Starting phenix.real_space_refine on Fri Feb 6 07:31:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zf2_14696/02_2026/7zf2_14696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zf2_14696/02_2026/7zf2_14696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zf2_14696/02_2026/7zf2_14696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zf2_14696/02_2026/7zf2_14696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zf2_14696/02_2026/7zf2_14696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zf2_14696/02_2026/7zf2_14696.map" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 87 5.16 5 C 14935 2.51 5 N 4230 2.21 5 O 4567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23822 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1704 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1781 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8699 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1059} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 9879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1264, 9879 Classifications: {'peptide': 1264} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1203} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 74} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1119 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} 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 19233 SG CYS D 891 77.823 25.379 97.890 1.00 77.37 S ATOM 19807 SG CYS D 968 78.667 28.744 97.624 1.00 71.40 S ATOM 19849 SG CYS D 975 74.930 27.669 98.642 1.00 61.72 S ATOM 19867 SG CYS D 978 77.642 27.763 101.091 1.00 63.75 S ATOM 12660 SG CYS D 60 66.937 42.577 33.661 1.00154.40 S ATOM 12678 SG CYS D 62 68.408 42.874 30.301 1.00163.42 S ATOM 12787 SG CYS D 75 67.845 39.336 31.624 1.00153.90 S ATOM 12813 SG CYS D 78 70.576 41.436 33.031 1.00153.87 S Time building chain proxies: 5.79, per 1000 atoms: 0.24 Number of scatterers: 23822 At special positions: 0 Unit cell: (181.5, 132, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 87 16.00 Mg 1 11.99 O 4567 8.00 N 4230 7.00 C 14935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 975 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " 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 75 " Number of angles added : 12 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5638 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 41 sheets defined 41.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.845A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.095A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.547A pdb=" N ARG A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 154 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 155 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 156 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.205A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.726A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.719A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.835A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.086A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 removed outlier: 4.018A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 302 removed outlier: 3.968A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.084A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.997A pdb=" N PHE C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.641A pdb=" N ARG C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.865A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 582 through 587 removed outlier: 4.546A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.575A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.542A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 removed outlier: 3.590A pdb=" N ALA C 615 " --> pdb=" O GLN C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 removed outlier: 4.480A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 783 removed outlier: 3.592A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 779 through 783' Processing helix chain 'C' and resid 815 through 825 removed outlier: 3.688A pdb=" N PHE C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.586A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.823A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.516A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 960 through 964 Processing helix chain 'C' and resid 981 through 990 removed outlier: 3.604A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.702A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1079 removed outlier: 3.787A pdb=" N TYR C1079 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1097 through 1109 Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 3.613A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.524A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 188 removed outlier: 4.950A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.786A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 285 through 306 removed outlier: 3.774A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 306 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 338 through 359 removed outlier: 3.942A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.395A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.020A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 removed outlier: 4.162A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 3.592A pdb=" N MET D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 removed outlier: 3.681A pdb=" N GLU D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.643A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.600A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 728 No H-bonds generated for 'chain 'D' and resid 726 through 728' Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.974A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.945A pdb=" N ARG D 857 " --> pdb=" O THR D 853 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR D 874 " --> pdb=" O SER D 870 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 876 " --> pdb=" O TYR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 3.632A pdb=" N ALA D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 995 through 1005 Processing helix chain 'D' and resid 1006 through 1009 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1146 removed outlier: 3.593A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.087A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 Processing helix chain 'D' and resid 1209 through 1216 removed outlier: 3.618A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.604A pdb=" N ASN D1239 " --> pdb=" O ASP D1235 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.980A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 4.030A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.515A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 Processing helix chain 'F' and resid 43 through 65 removed outlier: 4.148A pdb=" N GLU F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 89 Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.083A pdb=" N SER F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.254A pdb=" N GLN F 117 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 157 removed outlier: 3.673A pdb=" N TRP F 145 " --> pdb=" O TYR F 141 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN F 148 " --> pdb=" O TRP F 144 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 5.917A 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 99 removed outlier: 7.545A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.869A pdb=" N GLU B 24 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.869A pdb=" N GLU B 24 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.741A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.772A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 removed outlier: 7.028A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.513A pdb=" N THR C 136 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.663A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB6, first strand: chain 'C' and resid 212 through 216 Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.516A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.946A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.533A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 676 through 677 removed outlier: 3.645A pdb=" N ALA C 676 " --> pdb=" O ALA C 684 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.970A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 750 through 760 removed outlier: 3.647A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.538A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 806 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.597A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.677A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.704A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1144 through 1145 removed outlier: 4.420A pdb=" N VAL C1137 " --> pdb=" O ILE C1145 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.080A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 135 through 139 removed outlier: 7.167A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD7, first strand: chain 'D' and resid 392 through 393 Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 900 removed outlier: 4.521A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 902 through 903 Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1080 removed outlier: 3.724A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D1105 " --> pdb=" O GLY D1051 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 1034 hydrogen bonds defined for protein. 2865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8231 1.34 - 1.46: 4805 1.46 - 1.58: 11034 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 24223 Sorted by residual: bond pdb=" CA SER D 805 " pdb=" C SER D 805 " ideal model delta sigma weight residual 1.524 1.470 0.053 2.25e-02 1.98e+03 5.59e+00 bond pdb=" CB VAL D 543 " pdb=" CG2 VAL D 543 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB ILE D 509 " pdb=" CG2 ILE D 509 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB THR D 583 " pdb=" CG2 THR D 583 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB LYS D1152 " pdb=" CG LYS D1152 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 24218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 31472 1.35 - 2.70: 1074 2.70 - 4.05: 224 4.05 - 5.40: 36 5.40 - 6.75: 7 Bond angle restraints: 32813 Sorted by residual: angle pdb=" N GLY E 34 " pdb=" CA GLY E 34 " pdb=" C GLY E 34 " ideal model delta sigma weight residual 110.77 116.82 -6.05 1.93e+00 2.68e-01 9.82e+00 angle pdb=" C PRO C 725 " pdb=" N TRP C 726 " pdb=" CA TRP C 726 " ideal model delta sigma weight residual 122.76 118.34 4.42 1.63e+00 3.76e-01 7.35e+00 angle pdb=" C VAL D 880 " pdb=" CA VAL D 880 " pdb=" CB VAL D 880 " ideal model delta sigma weight residual 112.16 108.04 4.12 1.63e+00 3.76e-01 6.38e+00 angle pdb=" C PHE C 554 " pdb=" N VAL C 555 " pdb=" CA VAL C 555 " ideal model delta sigma weight residual 122.97 120.65 2.32 9.80e-01 1.04e+00 5.62e+00 angle pdb=" C LEU B 43 " pdb=" N SER B 44 " pdb=" CA SER B 44 " ideal model delta sigma weight residual 122.50 118.22 4.28 1.82e+00 3.02e-01 5.53e+00 ... (remaining 32808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13562 17.93 - 35.85: 1037 35.85 - 53.78: 205 53.78 - 71.71: 34 71.71 - 89.64: 13 Dihedral angle restraints: 14851 sinusoidal: 6076 harmonic: 8775 Sorted by residual: dihedral pdb=" CA GLY D 855 " pdb=" C GLY D 855 " pdb=" N ALA D 856 " pdb=" CA ALA D 856 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ARG D 414 " pdb=" C ARG D 414 " pdb=" N GLN D 415 " pdb=" CA GLN D 415 " ideal model delta harmonic sigma weight residual 180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY C 979 " pdb=" C GLY C 979 " pdb=" N ALA C 980 " pdb=" CA ALA C 980 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 14848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1951 0.029 - 0.059: 1104 0.059 - 0.088: 451 0.088 - 0.117: 194 0.117 - 0.146: 35 Chirality restraints: 3735 Sorted by residual: chirality pdb=" CA ILE C 594 " pdb=" N ILE C 594 " pdb=" C ILE C 594 " pdb=" CB ILE C 594 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA PHE C 300 " pdb=" N PHE C 300 " pdb=" C PHE C 300 " pdb=" CB PHE C 300 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE D 832 " pdb=" N ILE D 832 " pdb=" C ILE D 832 " pdb=" CB ILE D 832 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 3732 not shown) Planarity restraints: 4333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 24 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 25 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 320 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO D 321 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 815 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO C 816 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 816 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 816 " 0.023 5.00e-02 4.00e+02 ... (remaining 4330 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1048 2.71 - 3.26: 24549 3.26 - 3.80: 36677 3.80 - 4.35: 42734 4.35 - 4.90: 74852 Nonbonded interactions: 179860 Sorted by model distance: nonbonded pdb=" OG1 THR B 74 " pdb=" OE1 GLU B 75 " model vdw 2.162 3.040 nonbonded pdb=" OE2 GLU D 81 " pdb=" OG1 THR D 83 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR C 356 " pdb=" OE1 GLU C 362 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR E 56 " pdb=" O GLU E 105 " model vdw 2.214 3.040 nonbonded pdb=" O LEU D1176 " pdb=" OG SER D1179 " model vdw 2.223 3.040 ... (remaining 179855 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 3 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB )) or resid 162 through 226)) selection = (chain 'B' and (resid 3 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 226)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.350 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.007 0.053 24231 Z= 0.282 Angle : 0.634 11.955 32825 Z= 0.334 Chirality : 0.044 0.146 3735 Planarity : 0.004 0.045 4333 Dihedral : 13.324 89.635 9213 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.77 % Allowed : 11.06 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3054 helix: 1.11 (0.16), residues: 1084 sheet: -0.24 (0.27), residues: 374 loop : -0.66 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 295 TYR 0.019 0.002 TYR C 731 PHE 0.019 0.002 PHE C 906 TRP 0.013 0.002 TRP F 144 HIS 0.008 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00653 (24223) covalent geometry : angle 0.62259 (32813) hydrogen bonds : bond 0.16549 ( 1027) hydrogen bonds : angle 5.83418 ( 2865) metal coordination : bond 0.01053 ( 8) metal coordination : angle 6.22935 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 331 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.7918 (pt) cc_final: 0.7712 (pt) REVERT: A 72 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8500 (p0) REVERT: A 133 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8441 (mptt) REVERT: A 191 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8960 (ttpp) REVERT: A 208 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9274 (tt) REVERT: A 217 GLU cc_start: 0.7835 (tp30) cc_final: 0.7530 (tp30) REVERT: B 9 LEU cc_start: 0.8812 (mt) cc_final: 0.8313 (mt) REVERT: B 90 ASP cc_start: 0.7861 (t0) cc_final: 0.7505 (t0) REVERT: B 99 LYS cc_start: 0.8850 (tppt) cc_final: 0.8365 (tppt) REVERT: B 234 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.5868 (pt) REVERT: C 62 GLU cc_start: 0.8512 (tp30) cc_final: 0.8300 (tp30) REVERT: C 610 ASN cc_start: 0.9456 (OUTLIER) cc_final: 0.8856 (t0) REVERT: C 744 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: C 1119 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7559 (mt-10) REVERT: D 107 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8559 (p90) REVERT: D 218 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.8165 (mmm-85) REVERT: D 268 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7759 (t80) REVERT: D 312 MET cc_start: 0.8606 (mtm) cc_final: 0.8387 (mtm) REVERT: D 335 PHE cc_start: 0.5568 (OUTLIER) cc_final: 0.3850 (p90) REVERT: D 413 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.9088 (m-80) REVERT: D 475 MET cc_start: 0.8520 (ttp) cc_final: 0.8232 (ttm) REVERT: D 848 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7582 (mt-10) REVERT: D 975 CYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6575 (p) REVERT: D 1063 LYS cc_start: 0.7899 (tttm) cc_final: 0.7666 (tptt) REVERT: D 1155 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7433 (mt-10) REVERT: D 1227 GLN cc_start: 0.8102 (mt0) cc_final: 0.7611 (mt0) REVERT: E 66 ASP cc_start: 0.8315 (t70) cc_final: 0.7627 (t0) REVERT: E 102 ASP cc_start: 0.8770 (t0) cc_final: 0.8168 (t70) REVERT: E 103 LEU cc_start: 0.9435 (mp) cc_final: 0.9234 (mt) REVERT: E 104 LEU cc_start: 0.9388 (tp) cc_final: 0.9143 (tt) REVERT: F 114 ASP cc_start: 0.7596 (t70) cc_final: 0.7260 (t0) REVERT: F 115 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8821 (mm) REVERT: F 116 ILE cc_start: 0.9061 (tt) cc_final: 0.8691 (mt) REVERT: F 118 GLU cc_start: 0.8386 (pm20) cc_final: 0.7967 (pm20) REVERT: F 136 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7401 (t80) outliers start: 148 outliers final: 88 residues processed: 451 average time/residue: 0.1669 time to fit residues: 118.6448 Evaluate side-chains 375 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 275 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 712 THR Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1101 ASP Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 687 GLN D 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092757 restraints weight = 45250.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.092353 restraints weight = 30443.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092495 restraints weight = 36669.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093682 restraints weight = 23493.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.094358 restraints weight = 19473.013| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24231 Z= 0.176 Angle : 0.582 10.133 32825 Z= 0.299 Chirality : 0.043 0.142 3735 Planarity : 0.004 0.051 4333 Dihedral : 7.333 57.850 3537 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.67 % Allowed : 14.92 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3054 helix: 1.18 (0.16), residues: 1125 sheet: -0.10 (0.27), residues: 374 loop : -0.60 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 295 TYR 0.024 0.001 TYR E 56 PHE 0.014 0.001 PHE F 138 TRP 0.013 0.001 TRP F 145 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00413 (24223) covalent geometry : angle 0.57273 (32813) hydrogen bonds : bond 0.04813 ( 1027) hydrogen bonds : angle 4.61423 ( 2865) metal coordination : bond 0.00679 ( 8) metal coordination : angle 5.36012 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 310 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9299 (tt) REVERT: A 213 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.9010 (tptm) REVERT: B 79 ASN cc_start: 0.8983 (m-40) cc_final: 0.8760 (m-40) REVERT: B 99 LYS cc_start: 0.8677 (tppt) cc_final: 0.8446 (tppt) REVERT: B 152 ASN cc_start: 0.7694 (p0) cc_final: 0.7304 (p0) REVERT: B 215 LEU cc_start: 0.9552 (mt) cc_final: 0.9303 (mt) REVERT: B 234 ILE cc_start: 0.6751 (tt) cc_final: 0.5646 (pt) REVERT: C 121 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: C 239 LYS cc_start: 0.6918 (mmmt) cc_final: 0.6346 (mmmt) REVERT: C 610 ASN cc_start: 0.9363 (OUTLIER) cc_final: 0.8996 (t0) REVERT: C 744 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: C 768 GLU cc_start: 0.7417 (tt0) cc_final: 0.7201 (pt0) REVERT: D 76 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6920 (mm-30) REVERT: D 107 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8503 (p90) REVERT: D 143 MET cc_start: 0.8744 (ttp) cc_final: 0.8192 (ttp) REVERT: D 205 MET cc_start: 0.6243 (mmt) cc_final: 0.5708 (mmp) REVERT: D 211 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7864 (mmt-90) REVERT: D 268 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7358 (t80) REVERT: D 335 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.3925 (p90) REVERT: D 413 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8976 (m-80) REVERT: D 475 MET cc_start: 0.8172 (ttp) cc_final: 0.7918 (ttm) REVERT: D 693 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8823 (mt0) REVERT: D 975 CYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7487 (p) REVERT: D 983 MET cc_start: 0.8962 (mmp) cc_final: 0.8698 (mmp) REVERT: D 1063 LYS cc_start: 0.7844 (tttm) cc_final: 0.7576 (tptt) REVERT: D 1155 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7409 (mt-10) REVERT: E 66 ASP cc_start: 0.8155 (t70) cc_final: 0.7540 (t0) REVERT: E 102 ASP cc_start: 0.8507 (t0) cc_final: 0.8007 (t70) REVERT: E 105 GLU cc_start: 0.8376 (pp20) cc_final: 0.8092 (pp20) REVERT: F 114 ASP cc_start: 0.8234 (t70) cc_final: 0.7791 (t70) REVERT: F 115 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9162 (mm) REVERT: F 116 ILE cc_start: 0.9344 (tt) cc_final: 0.8956 (mt) REVERT: F 118 GLU cc_start: 0.8797 (pm20) cc_final: 0.8418 (pm20) REVERT: F 128 GLU cc_start: 0.8104 (pt0) cc_final: 0.7756 (mt-10) REVERT: F 136 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7417 (t80) outliers start: 120 outliers final: 84 residues processed: 406 average time/residue: 0.1532 time to fit residues: 99.4484 Evaluate side-chains 372 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 275 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 47 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 248 optimal weight: 0.8980 chunk 295 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 300 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN D 693 GLN D1227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093947 restraints weight = 44928.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093332 restraints weight = 37426.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094049 restraints weight = 33819.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.094572 restraints weight = 24087.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.095054 restraints weight = 21744.769| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24231 Z= 0.158 Angle : 0.553 9.187 32825 Z= 0.282 Chirality : 0.043 0.171 3735 Planarity : 0.004 0.053 4333 Dihedral : 6.674 57.464 3479 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.53 % Allowed : 15.86 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3054 helix: 1.27 (0.16), residues: 1127 sheet: -0.05 (0.27), residues: 372 loop : -0.59 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.021 0.001 TYR E 56 PHE 0.014 0.001 PHE F 138 TRP 0.010 0.001 TRP F 145 HIS 0.005 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00373 (24223) covalent geometry : angle 0.54506 (32813) hydrogen bonds : bond 0.04288 ( 1027) hydrogen bonds : angle 4.42579 ( 2865) metal coordination : bond 0.00615 ( 8) metal coordination : angle 4.76787 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 301 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9298 (tt) REVERT: A 213 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8941 (tptm) REVERT: B 234 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5738 (pt) REVERT: C 239 LYS cc_start: 0.6741 (mmmt) cc_final: 0.6158 (mmmt) REVERT: C 463 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8119 (pp) REVERT: C 610 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.8983 (t0) REVERT: C 618 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9281 (mt) REVERT: C 744 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: D 59 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7993 (tt0) REVERT: D 107 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8461 (p90) REVERT: D 205 MET cc_start: 0.6015 (mmt) cc_final: 0.5761 (mmm) REVERT: D 219 LEU cc_start: 0.8968 (tp) cc_final: 0.8685 (tp) REVERT: D 268 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7351 (t80) REVERT: D 335 PHE cc_start: 0.5667 (OUTLIER) cc_final: 0.3902 (p90) REVERT: D 354 LEU cc_start: 0.9319 (tt) cc_final: 0.8679 (tp) REVERT: D 413 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8992 (m-80) REVERT: D 475 MET cc_start: 0.8117 (ttp) cc_final: 0.7846 (ttt) REVERT: D 693 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8772 (mt0) REVERT: D 975 CYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7587 (p) REVERT: D 983 MET cc_start: 0.9033 (mmp) cc_final: 0.8689 (mmp) REVERT: D 1063 LYS cc_start: 0.7773 (tttm) cc_final: 0.7543 (tptt) REVERT: E 66 ASP cc_start: 0.8158 (t70) cc_final: 0.7543 (t0) REVERT: E 102 ASP cc_start: 0.8466 (t0) cc_final: 0.8232 (t0) REVERT: E 105 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: F 114 ASP cc_start: 0.8264 (t70) cc_final: 0.7916 (t70) REVERT: F 115 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9171 (mm) REVERT: F 116 ILE cc_start: 0.9370 (tt) cc_final: 0.9016 (mt) REVERT: F 117 GLN cc_start: 0.8346 (pt0) cc_final: 0.7735 (pt0) REVERT: F 128 GLU cc_start: 0.8010 (pt0) cc_final: 0.7587 (mt-10) REVERT: F 136 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7396 (t80) outliers start: 142 outliers final: 90 residues processed: 411 average time/residue: 0.1536 time to fit residues: 102.1235 Evaluate side-chains 386 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 280 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 163 optimal weight: 8.9990 chunk 195 optimal weight: 0.0980 chunk 245 optimal weight: 0.0870 chunk 214 optimal weight: 5.9990 chunk 283 optimal weight: 0.0570 chunk 159 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 137 optimal weight: 0.0050 chunk 231 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 overall best weight: 0.2290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS B 120 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1227 GLN F 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097546 restraints weight = 44641.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094849 restraints weight = 35928.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095687 restraints weight = 32471.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096261 restraints weight = 24679.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096863 restraints weight = 22305.898| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24231 Z= 0.096 Angle : 0.523 13.147 32825 Z= 0.262 Chirality : 0.042 0.487 3735 Planarity : 0.003 0.050 4333 Dihedral : 6.119 57.182 3470 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.25 % Allowed : 17.10 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3054 helix: 1.45 (0.16), residues: 1133 sheet: 0.21 (0.28), residues: 359 loop : -0.52 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 278 TYR 0.017 0.001 TYR E 56 PHE 0.016 0.001 PHE D 226 TRP 0.015 0.001 TRP D 223 HIS 0.005 0.000 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00205 (24223) covalent geometry : angle 0.51831 (32813) hydrogen bonds : bond 0.03331 ( 1027) hydrogen bonds : angle 4.13814 ( 2865) metal coordination : bond 0.00348 ( 8) metal coordination : angle 3.56183 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 328 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7941 (ppp80) REVERT: A 213 LYS cc_start: 0.9112 (tppt) cc_final: 0.8894 (tptm) REVERT: C 213 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: C 239 LYS cc_start: 0.6399 (mmmt) cc_final: 0.5828 (mmmt) REVERT: C 290 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: C 463 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8035 (pp) REVERT: C 610 ASN cc_start: 0.9426 (OUTLIER) cc_final: 0.9208 (t0) REVERT: C 744 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: D 107 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8404 (p90) REVERT: D 143 MET cc_start: 0.8679 (ttp) cc_final: 0.8313 (ttm) REVERT: D 205 MET cc_start: 0.6531 (mmt) cc_final: 0.6111 (mmm) REVERT: D 268 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7387 (t80) REVERT: D 354 LEU cc_start: 0.8827 (tt) cc_final: 0.8223 (tp) REVERT: D 428 SER cc_start: 0.9107 (t) cc_final: 0.8838 (m) REVERT: D 572 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8411 (mmp80) REVERT: D 858 LYS cc_start: 0.7776 (mttt) cc_final: 0.7441 (mttt) REVERT: D 950 ASP cc_start: 0.7870 (t0) cc_final: 0.7516 (t70) REVERT: D 975 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7844 (p) REVERT: D 1063 LYS cc_start: 0.7874 (tttm) cc_final: 0.7627 (tptt) REVERT: D 1276 GLU cc_start: 0.7534 (pm20) cc_final: 0.7063 (pm20) REVERT: E 66 ASP cc_start: 0.8097 (t70) cc_final: 0.7467 (t0) REVERT: E 102 ASP cc_start: 0.8407 (t0) cc_final: 0.8181 (t70) REVERT: E 105 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: F 116 ILE cc_start: 0.9385 (tt) cc_final: 0.9067 (mt) REVERT: F 128 GLU cc_start: 0.8138 (pt0) cc_final: 0.7814 (mt-10) REVERT: F 136 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7464 (t80) outliers start: 109 outliers final: 64 residues processed: 408 average time/residue: 0.1611 time to fit residues: 104.4209 Evaluate side-chains 355 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 177 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 240 optimal weight: 0.3980 chunk 158 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 174 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093904 restraints weight = 44828.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.093358 restraints weight = 29906.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093784 restraints weight = 33517.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.094694 restraints weight = 22546.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.095183 restraints weight = 19328.467| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24231 Z= 0.145 Angle : 0.558 11.637 32825 Z= 0.279 Chirality : 0.043 0.374 3735 Planarity : 0.003 0.047 4333 Dihedral : 5.721 57.367 3432 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.71 % Allowed : 17.41 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 3054 helix: 1.44 (0.16), residues: 1142 sheet: 0.12 (0.28), residues: 373 loop : -0.47 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.016 0.001 TYR E 56 PHE 0.022 0.001 PHE F 138 TRP 0.012 0.001 TRP D 223 HIS 0.008 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00343 (24223) covalent geometry : angle 0.55304 (32813) hydrogen bonds : bond 0.03744 ( 1027) hydrogen bonds : angle 4.19747 ( 2865) metal coordination : bond 0.00626 ( 8) metal coordination : angle 3.97265 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 294 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7921 (ppp80) REVERT: A 213 LYS cc_start: 0.9102 (tppt) cc_final: 0.8900 (tptm) REVERT: B 215 LEU cc_start: 0.9521 (mt) cc_final: 0.9217 (mt) REVERT: C 213 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: C 239 LYS cc_start: 0.6507 (mmmt) cc_final: 0.5881 (mmmt) REVERT: C 290 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: C 463 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8055 (pp) REVERT: C 744 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: C 1067 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7944 (ttm170) REVERT: D 107 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8472 (p90) REVERT: D 143 MET cc_start: 0.8747 (ttp) cc_final: 0.8099 (ttp) REVERT: D 205 MET cc_start: 0.6451 (mmt) cc_final: 0.6014 (mmm) REVERT: D 211 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7743 (mmt-90) REVERT: D 268 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7433 (t80) REVERT: D 572 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8430 (mmp80) REVERT: D 750 GLU cc_start: 0.8406 (pp20) cc_final: 0.8191 (tp30) REVERT: D 858 LYS cc_start: 0.7853 (mttt) cc_final: 0.7603 (mttt) REVERT: D 975 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7582 (p) REVERT: D 1063 LYS cc_start: 0.7844 (tttm) cc_final: 0.7594 (tptt) REVERT: E 66 ASP cc_start: 0.8174 (t70) cc_final: 0.7511 (t0) REVERT: E 102 ASP cc_start: 0.8448 (t0) cc_final: 0.8221 (t0) REVERT: F 116 ILE cc_start: 0.9378 (tt) cc_final: 0.9105 (mt) REVERT: F 128 GLU cc_start: 0.8050 (pt0) cc_final: 0.7707 (mt-10) REVERT: F 136 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7605 (t80) outliers start: 121 outliers final: 88 residues processed: 387 average time/residue: 0.1701 time to fit residues: 103.8052 Evaluate side-chains 380 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 281 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 290 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 285 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN C 407 GLN ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092963 restraints weight = 45236.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092113 restraints weight = 30707.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092189 restraints weight = 38722.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.093215 restraints weight = 23874.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094228 restraints weight = 19723.662| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24231 Z= 0.205 Angle : 0.602 10.274 32825 Z= 0.304 Chirality : 0.044 0.375 3735 Planarity : 0.004 0.045 4333 Dihedral : 5.971 59.929 3430 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.45 % Allowed : 17.65 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3054 helix: 1.33 (0.16), residues: 1136 sheet: 0.09 (0.28), residues: 363 loop : -0.58 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 278 TYR 0.018 0.001 TYR E 56 PHE 0.024 0.001 PHE F 138 TRP 0.012 0.001 TRP D 223 HIS 0.006 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00488 (24223) covalent geometry : angle 0.59544 (32813) hydrogen bonds : bond 0.04265 ( 1027) hydrogen bonds : angle 4.34889 ( 2865) metal coordination : bond 0.00857 ( 8) metal coordination : angle 4.70825 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 279 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9327 (tt) REVERT: A 213 LYS cc_start: 0.9143 (tppt) cc_final: 0.8862 (tptm) REVERT: C 213 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: C 239 LYS cc_start: 0.6682 (mmmt) cc_final: 0.6035 (mmmt) REVERT: C 290 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: C 463 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8001 (pp) REVERT: C 744 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: C 1067 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7894 (ttm170) REVERT: D 107 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8593 (p90) REVERT: D 205 MET cc_start: 0.6442 (mmt) cc_final: 0.5758 (mmp) REVERT: D 268 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7562 (t80) REVERT: D 572 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8474 (mmp80) REVERT: D 975 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7478 (p) REVERT: D 1112 MET cc_start: 0.8405 (mmm) cc_final: 0.7018 (mmm) REVERT: D 1279 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6711 (pmt-80) REVERT: E 66 ASP cc_start: 0.8294 (t70) cc_final: 0.7489 (t0) REVERT: E 104 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9206 (tt) REVERT: F 116 ILE cc_start: 0.9392 (tt) cc_final: 0.9160 (mt) REVERT: F 136 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7712 (t80) outliers start: 140 outliers final: 99 residues processed: 391 average time/residue: 0.1697 time to fit residues: 104.3988 Evaluate side-chains 379 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 267 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1169 ASP Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1279 ARG Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 249 optimal weight: 0.3980 chunk 143 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 209 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 189 optimal weight: 0.0970 chunk 207 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 120 ASN C 543 GLN ** C 730 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.128498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095042 restraints weight = 44528.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093960 restraints weight = 29466.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094513 restraints weight = 32564.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095458 restraints weight = 22597.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095960 restraints weight = 19357.476| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24231 Z= 0.105 Angle : 0.545 13.526 32825 Z= 0.271 Chirality : 0.042 0.314 3735 Planarity : 0.003 0.046 4333 Dihedral : 5.678 58.529 3428 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.13 % Allowed : 18.93 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 3054 helix: 1.53 (0.16), residues: 1128 sheet: 0.25 (0.28), residues: 359 loop : -0.52 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 278 TYR 0.019 0.001 TYR E 56 PHE 0.025 0.001 PHE F 138 TRP 0.011 0.001 TRP C 938 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00237 (24223) covalent geometry : angle 0.54039 (32813) hydrogen bonds : bond 0.03416 ( 1027) hydrogen bonds : angle 4.13401 ( 2865) metal coordination : bond 0.00481 ( 8) metal coordination : angle 3.78819 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 296 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7955 (ppp80) REVERT: A 213 LYS cc_start: 0.9070 (tppt) cc_final: 0.8852 (tptm) REVERT: C 213 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: C 239 LYS cc_start: 0.6532 (mmmt) cc_final: 0.5937 (mmmt) REVERT: C 290 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: C 463 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8125 (pp) REVERT: C 744 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: C 768 GLU cc_start: 0.6924 (tp30) cc_final: 0.6658 (tp30) REVERT: C 1067 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8214 (ttm170) REVERT: D 107 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8485 (p90) REVERT: D 143 MET cc_start: 0.8661 (ttp) cc_final: 0.7863 (ttp) REVERT: D 205 MET cc_start: 0.6379 (mmt) cc_final: 0.5975 (mmm) REVERT: D 251 TYR cc_start: 0.7252 (m-80) cc_final: 0.6887 (m-80) REVERT: D 256 MET cc_start: 0.7817 (ttm) cc_final: 0.7336 (ttm) REVERT: D 268 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7426 (t80) REVERT: D 572 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8425 (mmp80) REVERT: D 745 ILE cc_start: 0.9202 (mt) cc_final: 0.8932 (tp) REVERT: D 750 GLU cc_start: 0.8428 (pp20) cc_final: 0.8119 (tp30) REVERT: D 858 LYS cc_start: 0.7691 (mttt) cc_final: 0.7306 (mttt) REVERT: D 975 CYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7641 (p) REVERT: D 1063 LYS cc_start: 0.7861 (tttm) cc_final: 0.7600 (tptt) REVERT: D 1112 MET cc_start: 0.8340 (mmm) cc_final: 0.7775 (mmm) REVERT: D 1279 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6624 (pmt-80) REVERT: E 66 ASP cc_start: 0.8324 (t70) cc_final: 0.7408 (t0) REVERT: E 105 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: F 116 ILE cc_start: 0.9376 (tt) cc_final: 0.9125 (mt) REVERT: F 128 GLU cc_start: 0.8016 (pt0) cc_final: 0.7625 (mt-10) REVERT: F 136 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7797 (t80) outliers start: 106 outliers final: 83 residues processed: 375 average time/residue: 0.1706 time to fit residues: 100.6079 Evaluate side-chains 367 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 271 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1279 ARG Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 112 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 289 optimal weight: 0.0980 chunk 183 optimal weight: 0.3980 chunk 253 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 272 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095040 restraints weight = 44638.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093549 restraints weight = 28675.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094463 restraints weight = 29570.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094813 restraints weight = 22523.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095267 restraints weight = 19891.670| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24231 Z= 0.106 Angle : 0.548 11.618 32825 Z= 0.272 Chirality : 0.042 0.327 3735 Planarity : 0.003 0.044 4333 Dihedral : 5.548 58.635 3427 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.25 % Allowed : 19.28 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 3054 helix: 1.55 (0.16), residues: 1131 sheet: 0.28 (0.28), residues: 366 loop : -0.49 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 211 TYR 0.014 0.001 TYR E 56 PHE 0.028 0.001 PHE F 138 TRP 0.009 0.001 TRP D 223 HIS 0.004 0.000 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00248 (24223) covalent geometry : angle 0.54425 (32813) hydrogen bonds : bond 0.03353 ( 1027) hydrogen bonds : angle 4.07764 ( 2865) metal coordination : bond 0.00458 ( 8) metal coordination : angle 3.54080 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 281 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7986 (ppp80) REVERT: A 213 LYS cc_start: 0.9132 (tppt) cc_final: 0.8930 (tppt) REVERT: B 215 LEU cc_start: 0.9476 (mt) cc_final: 0.9236 (mt) REVERT: C 213 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: C 290 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: C 484 CYS cc_start: 0.9246 (t) cc_final: 0.8973 (t) REVERT: C 744 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: C 1067 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: D 107 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8512 (p90) REVERT: D 143 MET cc_start: 0.8653 (ttp) cc_final: 0.7844 (ttm) REVERT: D 205 MET cc_start: 0.6578 (mmt) cc_final: 0.6072 (mmm) REVERT: D 251 TYR cc_start: 0.7368 (m-80) cc_final: 0.6931 (m-80) REVERT: D 256 MET cc_start: 0.7873 (ttm) cc_final: 0.7399 (ttm) REVERT: D 268 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7604 (t80) REVERT: D 354 LEU cc_start: 0.8855 (tt) cc_final: 0.8494 (tp) REVERT: D 572 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8392 (mmp80) REVERT: D 745 ILE cc_start: 0.9170 (mt) cc_final: 0.8889 (tp) REVERT: D 750 GLU cc_start: 0.8515 (pp20) cc_final: 0.8229 (tp30) REVERT: D 858 LYS cc_start: 0.7680 (mttt) cc_final: 0.7294 (mttt) REVERT: D 975 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7781 (p) REVERT: D 1063 LYS cc_start: 0.7894 (tttm) cc_final: 0.7635 (tptt) REVERT: D 1112 MET cc_start: 0.8502 (mmm) cc_final: 0.7834 (mmm) REVERT: E 66 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8022 (t70) REVERT: F 116 ILE cc_start: 0.9386 (tt) cc_final: 0.9153 (mt) REVERT: F 128 GLU cc_start: 0.8094 (pt0) cc_final: 0.7742 (mt-10) REVERT: F 136 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7869 (t80) outliers start: 109 outliers final: 87 residues processed: 364 average time/residue: 0.1594 time to fit residues: 92.2748 Evaluate side-chains 375 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 277 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 0 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 292 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093399 restraints weight = 45152.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.092097 restraints weight = 28099.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092520 restraints weight = 33985.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093510 restraints weight = 22487.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093950 restraints weight = 18817.479| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24231 Z= 0.207 Angle : 0.618 13.599 32825 Z= 0.310 Chirality : 0.044 0.344 3735 Planarity : 0.004 0.049 4333 Dihedral : 5.858 59.970 3425 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.52 % Allowed : 19.17 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3054 helix: 1.37 (0.16), residues: 1136 sheet: 0.17 (0.28), residues: 369 loop : -0.54 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 211 TYR 0.019 0.001 TYR E 56 PHE 0.019 0.001 PHE D 226 TRP 0.014 0.001 TRP C 243 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00494 (24223) covalent geometry : angle 0.61290 (32813) hydrogen bonds : bond 0.04166 ( 1027) hydrogen bonds : angle 4.29184 ( 2865) metal coordination : bond 0.00836 ( 8) metal coordination : angle 4.38284 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 271 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7583 (tp30) REVERT: C 213 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: C 239 LYS cc_start: 0.5975 (mmtt) cc_final: 0.5322 (mmmt) REVERT: C 290 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: C 744 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 1067 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8358 (tpm170) REVERT: D 107 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8654 (p90) REVERT: D 143 MET cc_start: 0.8740 (ttp) cc_final: 0.8519 (ttp) REVERT: D 205 MET cc_start: 0.6533 (mmt) cc_final: 0.5968 (mmm) REVERT: D 268 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7553 (t80) REVERT: D 572 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8451 (mmp80) REVERT: D 745 ILE cc_start: 0.9203 (mt) cc_final: 0.8910 (tp) REVERT: D 858 LYS cc_start: 0.7864 (mttt) cc_final: 0.7513 (mttt) REVERT: D 975 CYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7600 (p) REVERT: D 1063 LYS cc_start: 0.7902 (tttm) cc_final: 0.7636 (tptt) REVERT: D 1279 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6680 (pmt-80) REVERT: E 66 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8127 (t70) REVERT: F 136 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7793 (t80) outliers start: 116 outliers final: 104 residues processed: 360 average time/residue: 0.1522 time to fit residues: 86.7719 Evaluate side-chains 379 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 264 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1279 ARG Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 116 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 272 optimal weight: 0.9980 chunk 280 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 304 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094167 restraints weight = 44886.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092544 restraints weight = 27525.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.092873 restraints weight = 34775.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.093960 restraints weight = 23216.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094755 restraints weight = 19260.082| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24231 Z= 0.159 Angle : 0.603 13.456 32825 Z= 0.301 Chirality : 0.043 0.339 3735 Planarity : 0.004 0.055 4333 Dihedral : 5.843 59.405 3425 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.75 % Allowed : 19.01 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3054 helix: 1.35 (0.16), residues: 1136 sheet: 0.18 (0.28), residues: 369 loop : -0.54 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 211 TYR 0.020 0.001 TYR E 56 PHE 0.029 0.001 PHE F 138 TRP 0.012 0.001 TRP C 243 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00382 (24223) covalent geometry : angle 0.59750 (32813) hydrogen bonds : bond 0.03915 ( 1027) hydrogen bonds : angle 4.24386 ( 2865) metal coordination : bond 0.00657 ( 8) metal coordination : angle 4.20249 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 271 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8029 (ppp80) REVERT: B 215 LEU cc_start: 0.9487 (mt) cc_final: 0.9261 (mt) REVERT: C 213 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: C 239 LYS cc_start: 0.5989 (mmtt) cc_final: 0.5339 (mmmt) REVERT: C 290 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6927 (mm-30) REVERT: C 744 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: C 1067 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8377 (tpm170) REVERT: D 107 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8541 (p90) REVERT: D 143 MET cc_start: 0.8722 (ttp) cc_final: 0.8128 (ttp) REVERT: D 205 MET cc_start: 0.6511 (mmt) cc_final: 0.5965 (mmm) REVERT: D 251 TYR cc_start: 0.7381 (m-80) cc_final: 0.7041 (m-80) REVERT: D 256 MET cc_start: 0.8028 (ttm) cc_final: 0.7531 (ttm) REVERT: D 268 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7476 (t80) REVERT: D 572 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8440 (mmp80) REVERT: D 745 ILE cc_start: 0.9175 (mt) cc_final: 0.8908 (tp) REVERT: D 750 GLU cc_start: 0.8615 (pp20) cc_final: 0.8129 (tp30) REVERT: D 858 LYS cc_start: 0.7770 (mttt) cc_final: 0.7416 (mttt) REVERT: D 975 CYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7643 (p) REVERT: D 1063 LYS cc_start: 0.7904 (tttm) cc_final: 0.7641 (tptt) REVERT: D 1112 MET cc_start: 0.8588 (mmm) cc_final: 0.8296 (mmm) REVERT: D 1279 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6684 (pmt-80) REVERT: E 66 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8044 (t70) REVERT: F 136 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7807 (t80) outliers start: 122 outliers final: 101 residues processed: 364 average time/residue: 0.1571 time to fit residues: 90.9755 Evaluate side-chains 380 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 267 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 712 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1279 ARG Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 288 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 221 optimal weight: 0.0040 chunk 263 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 overall best weight: 0.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098079 restraints weight = 44700.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097833 restraints weight = 34536.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098254 restraints weight = 36115.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099040 restraints weight = 24340.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099460 restraints weight = 20771.465| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24231 Z= 0.106 Angle : 0.577 12.539 32825 Z= 0.286 Chirality : 0.043 0.305 3735 Planarity : 0.004 0.055 4333 Dihedral : 5.537 58.819 3422 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.93 % Allowed : 19.75 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 3054 helix: 1.51 (0.16), residues: 1135 sheet: 0.40 (0.29), residues: 354 loop : -0.51 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 211 TYR 0.018 0.001 TYR E 56 PHE 0.020 0.001 PHE D 226 TRP 0.021 0.001 TRP C 243 HIS 0.004 0.000 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00246 (24223) covalent geometry : angle 0.57298 (32813) hydrogen bonds : bond 0.03285 ( 1027) hydrogen bonds : angle 4.07867 ( 2865) metal coordination : bond 0.00422 ( 8) metal coordination : angle 3.42924 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3682.16 seconds wall clock time: 64 minutes 31.70 seconds (3871.70 seconds total)