798 Planarity : 0.006 0.067 4204 Dihedral : 15.057 179.759 3827 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.73 % Allowed : 24.44 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 2921 helix: 0.27 (0.16), residues: 1054 sheet: -1.17 (0.28), residues: 352 loop : -2.10 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 54 HIS 0.008 0.001 HIS D 849 PHE 0.047 0.002 PHE F 88 TYR 0.018 0.002 TYR B 168 ARG 0.011 0.001 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 977) hydrogen bonds : angle 5.14653 ( 2721) metal coordination : bond 0.00870 ( 8) metal coordination : angle 6.90291 ( 12) covalent geometry : bond 0.00658 (24536) covalent geometry : angle 0.79328 (33441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 272 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6710 (tmm) cc_final: 0.6258 (tmm) REVERT: B 136 MET cc_start: 0.6681 (pmm) cc_final: 0.6032 (pmm) REVERT: C 263 LEU cc_start: 0.8817 (mt) cc_final: 0.8476 (mt) REVERT: C 616 MET cc_start: 0.7853 (mpp) cc_final: 0.7635 (mpp) REVERT: C 709 PHE cc_start: 0.4962 (OUTLIER) cc_final: 0.4248 (m-10) REVERT: C 1128 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6324 (mmp) REVERT: D 314 LEU cc_start: 0.7100 (mt) cc_final: 0.6887 (mt) REVERT: D 474 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.7972 (tpm170) REVERT: D 475 MET cc_start: 0.8197 (ptp) cc_final: 0.6511 (ptp) REVERT: D 494 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: D 637 ARG cc_start: 0.7329 (mmm160) cc_final: 0.6995 (mmm160) REVERT: D 784 MET cc_start: 0.7179 (tmm) cc_final: 0.6789 (tmm) REVERT: D 920 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5157 (mp) REVERT: D 946 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5390 (mm) REVERT: D 1218 ASP cc_start: 0.7443 (m-30) cc_final: 0.6994 (m-30) REVERT: F 103 MET cc_start: 0.6870 (ptp) cc_final: 0.6249 (ptp) outliers start: 92 outliers final: 63 residues processed: 333 average time/residue: 0.3510 time to fit residues: 186.4416 Evaluate side-chains 329 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 261 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 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 825 VAL 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 949 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 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 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 271 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 741 HIS ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.191370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.152864 restraints weight = 46609.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.153050 restraints weight = 33935.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.154685 restraints weight = 28936.807| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24544 Z= 0.188 Angle : 0.735 17.140 33453 Z= 0.367 Chirality : 0.046 0.267 3798 Planarity : 0.005 0.058 4204 Dihedral : 15.036 179.888 3827 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.98 % Favored : 91.99 % Rotamer: Outliers : 2.80 % Allowed : 25.74 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 2921 helix: 0.38 (0.16), residues: 1055 sheet: -1.21 (0.27), residues: 352 loop : -2.05 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 54 HIS 0.006 0.001 HIS D 849 PHE 0.049 0.002 PHE F 88 TYR 0.025 0.002 TYR C 266 ARG 0.012 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 977) hydrogen bonds : angle 5.02853 ( 2721) metal coordination : bond 0.00670 ( 8) metal coordination : angle 6.55629 ( 12) covalent geometry : bond 0.00445 (24536) covalent geometry : angle 0.72497 (33441) *********************** 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 340 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 271 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6726 (tmm) cc_final: 0.6321 (tmm) REVERT: B 95 MET cc_start: 0.6123 (tmm) cc_final: 0.5667 (tmm) REVERT: B 136 MET cc_start: 0.6759 (pmm) cc_final: 0.6159 (pmm) REVERT: B 177 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6444 (mmmt) REVERT: C 142 MET cc_start: 0.6244 (mmm) cc_final: 0.5394 (mpp) REVERT: C 209 MET cc_start: 0.7196 (mmp) cc_final: 0.6988 (mmp) REVERT: C 263 LEU cc_start: 0.8811 (mt) cc_final: 0.8470 (mt) REVERT: C 587 ASP cc_start: 0.5920 (p0) cc_final: 0.5525 (p0) REVERT: C 616 MET cc_start: 0.7986 (mpp) cc_final: 0.7731 (mpp) REVERT: C 709 PHE cc_start: 0.4773 (OUTLIER) cc_final: 0.4040 (m-80) REVERT: C 912 MET cc_start: 0.6982 (tpt) cc_final: 0.5679 (tpt) REVERT: C 1128 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6436 (mmp) REVERT: D 314 LEU cc_start: 0.7135 (mt) cc_final: 0.6907 (mt) REVERT: D 373 MET cc_start: 0.6754 (mmp) cc_final: 0.6000 (ttm) REVERT: D 494 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7474 (t-90) REVERT: D 637 ARG cc_start: 0.7350 (mmm160) cc_final: 0.7027 (mmm160) REVERT: D 784 MET cc_start: 0.7126 (tmm) cc_final: 0.6716 (tmm) REVERT: D 920 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5369 (mp) REVERT: D 946 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5155 (mm) REVERT: D 1218 ASP cc_start: 0.7484 (m-30) cc_final: 0.6974 (m-30) REVERT: F 103 MET cc_start: 0.6933 (ptp) cc_final: 0.6353 (ptp) outliers start: 69 outliers final: 59 residues processed: 316 average time/residue: 0.3582 time to fit residues: 181.6467 Evaluate side-chains 329 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 2.710 ------------------------------------------------------------------------------- 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 84 VAL 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 178 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 191 LYS 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 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 857 VAL 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 1128 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 671 LEU 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 954 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 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 251 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 288 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 157 optimal weight: 0.0870 chunk 170 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 111 optimal weight: 0.0470 chunk 116 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 C 600 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 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 = 0.4801 r_free = 0.4801 target = 0.194730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.156801 restraints weight = 46499.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.156497 restraints weight = 34927.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.157964 restraints weight = 28862.744| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24544 Z= 0.136 Angle : 0.716 16.441 33453 Z= 0.354 Chirality : 0.045 0.248 3798 Planarity : 0.005 0.059 4204 Dihedral : 14.968 179.270 3827 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.53 % Rotamer: Outliers : 2.43 % Allowed : 26.47 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2921 helix: 0.57 (0.16), residues: 1057 sheet: -0.98 (0.28), residues: 351 loop : -1.95 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 54 HIS 0.005 0.001 HIS D 849 PHE 0.051 0.001 PHE F 88 TYR 0.024 0.001 TYR C 266 ARG 0.013 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 977) hydrogen bonds : angle 4.86520 ( 2721) metal coordination : bond 0.00632 ( 8) metal coordination : angle 6.31295 ( 12) covalent geometry : bond 0.00315 (24536) covalent geometry : angle 0.70579 (33441) ********************** 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 335 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 2.792 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: 0.6820 (tmm) cc_final: 0.6408 (tmm) REVERT: B 63 PHE cc_start: 0.5300 (t80) cc_final: 0.4091 (m-80) REVERT: B 95 MET cc_start: 0.5995 (tmm) cc_final: 0.5645 (tmm) REVERT: B 136 MET cc_start: 0.6714 (pmm) cc_final: 0.6058 (pmm) REVERT: B 177 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6351 (mmmt) REVERT: C 142 MET cc_start: 0.6098 (mmm) cc_final: 0.5178 (mpp) REVERT: C 263 LEU cc_start: 0.8749 (mt) cc_final: 0.8414 (mt) REVERT: C 287 LEU cc_start: 0.8764 (tp) cc_final: 0.8441 (tp) REVERT: C 426 MET cc_start: 0.5677 (mmm) cc_final: 0.4297 (tpt) REVERT: C 616 MET cc_start: 0.7957 (mpp) cc_final: 0.7716 (mpp) REVERT: C 1128 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6376 (mmp) REVERT: D 373 MET cc_start: 0.6588 (mmp) cc_final: 0.5918 (ttm) REVERT: D 456 VAL cc_start: 0.8132 (t) cc_final: 0.7700 (t) REVERT: D 474 ARG cc_start: 0.8255 (tpm170) cc_final: 0.7920 (tpm170) REVERT: D 494 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7430 (t-90) REVERT: D 637 ARG cc_start: 0.7448 (mmm160) cc_final: 0.7232 (mmm160) REVERT: D 784 MET cc_start: 0.7044 (tmm) cc_final: 0.6673 (tmm) REVERT: D 920 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5376 (mp) REVERT: D 946 LEU cc_start: 0.5620 (OUTLIER) cc_final: 0.5123 (mm) REVERT: D 1218 ASP cc_start: 0.7397 (m-30) cc_final: 0.6901 (m-30) REVERT: F 103 MET cc_start: 0.7043 (ptp) cc_final: 0.6505 (ptp) outliers start: 60 outliers final: 53 residues processed: 313 average time/residue: 0.3540 time to fit residues: 176.4494 Evaluate side-chains 325 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 2.574 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 191 LYS 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 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 572 MET Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 664 SER 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 949 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1128 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1193 ILE Chi-restraints excluded: chain D residue 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 126 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 258 optimal weight: 0.1980 chunk 45 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 198 optimal weight: 0.0000 chunk 201 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 284 optimal weight: 20.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.193662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.154848 restraints weight = 46200.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.154833 restraints weight = 33159.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.156022 restraints weight = 27553.590| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24544 Z= 0.149 Angle : 0.718 18.951 33453 Z= 0.353 Chirality : 0.046 0.402 3798 Planarity : 0.005 0.063 4204 Dihedral : 14.961 178.715 3827 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.08 % Rotamer: Outliers : 2.72 % Allowed : 26.59 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 2921 helix: 0.61 (0.16), residues: 1059 sheet: -1.02 (0.27), residues: 357 loop : -1.92 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 54 HIS 0.006 0.001 HIS C 465 PHE 0.053 0.001 PHE F 88 TYR 0.019 0.001 TYR C 266 ARG 0.017 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 977) hydrogen bonds : angle 4.86549 ( 2721) metal coordination : bond 0.00634 ( 8) metal coordination : angle 6.14762 ( 12) covalent geometry : bond 0.00351 (24536) covalent geometry : angle 0.70839 (33441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9808.87 seconds wall clock time: 173 minutes 49.66 seconds (10429.66 seconds total)