Starting phenix.real_space_refine on Sat Jul 4 13:16:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lvv_23543/07_2026/7lvv_23543.cif" } resolution = 3.25 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= 0.050 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 Ca 4 9.91 5 P 110 5.49 5 S 44 5.16 5 C 12960 2.51 5 N 3709 2.21 5 O 4193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21020 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8216 Classifications: {'peptide': 1011} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 969} Chain breaks: 2 Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8219 Classifications: {'peptide': 1012} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 970} Chain breaks: 2 Chain: "C" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "D" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1149 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "E" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.82, per 1000 atoms: 0.23 Number of scatterers: 21020 At special positions: 0 Unit cell: (106.72, 107.88, 203, 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) Ca 4 19.99 S 44 16.00 P 110 15.00 O 4193 8.00 N 3709 7.00 C 12960 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: 1.80 Conformation dependent library (CDL) restraints added in 847.0 milliseconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4372 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 18 sheets defined 50.0% alpha, 8.3% beta 48 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.523A pdb=" N ARG A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.703A pdb=" N GLY A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.900A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.644A pdb=" N LEU A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 167 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.876A pdb=" N ASP A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 222 removed outlier: 3.582A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.859A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 243 removed outlier: 4.226A pdb=" N LEU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 274 through 292 removed outlier: 4.177A pdb=" N ARG A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.576A pdb=" N ARG A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.530A pdb=" N VAL A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 removed outlier: 3.699A pdb=" N GLU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 374 through 393 removed outlier: 3.533A pdb=" N TYR A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 440 Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.585A pdb=" N ARG A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.585A pdb=" N LYS A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.699A pdb=" N LYS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.569A pdb=" N THR A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 646 through 651' Processing helix chain 'A' and resid 674 through 678 removed outlier: 3.531A pdb=" N VAL A 678 " --> pdb=" O ASP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 703 removed outlier: 3.571A pdb=" N LEU A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'A' and resid 827 through 838 Processing helix chain 'A' and resid 844 through 858 Processing helix chain 'A' and resid 858 through 865 removed outlier: 3.719A pdb=" N ARG A 862 " --> pdb=" O HIS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 870 removed outlier: 3.543A pdb=" N LEU A 869 " --> pdb=" O TYR A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 898 Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 968 through 976 Processing helix chain 'A' and resid 985 through 991 removed outlier: 3.839A pdb=" N LYS A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 991 " --> pdb=" O ILE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1024 removed outlier: 3.722A pdb=" N MET A1024 " --> pdb=" O ILE A1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 19 removed outlier: 3.523A pdb=" N PHE B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 14 " --> pdb=" O GLN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.952A pdb=" N GLY B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 4.094A pdb=" N ASN B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 97 removed outlier: 3.880A pdb=" N GLN B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 144 through 176 removed outlier: 3.779A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 178 through 197 Processing helix chain 'B' and resid 201 through 220 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.589A pdb=" N LYS B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 292 removed outlier: 3.843A pdb=" N LYS B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 280 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 307 through 326 removed outlier: 3.535A pdb=" N LYS B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.265A pdb=" N GLN B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 387 removed outlier: 3.513A pdb=" N TYR B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 427 through 439 Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.989A pdb=" N ASN B 461 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 477 removed outlier: 3.702A pdb=" N ARG B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 491 through 504 removed outlier: 3.640A pdb=" N ARG B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.570A pdb=" N ARG B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 611 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 646 through 652 removed outlier: 3.566A pdb=" N THR B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 684 through 702 removed outlier: 3.518A pdb=" N ASP B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 710 Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 765 through 769 Processing helix chain 'B' and resid 770 through 774 Processing helix chain 'B' and resid 802 through 805 removed outlier: 4.156A pdb=" N LEU B 805 " --> pdb=" O LEU B 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 802 through 805' Processing helix chain 'B' and resid 827 through 838 Processing helix chain 'B' and resid 844 through 856 Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 881 through 898 removed outlier: 3.835A pdb=" N TRP B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 889 " --> pdb=" O TRP B 885 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 890 " --> pdb=" O ALA B 886 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 924 Processing helix chain 'B' and resid 968 through 977 Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 995 through 998 Processing helix chain 'B' and resid 999 through 1024 removed outlier: 3.562A pdb=" N ILE B1004 " --> pdb=" O LYS B1000 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B1005 " --> pdb=" O GLU B1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.510A pdb=" N ALA C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 43 removed outlier: 4.786A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 96 removed outlier: 3.685A pdb=" N GLU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.724A pdb=" N ILE D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.691A pdb=" N GLY D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 43 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 98 removed outlier: 3.705A pdb=" N GLY D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.483A pdb=" N GLY A 76 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ILE A 105 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR A 77 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU A 107 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU A 79 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 104 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 336 through 338 removed outlier: 6.342A pdb=" N GLU A 336 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 445 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 338 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY A 447 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA A 511 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 445 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL A 513 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY A 447 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N ASN A 515 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 510 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 538 " --> pdb=" O TRP A 591 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 667 through 668 removed outlier: 3.655A pdb=" N GLN A 809 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 740 through 744 Processing sheet with id=AA5, first strand: chain 'A' and resid 908 through 909 removed outlier: 7.676A pdb=" N GLN A 933 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA A 943 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 931 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 49 removed outlier: 3.541A pdb=" N GLY B 76 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 104 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 368 through 370 removed outlier: 6.434A pdb=" N ILE B 337 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU B 336 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE B 445 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 338 " --> pdb=" O ILE B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 508 through 514 removed outlier: 6.112A pdb=" N ILE B 538 " --> pdb=" O TRP B 591 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS B 593 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE B 540 " --> pdb=" O HIS B 593 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 667 through 668 Processing sheet with id=AB1, first strand: chain 'B' and resid 679 through 680 removed outlier: 10.820A pdb=" N LEU B 799 " --> pdb=" O ILE B 740 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 814 through 816 Processing sheet with id=AB3, first strand: chain 'B' and resid 908 through 911 removed outlier: 6.999A pdb=" N THR B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 48 through 49 removed outlier: 4.151A pdb=" N ILE C 48 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AB7, first strand: chain 'C' and resid 77 through 80 removed outlier: 6.372A pdb=" N ALA C 112 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG C 123 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU C 114 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 48 removed outlier: 3.810A pdb=" N ILE D 48 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.628A pdb=" N GLU D 107 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU D 114 " --> pdb=" O GLN D 122 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN D 122 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN D 116 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3415 1.31 - 1.44: 6258 1.44 - 1.57: 11709 1.57 - 1.70: 213 1.70 - 1.83: 86 Bond restraints: 21681 Sorted by residual: bond pdb=" C ASN A 712 " pdb=" N TRP A 713 " ideal model delta sigma weight residual 1.332 1.247 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" C SER B 844 " pdb=" N ARG B 845 " ideal model delta sigma weight residual 1.335 1.263 0.072 1.25e-02 6.40e+03 3.31e+01 bond pdb=" C VAL A 741 " pdb=" N PRO A 742 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.20e-02 6.94e+03 3.02e+01 bond pdb=" C LYS A 702 " pdb=" N LEU A 703 " ideal model delta sigma weight residual 1.328 1.405 -0.077 1.44e-02 4.82e+03 2.85e+01 bond pdb=" C PRO B 144 " pdb=" O PRO B 144 " ideal model delta sigma weight residual 1.240 1.182 0.058 1.12e-02 7.97e+03 2.69e+01 ... (remaining 21676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 25167 2.43 - 4.85: 4074 4.85 - 7.28: 445 7.28 - 9.71: 67 9.71 - 12.13: 18 Bond angle restraints: 29771 Sorted by residual: angle pdb=" N ILE A 987 " pdb=" CA ILE A 987 " pdb=" C ILE A 987 " ideal model delta sigma weight residual 113.47 104.56 8.91 1.01e+00 9.80e-01 7.79e+01 angle pdb=" N GLU B 299 " pdb=" CA GLU B 299 " pdb=" C GLU B 299 " ideal model delta sigma weight residual 114.04 103.10 10.94 1.24e+00 6.50e-01 7.78e+01 angle pdb=" N GLN B 728 " pdb=" CA GLN B 728 " pdb=" C GLN B 728 " ideal model delta sigma weight residual 112.72 102.92 9.80 1.14e+00 7.69e-01 7.40e+01 angle pdb=" N ARG A 929 " pdb=" CA ARG A 929 " pdb=" C ARG A 929 " ideal model delta sigma weight residual 112.97 104.07 8.90 1.06e+00 8.90e-01 7.04e+01 angle pdb=" C LYS A 486 " pdb=" N THR A 487 " pdb=" CA THR A 487 " ideal model delta sigma weight residual 123.07 110.94 12.13 1.46e+00 4.69e-01 6.91e+01 ... (remaining 29766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 11238 32.96 - 65.91: 1441 65.91 - 98.87: 59 98.87 - 131.83: 1 131.83 - 164.78: 2 Dihedral angle restraints: 12741 sinusoidal: 5969 harmonic: 6772 Sorted by residual: dihedral pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CA ASP C 69 " pdb=" CB ASP C 69 " ideal model delta harmonic sigma weight residual 122.80 140.99 -18.19 0 2.50e+00 1.60e-01 5.29e+01 dihedral pdb=" C ASP C 69 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " pdb=" CB ASP C 69 " ideal model delta harmonic sigma weight residual -122.60 -139.94 17.34 0 2.50e+00 1.60e-01 4.81e+01 dihedral pdb=" C GLN B 33 " pdb=" N GLN B 33 " pdb=" CA GLN B 33 " pdb=" CB GLN B 33 " ideal model delta harmonic sigma weight residual -122.60 -107.31 -15.29 0 2.50e+00 1.60e-01 3.74e+01 ... (remaining 12738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2578 0.149 - 0.298: 604 0.298 - 0.448: 30 0.448 - 0.597: 2 0.597 - 0.746: 1 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CA ASP C 69 " pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CB ASP C 69 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C3' DC E 19 " pdb=" C4' DC E 19 " pdb=" O3' DC E 19 " pdb=" C2' DC E 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" C3' DG H 3 " pdb=" C4' DG H 3 " pdb=" O3' DG H 3 " pdb=" C2' DG H 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.27 -0.46 2.00e-01 2.50e+01 5.23e+00 ... (remaining 3212 not shown) Planarity restraints: 3504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 926 " -0.027 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C LYS B 926 " 0.098 2.00e-02 2.50e+03 pdb=" O LYS B 926 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS B 927 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 646 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C ALA B 646 " -0.094 2.00e-02 2.50e+03 pdb=" O ALA B 646 " 0.036 2.00e-02 2.50e+03 pdb=" N ASP B 647 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 43 " 0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C SER D 43 " -0.092 2.00e-02 2.50e+03 pdb=" O SER D 43 " 0.034 2.00e-02 2.50e+03 pdb=" N GLY D 44 " 0.032 2.00e-02 2.50e+03 ... (remaining 3501 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 28 2.34 - 2.98: 10791 2.98 - 3.62: 30911 3.62 - 4.26: 55284 4.26 - 4.90: 84529 Nonbonded interactions: 181543 Sorted by model distance: nonbonded pdb=" OE2 GLU D 25 " pdb="CA CA D1101 " model vdw 1.705 2.510 nonbonded pdb=" OD1 ASP B 64 " pdb="CA CA B1102 " model vdw 1.754 2.510 nonbonded pdb=" OP1 DG F 9 " pdb="CA CA C1101 " model vdw 1.874 2.510 nonbonded pdb=" OP1 DG H 9 " pdb="CA CA D1101 " model vdw 2.036 2.510 nonbonded pdb=" OD1 ASP D 69 " pdb=" N SER D 70 " model vdw 2.074 3.120 ... (remaining 181538 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 2 through 578 or resid 587 through 1102)) selection = (chain 'B' and (resid 2 through 411 or resid 422 through 1102)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 2 through 144 or resid 1101)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.880 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.012 0.085 21681 Z= 0.926 Angle : 1.782 12.133 29771 Z= 1.306 Chirality : 0.118 0.746 3215 Planarity : 0.007 0.080 3504 Dihedral : 23.475 164.782 8369 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 1.31 % Allowed : 10.32 % Favored : 88.37 % Rotamer: Outliers : 13.97 % Allowed : 16.78 % Favored : 69.25 % Cbeta Deviations : 1.46 % Peptide Plane: Cis-proline : 2.25 % 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: -4.96 (0.13), residues: 2296 helix: -3.06 (0.12), residues: 1029 sheet: -3.38 (0.35), residues: 138 loop : -3.53 (0.14), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 12 TYR 0.037 0.003 TYR A 573 PHE 0.028 0.003 PHE A 326 TRP 0.021 0.003 TRP B 39 HIS 0.012 0.002 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.93 (21681) covalent geometry : angle 1.78225 / 1.31 (29771) hydrogen bonds : bond 0.20943 / 13.95 ( 917) hydrogen bonds : angle 9.21543 / 6.52 ( 2487) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 507 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7358 (mmt90) REVERT: A 52 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8045 (t) REVERT: A 185 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8446 (tmm-80) REVERT: A 237 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8177 (tp-100) REVERT: A 366 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6972 (pp20) REVERT: A 451 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: A 629 TRP cc_start: 0.8505 (m-10) cc_final: 0.8171 (m-10) REVERT: A 641 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.4805 (mm-30) REVERT: A 1024 MET cc_start: 0.8023 (mtt) cc_final: 0.7531 (mtm) REVERT: B 188 PHE cc_start: 0.7504 (t80) cc_final: 0.7285 (t80) REVERT: B 246 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: B 319 ASP cc_start: 0.8007 (t0) cc_final: 0.7370 (t0) REVERT: B 328 LYS cc_start: 0.8652 (mttt) cc_final: 0.7481 (mmtm) REVERT: B 472 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7578 (tmm160) REVERT: B 512 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8228 (m-10) REVERT: B 649 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: B 713 TRP cc_start: 0.6846 (p-90) cc_final: 0.6608 (p-90) REVERT: B 792 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: B 831 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8832 (tt) REVERT: B 857 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8385 (m90) REVERT: B 876 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8836 (mp) REVERT: B 983 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9091 (mmtm) REVERT: B 986 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9253 (p) REVERT: C 25 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: C 86 THR cc_start: 0.8651 (m) cc_final: 0.8390 (p) REVERT: D 88 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8137 (t70) REVERT: D 94 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5429 (mmtm) REVERT: D 132 LEU cc_start: 0.7770 (tp) cc_final: 0.7562 (tp) outliers start: 274 outliers final: 32 residues processed: 713 average time/residue: 0.2024 time to fit residues: 204.5606 Evaluate side-chains 293 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 983 LYS Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN A 212 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 325 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 464 ASN A 673 ASN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 116 GLN B 212 HIS B 229 HIS B 232 ASN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 448 ASN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN B 824 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 10 GLN D 59 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.092517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.074168 restraints weight = 66355.096| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.85 r_work: 0.3137 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 21681 Z= 0.254 Angle : 0.829 9.135 29771 Z= 0.449 Chirality : 0.052 0.285 3215 Planarity : 0.006 0.076 3504 Dihedral : 23.371 162.420 3838 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 4.79 % Allowed : 22.03 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -3.19 (0.15), residues: 2296 helix: -1.39 (0.14), residues: 1069 sheet: -2.65 (0.33), residues: 194 loop : -2.77 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 46 TYR 0.026 0.002 TYR A 814 PHE 0.036 0.003 PHE B 882 TRP 0.014 0.002 TRP C 39 HIS 0.011 0.002 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (21681) covalent geometry : angle 0.82943 / 0.45 (29771) hydrogen bonds : bond 0.06967 / 4.60 ( 917) hydrogen bonds : angle 5.56026 / 3.92 ( 2487) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 252 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.4440 (OUTLIER) cc_final: 0.4004 (ttp-110) REVERT: A 34 GLN cc_start: 0.7738 (tt0) cc_final: 0.7475 (mt0) REVERT: A 185 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8186 (tmm-80) REVERT: A 291 ARG cc_start: 0.8824 (mtt-85) cc_final: 0.8487 (mtt-85) REVERT: A 488 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7656 (mtpt) REVERT: A 719 MET cc_start: 0.9254 (mmm) cc_final: 0.8855 (mmm) REVERT: A 766 MET cc_start: 0.9108 (tpp) cc_final: 0.8871 (tpp) REVERT: A 793 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8122 (p) REVERT: A 1029 MET cc_start: 0.6612 (tpt) cc_final: 0.6393 (tpt) REVERT: B 19 TYR cc_start: 0.8230 (m-10) cc_final: 0.7987 (m-80) REVERT: B 70 SER cc_start: 0.8746 (m) cc_final: 0.8526 (t) REVERT: B 188 PHE cc_start: 0.8134 (t80) cc_final: 0.7524 (t80) REVERT: B 245 PHE cc_start: 0.7848 (p90) cc_final: 0.7551 (p90) REVERT: B 246 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7197 (m-10) REVERT: B 259 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7726 (pttm) REVERT: B 282 LEU cc_start: 0.9475 (mt) cc_final: 0.9250 (mt) REVERT: B 312 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7689 (mtm-85) REVERT: B 498 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8606 (tpp-160) REVERT: B 512 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: B 570 VAL cc_start: 0.8466 (t) cc_final: 0.8242 (m) REVERT: B 648 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8942 (pttt) REVERT: B 664 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7880 (tptp) REVERT: B 719 MET cc_start: 0.9286 (mtp) cc_final: 0.8416 (mmm) REVERT: B 762 MET cc_start: 0.9082 (mmm) cc_final: 0.8796 (mmt) REVERT: B 806 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: B 810 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8704 (p) REVERT: B 912 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6118 (mp0) REVERT: B 983 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8940 (mmtm) REVERT: C 46 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7543 (mmt180) REVERT: C 93 LYS cc_start: 0.9169 (mttt) cc_final: 0.8875 (mtmm) REVERT: C 115 MET cc_start: 0.8727 (mmm) cc_final: 0.8454 (tpp) REVERT: C 123 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7916 (ttm-80) REVERT: C 141 GLU cc_start: 0.8045 (pp20) cc_final: 0.7759 (pp20) REVERT: C 143 GLU cc_start: 0.7906 (pm20) cc_final: 0.7644 (pp20) REVERT: D 90 GLU cc_start: 0.5478 (mm-30) cc_final: 0.5146 (tp30) REVERT: D 136 LEU cc_start: 0.6912 (mt) cc_final: 0.6638 (pp) outliers start: 94 outliers final: 43 residues processed: 334 average time/residue: 0.1600 time to fit residues: 79.6258 Evaluate side-chains 257 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 983 LYS Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.4980 chunk 169 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 232 ASN A 271 GLN A 275 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 233 ASN B 537 HIS B 563 ASN B 620 HIS B 763 GLN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.073262 restraints weight = 66736.750| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.85 r_work: 0.3111 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21681 Z= 0.177 Angle : 0.701 10.682 29771 Z= 0.377 Chirality : 0.047 0.251 3215 Planarity : 0.005 0.056 3504 Dihedral : 22.798 160.761 3779 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 4.03 % Allowed : 20.91 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.16), residues: 2296 helix: -0.54 (0.15), residues: 1057 sheet: -1.90 (0.38), residues: 173 loop : -2.42 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 260 TYR 0.030 0.002 TYR B 262 PHE 0.035 0.002 PHE D 140 TRP 0.017 0.001 TRP D 39 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (21681) covalent geometry : angle 0.70065 / 0.38 (29771) hydrogen bonds : bond 0.05349 / 3.51 ( 917) hydrogen bonds : angle 4.91431 / 3.47 ( 2487) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 218 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8284 (tmm-80) REVERT: A 451 TYR cc_start: 0.8873 (m-10) cc_final: 0.8616 (m-80) REVERT: A 719 MET cc_start: 0.9223 (mmm) cc_final: 0.8592 (mmm) REVERT: A 753 MET cc_start: 0.7938 (ttm) cc_final: 0.7641 (ttm) REVERT: A 766 MET cc_start: 0.9165 (tpp) cc_final: 0.8741 (tpp) REVERT: A 1029 MET cc_start: 0.6820 (tpt) cc_final: 0.6574 (tpt) REVERT: B 11 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8764 (ttpt) REVERT: B 19 TYR cc_start: 0.8215 (m-10) cc_final: 0.7920 (m-80) REVERT: B 126 MET cc_start: 0.8529 (mmm) cc_final: 0.8250 (mmm) REVERT: B 146 GLN cc_start: 0.8518 (pm20) cc_final: 0.8303 (pm20) REVERT: B 152 LYS cc_start: 0.9266 (mmmt) cc_final: 0.9007 (mmmt) REVERT: B 158 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8778 (ptpp) REVERT: B 232 ASN cc_start: 0.8286 (t0) cc_final: 0.8067 (t0) REVERT: B 245 PHE cc_start: 0.7905 (p90) cc_final: 0.7224 (p90) REVERT: B 246 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: B 259 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7738 (pttm) REVERT: B 282 LEU cc_start: 0.9490 (mt) cc_final: 0.9218 (mt) REVERT: B 648 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8893 (pttt) REVERT: B 649 ASP cc_start: 0.9296 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: B 664 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8102 (tptp) REVERT: B 719 MET cc_start: 0.9116 (mtp) cc_final: 0.8454 (mmm) REVERT: B 912 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6011 (mp0) REVERT: C 50 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: C 51 VAL cc_start: 0.9240 (t) cc_final: 0.9033 (p) REVERT: C 85 ASP cc_start: 0.7393 (t0) cc_final: 0.6851 (t0) REVERT: C 90 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9012 (mm-30) REVERT: C 93 LYS cc_start: 0.9164 (mttt) cc_final: 0.8839 (mtmm) REVERT: C 102 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8387 (p0) REVERT: C 103 ASN cc_start: 0.8355 (t0) cc_final: 0.7646 (p0) REVERT: C 115 MET cc_start: 0.8767 (mmm) cc_final: 0.8536 (tpp) REVERT: C 123 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7960 (ttm-80) REVERT: C 141 GLU cc_start: 0.8046 (pp20) cc_final: 0.7801 (pp20) REVERT: D 3 LEU cc_start: 0.8403 (pt) cc_final: 0.8185 (mt) REVERT: D 90 GLU cc_start: 0.5050 (mm-30) cc_final: 0.4793 (tp30) REVERT: D 136 LEU cc_start: 0.6997 (mt) cc_final: 0.6756 (pp) outliers start: 79 outliers final: 41 residues processed: 280 average time/residue: 0.1780 time to fit residues: 75.6791 Evaluate side-chains 223 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 875 ARG Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 80 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS A 275 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 34 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071965 restraints weight = 65848.546| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.76 r_work: 0.3092 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21681 Z= 0.149 Angle : 0.641 9.251 29771 Z= 0.344 Chirality : 0.045 0.312 3215 Planarity : 0.005 0.056 3504 Dihedral : 22.358 169.075 3759 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 3.77 % Allowed : 21.16 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.17), residues: 2296 helix: -0.17 (0.15), residues: 1066 sheet: -1.62 (0.35), residues: 199 loop : -2.20 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 365 TYR 0.024 0.001 TYR B 261 PHE 0.027 0.002 PHE B 188 TRP 0.013 0.001 TRP D 39 HIS 0.010 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (21681) covalent geometry : angle 0.64085 / 0.34 (29771) hydrogen bonds : bond 0.04769 / 3.14 ( 917) hydrogen bonds : angle 4.62332 / 3.25 ( 2487) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 191 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8281 (tmm-80) REVERT: A 316 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7954 (pp20) REVERT: A 393 MET cc_start: 0.8461 (tpp) cc_final: 0.8063 (tpp) REVERT: A 451 TYR cc_start: 0.8812 (m-10) cc_final: 0.8575 (m-80) REVERT: A 688 ASP cc_start: 0.8812 (m-30) cc_final: 0.8410 (m-30) REVERT: A 719 MET cc_start: 0.9217 (mmm) cc_final: 0.9016 (mmm) REVERT: A 766 MET cc_start: 0.9172 (tpp) cc_final: 0.8756 (tpp) REVERT: A 1024 MET cc_start: 0.8474 (mtm) cc_final: 0.7794 (mtm) REVERT: A 1029 MET cc_start: 0.6901 (tpt) cc_final: 0.6658 (tpt) REVERT: B 11 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8861 (ttpt) REVERT: B 19 TYR cc_start: 0.8265 (m-10) cc_final: 0.8019 (m-10) REVERT: B 126 MET cc_start: 0.8555 (mmm) cc_final: 0.8206 (mmm) REVERT: B 138 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8690 (tt) REVERT: B 152 LYS cc_start: 0.9281 (mmmt) cc_final: 0.9042 (mmmt) REVERT: B 246 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: B 259 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7871 (pttm) REVERT: B 282 LEU cc_start: 0.9511 (mt) cc_final: 0.9258 (mt) REVERT: B 648 LYS cc_start: 0.9287 (mtmt) cc_final: 0.9002 (pttt) REVERT: B 649 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: B 664 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8091 (tptp) REVERT: B 719 MET cc_start: 0.9153 (mtp) cc_final: 0.8394 (mmm) REVERT: B 762 MET cc_start: 0.9209 (mmm) cc_final: 0.8886 (mmt) REVERT: B 806 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: B 912 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6070 (mp0) REVERT: C 7 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8235 (ptpp) REVERT: C 8 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8100 (ttmm) REVERT: C 93 LYS cc_start: 0.9235 (mttt) cc_final: 0.8857 (mtmm) REVERT: C 102 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8509 (p0) REVERT: C 115 MET cc_start: 0.8789 (mmm) cc_final: 0.8586 (tpp) REVERT: C 120 GLU cc_start: 0.8223 (tt0) cc_final: 0.7923 (tt0) REVERT: C 141 GLU cc_start: 0.8005 (pp20) cc_final: 0.7799 (pp20) REVERT: D 90 GLU cc_start: 0.5075 (mm-30) cc_final: 0.4811 (tp30) REVERT: D 136 LEU cc_start: 0.6802 (mt) cc_final: 0.6371 (pp) outliers start: 74 outliers final: 35 residues processed: 249 average time/residue: 0.1715 time to fit residues: 65.4928 Evaluate side-chains 208 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN B 758 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN D 24 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.088772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070540 restraints weight = 65947.398| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.80 r_work: 0.3062 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21681 Z= 0.160 Angle : 0.614 9.641 29771 Z= 0.330 Chirality : 0.044 0.367 3215 Planarity : 0.004 0.057 3504 Dihedral : 22.130 174.180 3753 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 3.82 % Allowed : 21.32 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.17), residues: 2296 helix: 0.12 (0.16), residues: 1063 sheet: -1.52 (0.33), residues: 213 loop : -2.00 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 123 TYR 0.013 0.001 TYR A 592 PHE 0.020 0.002 PHE A 281 TRP 0.008 0.001 TRP B 713 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (21681) covalent geometry : angle 0.61395 / 0.33 (29771) hydrogen bonds : bond 0.04516 / 2.98 ( 917) hydrogen bonds : angle 4.46970 / 3.12 ( 2487) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 177 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8322 (tmm-80) REVERT: A 316 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7851 (pp20) REVERT: A 719 MET cc_start: 0.9210 (mmm) cc_final: 0.8990 (mmm) REVERT: A 1029 MET cc_start: 0.7100 (tpt) cc_final: 0.6701 (tpp) REVERT: B 19 TYR cc_start: 0.8315 (m-10) cc_final: 0.8082 (m-10) REVERT: B 126 MET cc_start: 0.8481 (mmm) cc_final: 0.8239 (mmm) REVERT: B 138 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8714 (tt) REVERT: B 152 LYS cc_start: 0.9279 (mmmt) cc_final: 0.9021 (mmmt) REVERT: B 245 PHE cc_start: 0.7376 (p90) cc_final: 0.7131 (p90) REVERT: B 246 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7960 (m-10) REVERT: B 282 LEU cc_start: 0.9529 (mt) cc_final: 0.9317 (mt) REVERT: B 366 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: B 649 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: B 664 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7767 (tptp) REVERT: B 719 MET cc_start: 0.9134 (mtp) cc_final: 0.8324 (mmm) REVERT: B 806 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: C 7 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8450 (ptpp) REVERT: C 8 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8265 (ttmm) REVERT: C 89 ASP cc_start: 0.9365 (m-30) cc_final: 0.9119 (p0) REVERT: C 90 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8990 (mm-30) REVERT: C 93 LYS cc_start: 0.9276 (mttt) cc_final: 0.8913 (mtmm) REVERT: C 102 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8408 (p0) REVERT: C 116 GLN cc_start: 0.7760 (mt0) cc_final: 0.7442 (mt0) REVERT: C 141 GLU cc_start: 0.8125 (pp20) cc_final: 0.7824 (pp20) REVERT: D 114 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5433 (mp) REVERT: D 115 MET cc_start: 0.1499 (tpt) cc_final: 0.1042 (tpt) REVERT: D 120 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7367 (tp30) REVERT: D 136 LEU cc_start: 0.6900 (mt) cc_final: 0.6496 (pp) outliers start: 75 outliers final: 37 residues processed: 237 average time/residue: 0.1687 time to fit residues: 61.7765 Evaluate side-chains 208 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 223 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS B 362 GLN B 858 HIS ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 103 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.089581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071266 restraints weight = 65728.083| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.81 r_work: 0.3070 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21681 Z= 0.124 Angle : 0.583 11.437 29771 Z= 0.313 Chirality : 0.042 0.355 3215 Planarity : 0.004 0.057 3504 Dihedral : 21.978 176.362 3748 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 3.31 % Allowed : 21.42 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2296 helix: 0.36 (0.16), residues: 1069 sheet: -1.19 (0.35), residues: 199 loop : -1.91 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 123 TYR 0.011 0.001 TYR B 962 PHE 0.014 0.001 PHE B 289 TRP 0.014 0.001 TRP B 888 HIS 0.009 0.001 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (21681) covalent geometry : angle 0.58349 / 0.31 (29771) hydrogen bonds : bond 0.04068 / 2.70 ( 917) hydrogen bonds : angle 4.31636 / 3.03 ( 2487) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 182 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8351 (tmm-80) REVERT: A 275 HIS cc_start: 0.7720 (t70) cc_final: 0.7279 (t-90) REVERT: A 279 GLN cc_start: 0.8586 (pt0) cc_final: 0.8329 (pt0) REVERT: A 393 MET cc_start: 0.8474 (tpp) cc_final: 0.8015 (tpp) REVERT: A 719 MET cc_start: 0.9213 (mmm) cc_final: 0.8992 (mmm) REVERT: A 895 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 978 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8824 (mttt) REVERT: A 1029 MET cc_start: 0.7200 (tpt) cc_final: 0.6647 (tpt) REVERT: B 126 MET cc_start: 0.8539 (mmm) cc_final: 0.8290 (mmm) REVERT: B 152 LYS cc_start: 0.9285 (mmmt) cc_final: 0.9038 (mmmt) REVERT: B 245 PHE cc_start: 0.7213 (p90) cc_final: 0.6979 (p90) REVERT: B 246 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: B 323 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8522 (mm-30) REVERT: B 362 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7717 (tp-100) REVERT: B 366 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: B 649 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: B 664 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8261 (tptp) REVERT: B 719 MET cc_start: 0.9103 (mtp) cc_final: 0.8345 (mmm) REVERT: B 762 MET cc_start: 0.9222 (mmm) cc_final: 0.8860 (mmt) REVERT: C 8 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8285 (ttmm) REVERT: C 50 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: C 69 ASP cc_start: 0.7366 (t70) cc_final: 0.6791 (t0) REVERT: C 73 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7913 (tm-30) REVERT: C 102 ASP cc_start: 0.8867 (m-30) cc_final: 0.8525 (p0) REVERT: C 107 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7432 (pp20) REVERT: C 119 GLU cc_start: 0.9132 (mp0) cc_final: 0.8895 (pm20) REVERT: C 141 GLU cc_start: 0.8210 (pp20) cc_final: 0.7927 (pp20) REVERT: D 114 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5647 (mp) REVERT: D 115 MET cc_start: 0.2442 (tpt) cc_final: 0.1640 (tpt) REVERT: D 120 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7461 (tp30) outliers start: 65 outliers final: 34 residues processed: 231 average time/residue: 0.1733 time to fit residues: 61.2662 Evaluate side-chains 212 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 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 = 0.3609 r_free = 0.3609 target = 0.089274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.071088 restraints weight = 66642.272| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.81 r_work: 0.3069 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21681 Z= 0.138 Angle : 0.610 13.119 29771 Z= 0.321 Chirality : 0.043 0.313 3215 Planarity : 0.004 0.057 3504 Dihedral : 21.931 177.262 3746 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 2.91 % Allowed : 21.88 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2296 helix: 0.45 (0.16), residues: 1067 sheet: -1.12 (0.34), residues: 210 loop : -1.79 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 123 TYR 0.011 0.001 TYR B 861 PHE 0.014 0.001 PHE A 326 TRP 0.006 0.001 TRP B 499 HIS 0.017 0.001 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (21681) covalent geometry : angle 0.61030 / 0.32 (29771) hydrogen bonds : bond 0.04095 / 2.71 ( 917) hydrogen bonds : angle 4.30042 / 3.02 ( 2487) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7985 (ttm170) REVERT: A 275 HIS cc_start: 0.7733 (t70) cc_final: 0.7203 (t-90) REVERT: A 279 GLN cc_start: 0.8572 (pt0) cc_final: 0.8306 (pt0) REVERT: A 326 PHE cc_start: 0.7282 (m-80) cc_final: 0.7082 (m-10) REVERT: A 393 MET cc_start: 0.8533 (tpp) cc_final: 0.7833 (tmm) REVERT: A 719 MET cc_start: 0.9215 (mmm) cc_final: 0.8967 (mmm) REVERT: A 766 MET cc_start: 0.9067 (tpp) cc_final: 0.8312 (mpp) REVERT: A 895 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 978 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8832 (mttt) REVERT: A 1029 MET cc_start: 0.7262 (tpt) cc_final: 0.6776 (tpt) REVERT: B 126 MET cc_start: 0.8487 (mmm) cc_final: 0.8228 (mmm) REVERT: B 152 LYS cc_start: 0.9291 (mmmt) cc_final: 0.9050 (mmmt) REVERT: B 245 PHE cc_start: 0.7391 (p90) cc_final: 0.7165 (p90) REVERT: B 246 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8069 (m-10) REVERT: B 323 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8483 (mm-30) REVERT: B 649 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8745 (m-30) REVERT: B 719 MET cc_start: 0.9135 (mtp) cc_final: 0.8323 (mmm) REVERT: B 762 MET cc_start: 0.9170 (mmm) cc_final: 0.8832 (mmt) REVERT: B 806 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: C 8 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8230 (ttmm) REVERT: C 50 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: C 69 ASP cc_start: 0.7368 (t70) cc_final: 0.6738 (t0) REVERT: C 73 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 90 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9078 (mm-30) REVERT: C 102 ASP cc_start: 0.8874 (m-30) cc_final: 0.8531 (p0) REVERT: C 141 GLU cc_start: 0.8223 (pp20) cc_final: 0.7925 (pp20) REVERT: D 114 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5713 (mp) REVERT: D 115 MET cc_start: 0.2032 (tpt) cc_final: 0.1337 (tpt) REVERT: D 120 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7405 (tp30) outliers start: 57 outliers final: 35 residues processed: 226 average time/residue: 0.1716 time to fit residues: 58.9719 Evaluate side-chains 210 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 175 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 362 GLN ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.088037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069628 restraints weight = 66059.318| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.78 r_work: 0.3038 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21681 Z= 0.159 Angle : 0.616 10.747 29771 Z= 0.326 Chirality : 0.043 0.272 3215 Planarity : 0.004 0.056 3504 Dihedral : 21.908 178.485 3746 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.75 % Allowed : 22.18 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.84 (0.17), residues: 2296 helix: 0.58 (0.16), residues: 1066 sheet: -0.94 (0.34), residues: 209 loop : -1.70 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 875 TYR 0.013 0.001 TYR B 861 PHE 0.019 0.001 PHE C 139 TRP 0.010 0.001 TRP A 39 HIS 0.011 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (21681) covalent geometry : angle 0.61592 / 0.33 (29771) hydrogen bonds : bond 0.04210 / 2.79 ( 917) hydrogen bonds : angle 4.29038 / 3.00 ( 2487) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8016 (ttm110) REVERT: A 275 HIS cc_start: 0.7605 (t70) cc_final: 0.7058 (t-90) REVERT: A 279 GLN cc_start: 0.8599 (pt0) cc_final: 0.8318 (pt0) REVERT: A 287 GLU cc_start: 0.8986 (tt0) cc_final: 0.8313 (tp30) REVERT: A 326 PHE cc_start: 0.7448 (m-80) cc_final: 0.6661 (m-10) REVERT: A 393 MET cc_start: 0.8610 (tpp) cc_final: 0.7881 (tmm) REVERT: A 895 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 978 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8865 (mttt) REVERT: A 1029 MET cc_start: 0.7348 (tpt) cc_final: 0.7079 (tpp) REVERT: B 152 LYS cc_start: 0.9306 (mmmt) cc_final: 0.9078 (mmmt) REVERT: B 246 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.8135 (m-10) REVERT: B 323 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8502 (mm-30) REVERT: B 362 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8100 (tp40) REVERT: B 649 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8879 (m-30) REVERT: B 719 MET cc_start: 0.9179 (mtp) cc_final: 0.8348 (mmm) REVERT: B 806 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: C 8 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8258 (ttmm) REVERT: C 50 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: C 73 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8021 (tm-30) REVERT: C 102 ASP cc_start: 0.8873 (m-30) cc_final: 0.8559 (p0) REVERT: C 120 GLU cc_start: 0.8232 (tt0) cc_final: 0.7834 (tt0) REVERT: C 123 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8423 (ttm110) REVERT: C 141 GLU cc_start: 0.8240 (pp20) cc_final: 0.7933 (pp20) REVERT: D 114 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5555 (mp) REVERT: D 115 MET cc_start: 0.2380 (tpt) cc_final: 0.1192 (tpt) REVERT: D 120 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7262 (tp30) outliers start: 54 outliers final: 39 residues processed: 218 average time/residue: 0.1765 time to fit residues: 58.5521 Evaluate side-chains 216 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 102 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** D 60 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 = 0.3598 r_free = 0.3598 target = 0.088753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070709 restraints weight = 66329.675| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.74 r_work: 0.3050 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21681 Z= 0.129 Angle : 0.602 11.078 29771 Z= 0.320 Chirality : 0.042 0.265 3215 Planarity : 0.004 0.059 3504 Dihedral : 21.860 179.090 3746 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 2.29 % Allowed : 22.85 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.67 (0.17), residues: 2296 helix: 0.70 (0.16), residues: 1062 sheet: -0.86 (0.35), residues: 214 loop : -1.60 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 123 TYR 0.013 0.001 TYR A 305 PHE 0.020 0.001 PHE B 642 TRP 0.009 0.001 TRP A 39 HIS 0.010 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (21681) covalent geometry : angle 0.60175 / 0.32 (29771) hydrogen bonds : bond 0.04002 / 2.67 ( 917) hydrogen bonds : angle 4.24817 / 2.97 ( 2487) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8011 (ttm110) REVERT: A 275 HIS cc_start: 0.7479 (t70) cc_final: 0.6884 (t-90) REVERT: A 279 GLN cc_start: 0.8571 (pt0) cc_final: 0.8335 (pt0) REVERT: A 287 GLU cc_start: 0.8988 (tt0) cc_final: 0.8425 (tp30) REVERT: A 326 PHE cc_start: 0.7427 (m-80) cc_final: 0.6549 (m-10) REVERT: A 393 MET cc_start: 0.8617 (tpp) cc_final: 0.7928 (tmm) REVERT: A 719 MET cc_start: 0.9227 (mmm) cc_final: 0.8734 (mmm) REVERT: A 766 MET cc_start: 0.9078 (tpp) cc_final: 0.8807 (mmt) REVERT: A 895 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 978 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8844 (mttt) REVERT: A 1029 MET cc_start: 0.7375 (tpt) cc_final: 0.7127 (tpp) REVERT: B 152 LYS cc_start: 0.9307 (mmmt) cc_final: 0.9078 (mmmt) REVERT: B 246 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8165 (m-10) REVERT: B 323 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8483 (mm-30) REVERT: B 649 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8798 (m-30) REVERT: B 719 MET cc_start: 0.9140 (mtp) cc_final: 0.8321 (mmm) REVERT: B 753 MET cc_start: 0.8817 (ppp) cc_final: 0.8308 (ppp) REVERT: B 762 MET cc_start: 0.9151 (mmm) cc_final: 0.8809 (mmt) REVERT: C 8 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8267 (ttmm) REVERT: C 50 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: C 69 ASP cc_start: 0.7743 (t70) cc_final: 0.7326 (t0) REVERT: C 102 ASP cc_start: 0.8906 (m-30) cc_final: 0.8607 (p0) REVERT: C 141 GLU cc_start: 0.8284 (pp20) cc_final: 0.7934 (pp20) REVERT: D 114 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5542 (mp) REVERT: D 115 MET cc_start: 0.2568 (tpt) cc_final: 0.1498 (tpt) REVERT: D 120 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7269 (tp30) outliers start: 45 outliers final: 33 residues processed: 209 average time/residue: 0.1757 time to fit residues: 55.6820 Evaluate side-chains 201 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 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 = 0.3584 r_free = 0.3584 target = 0.088069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070042 restraints weight = 66807.478| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.74 r_work: 0.3042 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21681 Z= 0.148 Angle : 0.611 11.283 29771 Z= 0.324 Chirality : 0.042 0.251 3215 Planarity : 0.004 0.054 3504 Dihedral : 21.821 179.529 3746 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.24 % Allowed : 22.69 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.60 (0.17), residues: 2296 helix: 0.73 (0.16), residues: 1062 sheet: -0.77 (0.35), residues: 216 loop : -1.54 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 123 TYR 0.014 0.001 TYR A 305 PHE 0.018 0.001 PHE C 139 TRP 0.008 0.001 TRP A 39 HIS 0.009 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (21681) covalent geometry : angle 0.61143 / 0.32 (29771) hydrogen bonds : bond 0.04043 / 2.70 ( 917) hydrogen bonds : angle 4.22025 / 2.95 ( 2487) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8248 (tmm-80) REVERT: A 275 HIS cc_start: 0.7517 (t70) cc_final: 0.6869 (t-90) REVERT: A 279 GLN cc_start: 0.8632 (pt0) cc_final: 0.8359 (pt0) REVERT: A 326 PHE cc_start: 0.7118 (m-80) cc_final: 0.6394 (m-10) REVERT: A 393 MET cc_start: 0.8637 (tpp) cc_final: 0.7952 (tmm) REVERT: A 719 MET cc_start: 0.9219 (mmm) cc_final: 0.8787 (mmm) REVERT: A 766 MET cc_start: 0.9123 (tpp) cc_final: 0.8802 (mmt) REVERT: A 978 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8852 (mttt) REVERT: B 152 LYS cc_start: 0.9312 (mmmt) cc_final: 0.9089 (mmmt) REVERT: B 246 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: B 323 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 719 MET cc_start: 0.9144 (mtp) cc_final: 0.8320 (mmm) REVERT: B 753 MET cc_start: 0.8841 (ppp) cc_final: 0.8333 (ppp) REVERT: B 762 MET cc_start: 0.9171 (mmm) cc_final: 0.8848 (mmt) REVERT: C 8 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8307 (ttmm) REVERT: C 73 GLN cc_start: 0.8590 (tm-30) cc_final: 0.7805 (tm-30) REVERT: C 102 ASP cc_start: 0.8955 (m-30) cc_final: 0.8670 (p0) REVERT: C 141 GLU cc_start: 0.8290 (pp20) cc_final: 0.7952 (pp20) REVERT: D 114 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5669 (mp) REVERT: D 115 MET cc_start: 0.2448 (tpt) cc_final: 0.1917 (tpp) REVERT: D 120 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7394 (tp30) outliers start: 44 outliers final: 34 residues processed: 207 average time/residue: 0.1671 time to fit residues: 52.9607 Evaluate side-chains 203 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 86 optimal weight: 0.0370 chunk 219 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 HIS ** D 60 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 = 0.3601 r_free = 0.3601 target = 0.088971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070852 restraints weight = 66833.279| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.79 r_work: 0.3058 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21681 Z= 0.122 Angle : 0.591 11.229 29771 Z= 0.314 Chirality : 0.041 0.240 3215 Planarity : 0.004 0.065 3504 Dihedral : 21.748 179.869 3744 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.94 % Allowed : 23.00 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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 (0.17), residues: 2296 helix: 0.78 (0.16), residues: 1068 sheet: -0.76 (0.34), residues: 225 loop : -1.45 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 123 TYR 0.013 0.001 TYR A 305 PHE 0.018 0.001 PHE C 139 TRP 0.010 0.001 TRP B 888 HIS 0.010 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21681) covalent geometry : angle 0.59138 / 0.31 (29771) hydrogen bonds : bond 0.03770 / 2.53 ( 917) hydrogen bonds : angle 4.16084 / 2.91 ( 2487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5430.31 seconds wall clock time: 94 minutes 8.56 seconds (5648.56 seconds total)