Starting phenix.real_space_refine on Sun Sep 13 05:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lvv_23543/09_2026/7lvv_23543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lvv_23543/09_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_23543/09_2026/7lvv_23543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lvv_23543/09_2026/7lvv_23543.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lvv_23543/09_2026/7lvv_23543.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lvv_23543/09_2026/7lvv_23543.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lvv_23543/09_2026/7lvv_23543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lvv_23543/09_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-2.2.1-6174/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: 5.11, per 1000 atoms: 0.24 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: 1.89 Conformation dependent library (CDL) restraints added in 874.0 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: 2.75 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: 4.26 Time building geometry restraints manager: 2.47 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: 25156 2.43 - 4.85: 4084 4.85 - 7.28: 446 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.600 Find NCS groups from input model: 0.480 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- 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= 0.929 Angle : 1.784 12.133 29771 Z= 1.308 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 1.78373 / 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 : 0.776 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: 0.7359 (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: 0.8445 (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: 0.7841 (m-80) REVERT: A 629 TRP cc_start: 0.8505 (m-10) cc_final: 0.8173 (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: 0.7530 (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: 0.6677 (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: 0.7579 (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: 0.8833 (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: 0.8835 (mp) REVERT: B 983 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9092 (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: 0.8120 (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: 0.7561 (tp) outliers start: 274 outliers final: 32 residues processed: 713 average time/residue: 0.1959 time to fit residues: 198.4173 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 : 0.527 ------------------------------------------------------------------------------- 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: 9.9990 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 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 C 72 GLN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.073978 restraints weight = 66205.466| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.85 r_work: 0.3137 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 21681 Z= 0.260 Angle : 0.848 9.590 29771 Z= 0.454 Chirality : 0.052 0.307 3215 Planarity : 0.006 0.076 3504 Dihedral : 23.281 161.848 3838 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 4.84 % Allowed : 21.72 % Favored : 73.43 % 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: -3.12 (0.15), residues: 2296 helix: -1.31 (0.14), residues: 1067 sheet: -2.60 (0.33), residues: 194 loop : -2.76 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 46 TYR 0.034 0.002 TYR A 814 PHE 0.036 0.003 PHE B 882 TRP 0.016 0.002 TRP C 39 HIS 0.011 0.002 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.26 (21681) covalent geometry : angle 0.84792 / 0.45 (29771) hydrogen bonds : bond 0.06692 / 4.42 ( 917) hydrogen bonds : angle 5.49805 / 3.87 ( 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 350 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 255 time to evaluate : 0.698 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: A 23 ARG cc_start: 0.4417 (OUTLIER) cc_final: 0.3962 (ttp-110) REVERT: A 34 GLN cc_start: 0.7734 (tt0) cc_final: 0.7475 (mt0) REVERT: A 185 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8351 (tmm-80) REVERT: A 291 ARG cc_start: 0.8818 (mtt-85) cc_final: 0.8487 (mtt-85) REVERT: A 372 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8680 (tp30) REVERT: A 488 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7688 (mtpt) REVERT: A 719 MET cc_start: 0.9248 (mmm) cc_final: 0.8890 (mmm) REVERT: A 793 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 1029 MET cc_start: 0.6673 (tpt) cc_final: 0.6456 (tpt) REVERT: B 19 TYR cc_start: 0.8256 (m-10) cc_final: 0.8040 (m-80) REVERT: B 69 ASP cc_start: 0.7035 (p0) cc_final: 0.6747 (p0) REVERT: B 245 PHE cc_start: 0.7924 (p90) cc_final: 0.7613 (p90) REVERT: B 246 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7223 (m-10) REVERT: B 259 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7784 (pttm) REVERT: B 282 LEU cc_start: 0.9477 (mt) cc_final: 0.9252 (mt) REVERT: B 498 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8602 (tpp-160) REVERT: B 512 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8283 (m-10) REVERT: B 648 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8951 (pttt) REVERT: B 664 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7802 (tptp) REVERT: B 719 MET cc_start: 0.9298 (mtp) cc_final: 0.8474 (mmm) REVERT: B 762 MET cc_start: 0.9109 (mmm) cc_final: 0.8813 (mmt) REVERT: B 806 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: B 810 CYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8814 (p) REVERT: B 912 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6143 (mp0) REVERT: B 983 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8923 (mmtm) REVERT: C 69 ASP cc_start: 0.7483 (t0) cc_final: 0.7266 (t70) REVERT: C 93 LYS cc_start: 0.9163 (mttt) cc_final: 0.8869 (mtmm) REVERT: C 115 MET cc_start: 0.8693 (mmm) cc_final: 0.8435 (tpp) REVERT: C 123 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: C 125 ASP cc_start: 0.7567 (t0) cc_final: 0.7347 (t0) REVERT: C 141 GLU cc_start: 0.8037 (pp20) cc_final: 0.7740 (pp20) REVERT: C 143 GLU cc_start: 0.7835 (pm20) cc_final: 0.7552 (pp20) REVERT: D 90 GLU cc_start: 0.5320 (mm-30) cc_final: 0.4981 (tp30) REVERT: D 136 LEU cc_start: 0.6952 (mt) cc_final: 0.6692 (pp) outliers start: 95 outliers final: 44 residues processed: 338 average time/residue: 0.1612 time to fit residues: 81.2134 Evaluate side-chains 245 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 372 GLU 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 893 MET 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 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 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 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: 0.3980 chunk 169 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 59 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.091312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.073073 restraints weight = 66391.447| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.87 r_work: 0.3110 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21681 Z= 0.171 Angle : 0.688 8.915 29771 Z= 0.373 Chirality : 0.047 0.276 3215 Planarity : 0.005 0.058 3504 Dihedral : 22.736 162.948 3778 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 3.62 % Allowed : 21.37 % Favored : 75.01 % 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: -2.30 (0.16), residues: 2296 helix: -0.59 (0.15), residues: 1062 sheet: -1.90 (0.38), residues: 174 loop : -2.46 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 365 TYR 0.020 0.002 TYR B 262 PHE 0.031 0.002 PHE D 140 TRP 0.015 0.001 TRP D 39 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (21681) covalent geometry : angle 0.68810 / 0.37 (29771) hydrogen bonds : bond 0.05404 / 3.54 ( 917) hydrogen bonds : angle 4.93287 / 3.48 ( 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 281 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 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: A 185 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8278 (tmm-80) REVERT: A 393 MET cc_start: 0.8399 (tpp) cc_final: 0.8000 (tpp) REVERT: A 451 TYR cc_start: 0.8987 (m-10) cc_final: 0.8726 (m-80) REVERT: A 719 MET cc_start: 0.9225 (mmm) cc_final: 0.8637 (mmm) REVERT: A 1029 MET cc_start: 0.6820 (tpt) cc_final: 0.6509 (tpt) REVERT: B 19 TYR cc_start: 0.8181 (m-10) cc_final: 0.7932 (m-80) REVERT: B 126 MET cc_start: 0.8437 (mmm) cc_final: 0.8086 (mmm) REVERT: B 146 GLN cc_start: 0.8539 (pm20) cc_final: 0.8325 (pm20) REVERT: B 152 LYS cc_start: 0.9283 (mmmt) cc_final: 0.9027 (mmmt) REVERT: B 158 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8787 (ptpp) REVERT: B 232 ASN cc_start: 0.8271 (t0) cc_final: 0.8058 (t0) REVERT: B 245 PHE cc_start: 0.7885 (p90) cc_final: 0.7184 (p90) REVERT: B 246 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7284 (m-10) REVERT: B 259 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7749 (pttm) REVERT: B 282 LEU cc_start: 0.9482 (mt) cc_final: 0.9187 (mt) REVERT: B 648 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8932 (pttt) REVERT: B 649 ASP cc_start: 0.9273 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: B 664 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8086 (tptp) REVERT: B 719 MET cc_start: 0.9088 (mtp) cc_final: 0.8430 (mmm) REVERT: B 890 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7827 (mpt-90) REVERT: B 912 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6010 (mp0) REVERT: C 90 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8960 (mm-30) REVERT: C 93 LYS cc_start: 0.9184 (mttt) cc_final: 0.8826 (mtmm) REVERT: C 102 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8467 (p0) REVERT: C 115 MET cc_start: 0.8675 (mmm) cc_final: 0.8462 (tpp) REVERT: C 125 ASP cc_start: 0.7407 (t0) cc_final: 0.7153 (t0) REVERT: C 141 GLU cc_start: 0.7911 (pp20) cc_final: 0.7659 (pp20) REVERT: D 3 LEU cc_start: 0.8358 (pt) cc_final: 0.7894 (mt) REVERT: D 4 GLN cc_start: 0.8288 (pm20) cc_final: 0.7904 (pm20) REVERT: D 90 GLU cc_start: 0.5094 (mm-30) cc_final: 0.4839 (tp30) REVERT: D 136 LEU cc_start: 0.7007 (mt) cc_final: 0.6733 (pp) outliers start: 71 outliers final: 37 residues processed: 268 average time/residue: 0.1691 time to fit residues: 68.4678 Evaluate side-chains 211 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 B residue 149 GLU 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 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 890 ARG Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 3 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN 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 = 0.3632 r_free = 0.3632 target = 0.090428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072345 restraints weight = 65650.565| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.77 r_work: 0.3100 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21681 Z= 0.147 Angle : 0.642 9.279 29771 Z= 0.344 Chirality : 0.045 0.286 3215 Planarity : 0.004 0.055 3504 Dihedral : 22.346 170.293 3763 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 3.37 % Allowed : 21.11 % Favored : 75.52 % 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: -1.84 (0.17), residues: 2296 helix: -0.20 (0.16), residues: 1067 sheet: -1.70 (0.36), residues: 192 loop : -2.23 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 75 TYR 0.020 0.001 TYR B 262 PHE 0.017 0.001 PHE B 289 TRP 0.012 0.001 TRP B 713 HIS 0.010 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (21681) covalent geometry : angle 0.64164 / 0.34 (29771) hydrogen bonds : bond 0.04787 / 3.15 ( 917) hydrogen bonds : angle 4.64103 / 3.26 ( 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 247 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 181 time to evaluate : 0.780 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: 0.8668 (OUTLIER) cc_final: 0.8313 (tmm-80) REVERT: A 316 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7989 (pp20) REVERT: A 451 TYR cc_start: 0.8918 (m-10) cc_final: 0.8667 (m-80) REVERT: A 688 ASP cc_start: 0.8738 (m-30) cc_final: 0.8485 (m-30) REVERT: A 766 MET cc_start: 0.9164 (tpp) cc_final: 0.8892 (tpp) REVERT: A 1024 MET cc_start: 0.8544 (mtm) cc_final: 0.7749 (mtm) REVERT: A 1029 MET cc_start: 0.6916 (tpt) cc_final: 0.6667 (tpt) REVERT: B 11 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8853 (ttpt) REVERT: B 126 MET cc_start: 0.8546 (mmm) cc_final: 0.8229 (mmm) REVERT: B 152 LYS cc_start: 0.9285 (mmmt) cc_final: 0.9037 (mmmt) REVERT: B 246 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: B 259 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7889 (pttm) REVERT: B 282 LEU cc_start: 0.9522 (mt) cc_final: 0.9268 (mt) REVERT: B 366 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: B 648 LYS cc_start: 0.9295 (mtmt) cc_final: 0.9047 (pttt) REVERT: B 649 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: B 664 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8110 (tptp) REVERT: B 719 MET cc_start: 0.9116 (mtp) cc_final: 0.8402 (mmm) REVERT: B 753 MET cc_start: 0.8692 (ppp) cc_final: 0.8286 (ppp) REVERT: B 762 MET cc_start: 0.9190 (mmm) cc_final: 0.8880 (mmt) REVERT: B 806 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: B 912 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6068 (mp0) REVERT: C 7 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8234 (ptpp) REVERT: C 8 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8152 (ttmm) REVERT: C 102 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8433 (p0) REVERT: C 115 MET cc_start: 0.8766 (mmm) cc_final: 0.8525 (tpp) REVERT: C 116 GLN cc_start: 0.8432 (mt0) cc_final: 0.7854 (mp10) REVERT: C 125 ASP cc_start: 0.7461 (t0) cc_final: 0.7203 (t0) REVERT: C 142 PHE cc_start: 0.6996 (t80) cc_final: 0.6692 (t80) REVERT: D 120 GLU cc_start: 0.7246 (tm-30) cc_final: 0.7008 (tp30) REVERT: D 136 LEU cc_start: 0.6878 (mt) cc_final: 0.6474 (pp) outliers start: 66 outliers final: 35 residues processed: 233 average time/residue: 0.1588 time to fit residues: 56.3602 Evaluate side-chains 207 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 315 ILE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 455 GLN 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 149 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 523 THR 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 806 GLU Chi-restraints excluded: chain B residue 875 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 565 GLN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.089925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071848 restraints weight = 65766.830| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.79 r_work: 0.3092 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5103 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= 0.138 Angle : 0.604 9.742 29771 Z= 0.325 Chirality : 0.043 0.372 3215 Planarity : 0.004 0.064 3504 Dihedral : 22.050 175.312 3752 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 3.62 % Allowed : 21.21 % Favored : 75.17 % 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: -1.50 (0.17), residues: 2296 helix: 0.06 (0.16), residues: 1073 sheet: -1.59 (0.34), residues: 212 loop : -2.02 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 123 TYR 0.018 0.001 TYR B 19 PHE 0.017 0.001 PHE D 140 TRP 0.009 0.001 TRP B 713 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (21681) covalent geometry : angle 0.60376 / 0.32 (29771) hydrogen bonds : bond 0.04364 / 2.89 ( 917) hydrogen bonds : angle 4.44574 / 3.11 ( 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 248 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 177 time to evaluate : 0.785 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: 0.8647 (OUTLIER) cc_final: 0.8344 (tmm-80) REVERT: A 316 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: A 393 MET cc_start: 0.8448 (tpp) cc_final: 0.8024 (tpp) REVERT: A 451 TYR cc_start: 0.8917 (m-10) cc_final: 0.8651 (m-80) REVERT: A 719 MET cc_start: 0.9257 (mmm) cc_final: 0.8839 (mmm) REVERT: A 766 MET cc_start: 0.9145 (tpp) cc_final: 0.8822 (tpp) REVERT: A 978 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8829 (mttt) REVERT: A 1024 MET cc_start: 0.8593 (mtm) cc_final: 0.7833 (mtm) REVERT: A 1029 MET cc_start: 0.7045 (tpt) cc_final: 0.6627 (tpp) REVERT: B 126 MET cc_start: 0.8600 (mmm) cc_final: 0.8295 (mmm) REVERT: B 152 LYS cc_start: 0.9271 (mmmt) cc_final: 0.9012 (mmmt) REVERT: B 170 GLU cc_start: 0.9162 (tp30) cc_final: 0.8808 (tm-30) REVERT: B 246 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7679 (m-10) REVERT: B 266 GLN cc_start: 0.8566 (mt0) cc_final: 0.8206 (mm110) REVERT: B 366 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: B 649 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: B 664 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8153 (tptp) REVERT: B 719 MET cc_start: 0.9072 (mtp) cc_final: 0.8340 (mmm) REVERT: B 753 MET cc_start: 0.8761 (ppp) cc_final: 0.8286 (ppp) REVERT: B 806 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: C 8 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8181 (ttmm) REVERT: C 93 LYS cc_start: 0.9235 (mttt) cc_final: 0.8902 (mtmm) REVERT: C 102 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8410 (p0) REVERT: C 114 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7536 (tt) REVERT: C 115 MET cc_start: 0.8726 (mmm) cc_final: 0.8486 (tpp) REVERT: C 125 ASP cc_start: 0.7405 (t0) cc_final: 0.7189 (t0) REVERT: D 136 LEU cc_start: 0.6902 (mt) cc_final: 0.6475 (pp) outliers start: 71 outliers final: 33 residues processed: 233 average time/residue: 0.1646 time to fit residues: 58.6908 Evaluate side-chains 202 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 455 GLN 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 779 VAL Chi-restraints excluded: chain A residue 810 CYS 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 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL 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 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 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 C residue 114 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 114 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 223 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 189 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS B 362 GLN B 712 ASN B 858 HIS ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN C 72 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.088659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070268 restraints weight = 65998.313| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.79 r_work: 0.3051 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5390 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= 0.159 Angle : 0.607 11.228 29771 Z= 0.324 Chirality : 0.043 0.339 3215 Planarity : 0.004 0.055 3504 Dihedral : 21.937 177.231 3747 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 3.62 % Allowed : 21.42 % Favored : 74.96 % 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: -1.24 (0.17), residues: 2296 helix: 0.28 (0.16), residues: 1072 sheet: -1.34 (0.34), residues: 211 loop : -1.92 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 46 TYR 0.014 0.001 TYR B 861 PHE 0.014 0.001 PHE D 140 TRP 0.012 0.001 TRP B 888 HIS 0.011 0.002 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (21681) covalent geometry : angle 0.60666 / 0.32 (29771) hydrogen bonds : bond 0.04385 / 2.89 ( 917) hydrogen bonds : angle 4.34241 / 3.05 ( 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 252 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 0.747 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: 0.8629 (OUTLIER) cc_final: 0.8372 (tmm-80) REVERT: A 316 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: A 393 MET cc_start: 0.8519 (tpp) cc_final: 0.7819 (tmm) REVERT: A 719 MET cc_start: 0.9254 (mmm) cc_final: 0.8676 (mmm) REVERT: A 766 MET cc_start: 0.9273 (tpp) cc_final: 0.8929 (tpp) REVERT: A 978 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8828 (mttt) REVERT: A 1029 MET cc_start: 0.7240 (tpt) cc_final: 0.6717 (tpt) REVERT: B 126 MET cc_start: 0.8579 (mmm) cc_final: 0.8283 (mmm) REVERT: B 152 LYS cc_start: 0.9297 (mmmt) cc_final: 0.9040 (mmmt) REVERT: B 170 GLU cc_start: 0.9199 (tp30) cc_final: 0.8925 (tm-30) REVERT: B 246 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: B 266 GLN cc_start: 0.8674 (mt0) cc_final: 0.8405 (tp40) REVERT: B 323 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8535 (mm-30) REVERT: B 362 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7567 (tp-100) REVERT: B 366 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: B 649 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8431 (m-30) REVERT: B 664 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8286 (tptp) REVERT: B 719 MET cc_start: 0.9101 (mtp) cc_final: 0.8338 (mmm) REVERT: B 762 MET cc_start: 0.9222 (mmm) cc_final: 0.8864 (mmt) REVERT: B 806 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: C 8 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8204 (ttmm) REVERT: C 102 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8434 (p0) REVERT: C 107 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7428 (pp20) REVERT: C 114 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7491 (tt) REVERT: C 116 GLN cc_start: 0.8266 (mt0) cc_final: 0.7756 (mp10) REVERT: C 119 GLU cc_start: 0.9063 (mp0) cc_final: 0.8837 (pm20) REVERT: D 90 GLU cc_start: 0.4950 (mm-30) cc_final: 0.4707 (tp30) outliers start: 71 outliers final: 39 residues processed: 236 average time/residue: 0.1549 time to fit residues: 55.8446 Evaluate side-chains 225 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 513 VAL 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 753 MET 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 A residue 978 LYS 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 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 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 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 939 GLN 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 102 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 17 VAL 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: 0.7980 chunk 94 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 211 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 169 optimal weight: 0.4980 chunk 223 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN C 72 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 = 0.3611 r_free = 0.3611 target = 0.089524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071149 restraints weight = 66029.214| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.83 r_work: 0.3074 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5528 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= 0.123 Angle : 0.605 12.365 29771 Z= 0.321 Chirality : 0.042 0.323 3215 Planarity : 0.004 0.054 3504 Dihedral : 21.874 178.378 3746 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 2.65 % Allowed : 22.49 % 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: -1.07 (0.17), residues: 2296 helix: 0.40 (0.16), residues: 1074 sheet: -1.20 (0.34), residues: 208 loop : -1.82 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 123 TYR 0.011 0.001 TYR B 962 PHE 0.022 0.001 PHE C 142 TRP 0.010 0.001 TRP A 39 HIS 0.014 0.001 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21681) covalent geometry : angle 0.60460 / 0.32 (29771) hydrogen bonds : bond 0.04074 / 2.73 ( 917) hydrogen bonds : angle 4.28145 / 3.01 ( 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 240 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.906 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: 0.8540 (OUTLIER) cc_final: 0.8310 (tmm-80) REVERT: A 279 GLN cc_start: 0.8568 (pt0) cc_final: 0.8291 (pt0) REVERT: A 326 PHE cc_start: 0.7136 (m-10) cc_final: 0.6482 (m-10) REVERT: A 393 MET cc_start: 0.8582 (tpp) cc_final: 0.7924 (tmm) REVERT: A 451 TYR cc_start: 0.8922 (m-10) cc_final: 0.8601 (m-80) REVERT: A 680 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 719 MET cc_start: 0.9230 (mmm) cc_final: 0.8622 (mmm) REVERT: A 895 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8679 (mp) REVERT: A 978 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8773 (mttt) REVERT: A 1029 MET cc_start: 0.7224 (tpt) cc_final: 0.6895 (tpp) REVERT: B 126 MET cc_start: 0.8554 (mmm) cc_final: 0.8339 (mmm) REVERT: B 152 LYS cc_start: 0.9287 (mmmt) cc_final: 0.9052 (mmmt) REVERT: B 170 GLU cc_start: 0.9236 (tp30) cc_final: 0.8961 (tm-30) REVERT: B 246 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: B 266 GLN cc_start: 0.8622 (mt0) cc_final: 0.8402 (mm110) REVERT: B 323 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8473 (mm-30) REVERT: B 649 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: B 664 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8277 (tptp) REVERT: B 719 MET cc_start: 0.9109 (mtp) cc_final: 0.8287 (mmm) REVERT: B 762 MET cc_start: 0.9197 (mmm) cc_final: 0.8831 (mmt) REVERT: B 939 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8744 (mm-40) REVERT: C 8 LYS cc_start: 0.8426 (mmmm) cc_final: 0.8171 (ttmm) REVERT: C 73 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8067 (tm-30) REVERT: C 102 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8427 (p0) REVERT: C 115 MET cc_start: 0.8652 (tpp) cc_final: 0.8331 (tpp) REVERT: C 116 GLN cc_start: 0.8417 (mt0) cc_final: 0.8156 (mt0) outliers start: 52 outliers final: 31 residues processed: 228 average time/residue: 0.1652 time to fit residues: 57.6658 Evaluate side-chains 217 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 680 SER Chi-restraints excluded: chain A residue 753 MET 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 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 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL 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 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 102 ASP 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 88 ASP 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: 10.0000 chunk 112 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN ** A 275 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 116 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.089238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070792 restraints weight = 65688.752| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.84 r_work: 0.3069 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5662 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= 0.132 Angle : 0.606 12.686 29771 Z= 0.319 Chirality : 0.042 0.296 3215 Planarity : 0.004 0.053 3504 Dihedral : 21.828 178.884 3746 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 2.91 % Allowed : 22.28 % Favored : 74.81 % 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: -0.94 (0.17), residues: 2296 helix: 0.48 (0.16), residues: 1078 sheet: -1.05 (0.34), residues: 208 loop : -1.75 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 46 TYR 0.012 0.001 TYR B 861 PHE 0.020 0.001 PHE C 142 TRP 0.011 0.001 TRP B 888 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21681) covalent geometry : angle 0.60564 / 0.32 (29771) hydrogen bonds : bond 0.04003 / 2.66 ( 917) hydrogen bonds : angle 4.21558 / 2.95 ( 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 247 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.908 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: 0.8531 (OUTLIER) cc_final: 0.8017 (ttm170) REVERT: A 279 GLN cc_start: 0.8574 (pt0) cc_final: 0.8301 (pt0) REVERT: A 326 PHE cc_start: 0.7155 (m-80) cc_final: 0.6466 (m-10) REVERT: A 393 MET cc_start: 0.8614 (tpp) cc_final: 0.7940 (tmm) REVERT: A 451 TYR cc_start: 0.8929 (m-10) cc_final: 0.8601 (m-80) REVERT: A 719 MET cc_start: 0.9229 (mmm) cc_final: 0.8622 (mmm) REVERT: A 766 MET cc_start: 0.9170 (tpp) cc_final: 0.8942 (tpp) REVERT: A 978 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8782 (mttt) REVERT: A 1029 MET cc_start: 0.7246 (tpt) cc_final: 0.6935 (tpp) REVERT: B 126 MET cc_start: 0.8495 (mmm) cc_final: 0.8267 (mmm) REVERT: B 152 LYS cc_start: 0.9288 (mmmt) cc_final: 0.9055 (mmmt) REVERT: B 170 GLU cc_start: 0.9247 (tp30) cc_final: 0.8962 (tm-30) REVERT: B 246 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7926 (m-10) REVERT: B 266 GLN cc_start: 0.8626 (mt0) cc_final: 0.8406 (mm110) REVERT: B 323 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8466 (mm-30) REVERT: B 649 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8754 (m-30) REVERT: B 719 MET cc_start: 0.9112 (mtp) cc_final: 0.8284 (mmm) REVERT: C 8 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8224 (ttmm) REVERT: C 73 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 102 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8359 (p0) REVERT: C 115 MET cc_start: 0.8563 (tpp) cc_final: 0.8183 (tpp) REVERT: C 120 GLU cc_start: 0.8223 (tt0) cc_final: 0.7964 (tt0) outliers start: 57 outliers final: 39 residues processed: 229 average time/residue: 0.1716 time to fit residues: 60.0196 Evaluate side-chains 221 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 779 VAL Chi-restraints excluded: chain A residue 810 CYS 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 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL 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 37 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain D residue 13 LEU 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 71 LEU Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 102 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 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 279 GLN B 563 ASN B 758 ASN ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.085697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067301 restraints weight = 66577.494| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.77 r_work: 0.2982 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 21681 Z= 0.251 Angle : 0.701 11.282 29771 Z= 0.369 Chirality : 0.046 0.319 3215 Planarity : 0.005 0.052 3504 Dihedral : 21.900 179.937 3746 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 2.60 % Allowed : 22.79 % Favored : 74.60 % 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: -0.98 (0.17), residues: 2296 helix: 0.44 (0.16), residues: 1072 sheet: -0.96 (0.34), residues: 217 loop : -1.78 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 123 TYR 0.018 0.002 TYR B 861 PHE 0.021 0.002 PHE C 142 TRP 0.014 0.002 TRP B 599 HIS 0.010 0.002 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (21681) covalent geometry : angle 0.70118 / 0.37 (29771) hydrogen bonds : bond 0.05157 / 3.43 ( 917) hydrogen bonds : angle 4.44450 / 3.10 ( 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 233 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8083 (ttm110) REVERT: A 287 GLU cc_start: 0.9007 (tt0) cc_final: 0.8393 (tp30) REVERT: A 326 PHE cc_start: 0.7588 (m-80) cc_final: 0.6906 (m-10) REVERT: A 393 MET cc_start: 0.8656 (tpp) cc_final: 0.8000 (tmm) REVERT: A 766 MET cc_start: 0.9307 (tpp) cc_final: 0.9075 (tpp) REVERT: A 810 CYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8885 (p) REVERT: A 978 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8944 (mttt) REVERT: B 152 LYS cc_start: 0.9310 (mmmt) cc_final: 0.9060 (mmmt) REVERT: B 170 GLU cc_start: 0.9284 (tp30) cc_final: 0.9039 (tm-30) REVERT: B 246 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: B 266 GLN cc_start: 0.8819 (mt0) cc_final: 0.8521 (mm-40) REVERT: B 323 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8606 (mm-30) REVERT: B 649 ASP cc_start: 0.9262 (OUTLIER) cc_final: 0.8780 (m-30) REVERT: B 664 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8314 (tptp) REVERT: B 719 MET cc_start: 0.9209 (mtp) cc_final: 0.8414 (mmm) REVERT: B 753 MET cc_start: 0.8880 (ppp) cc_final: 0.8362 (ppp) REVERT: B 762 MET cc_start: 0.9121 (mmm) cc_final: 0.8805 (mmt) REVERT: B 806 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: C 73 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 102 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8526 (p0) REVERT: C 115 MET cc_start: 0.8503 (tpp) cc_final: 0.8261 (tpp) REVERT: C 116 GLN cc_start: 0.8450 (mt0) cc_final: 0.8047 (mp10) REVERT: D 114 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.5971 (mp) REVERT: D 115 MET cc_start: 0.0998 (tpt) cc_final: 0.0702 (tpt) REVERT: D 119 GLU cc_start: 0.6805 (pm20) cc_final: 0.6405 (pm20) outliers start: 51 outliers final: 34 residues processed: 217 average time/residue: 0.1736 time to fit residues: 57.0400 Evaluate side-chains 214 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 512 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 753 MET 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 A residue 978 LYS 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 346 THR Chi-restraints excluded: chain B residue 451 TYR 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 17 VAL Chi-restraints excluded: chain C residue 37 SER 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 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: 1.9990 chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 127 optimal weight: 0.1980 chunk 152 optimal weight: 0.5980 chunk 230 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** 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 = 0.3566 r_free = 0.3566 target = 0.087145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068754 restraints weight = 66465.237| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.82 r_work: 0.3020 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.6111 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= 0.144 Angle : 0.644 11.347 29771 Z= 0.339 Chirality : 0.043 0.321 3215 Planarity : 0.004 0.069 3504 Dihedral : 21.824 179.323 3746 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.09 % Allowed : 23.76 % Favored : 74.15 % 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: -0.78 (0.17), residues: 2296 helix: 0.61 (0.16), residues: 1068 sheet: -0.83 (0.34), residues: 215 loop : -1.69 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 123 TYR 0.017 0.001 TYR A 764 PHE 0.013 0.001 PHE A 223 TRP 0.009 0.001 TRP A 888 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21681) covalent geometry : angle 0.64377 / 0.34 (29771) hydrogen bonds : bond 0.04301 / 2.87 ( 917) hydrogen bonds : angle 4.28959 / 2.99 ( 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 221 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.785 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: 0.8549 (OUTLIER) cc_final: 0.8268 (tmm-80) REVERT: A 326 PHE cc_start: 0.7324 (m-80) cc_final: 0.6692 (m-10) REVERT: A 393 MET cc_start: 0.8618 (tpp) cc_final: 0.7942 (tmm) REVERT: A 451 TYR cc_start: 0.8848 (m-10) cc_final: 0.8499 (m-80) REVERT: A 719 MET cc_start: 0.9242 (mmm) cc_final: 0.8786 (mmm) REVERT: A 978 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8855 (mttt) REVERT: B 152 LYS cc_start: 0.9316 (mmmt) cc_final: 0.9095 (mmmt) REVERT: B 170 GLU cc_start: 0.9319 (tp30) cc_final: 0.9107 (tm-30) REVERT: B 246 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: B 323 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8548 (mm-30) REVERT: B 719 MET cc_start: 0.9141 (mtp) cc_final: 0.8356 (mmm) REVERT: B 753 MET cc_start: 0.8840 (ppp) cc_final: 0.8320 (ppp) REVERT: B 762 MET cc_start: 0.9082 (mmm) cc_final: 0.8716 (mmt) REVERT: B 960 TRP cc_start: 0.8703 (OUTLIER) cc_final: 0.8486 (m100) REVERT: C 73 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8107 (tm-30) REVERT: C 102 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8516 (p0) REVERT: C 115 MET cc_start: 0.8558 (tpp) cc_final: 0.8335 (tpp) REVERT: C 116 GLN cc_start: 0.8496 (mt0) cc_final: 0.8070 (mp10) REVERT: D 14 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8331 (pm20) REVERT: D 114 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5904 (mp) outliers start: 41 outliers final: 31 residues processed: 211 average time/residue: 0.1732 time to fit residues: 55.2969 Evaluate side-chains 209 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 779 VAL Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 978 LYS 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 346 THR Chi-restraints excluded: chain B residue 451 TYR 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 960 TRP Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 17 VAL 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: 0.0980 chunk 219 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 226 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 279 GLN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** 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 = 0.3540 r_free = 0.3540 target = 0.085863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067565 restraints weight = 66824.113| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.78 r_work: 0.2991 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21681 Z= 0.194 Angle : 0.667 15.905 29771 Z= 0.349 Chirality : 0.044 0.330 3215 Planarity : 0.004 0.070 3504 Dihedral : 21.824 179.638 3744 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.19 % Allowed : 23.76 % Favored : 74.04 % 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: -0.86 (0.17), residues: 2296 helix: 0.53 (0.16), residues: 1083 sheet: -0.89 (0.34), residues: 225 loop : -1.74 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 123 TYR 0.027 0.001 TYR A 764 PHE 0.014 0.002 PHE A 326 TRP 0.008 0.001 TRP A 885 HIS 0.011 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (21681) covalent geometry : angle 0.66666 / 0.35 (29771) hydrogen bonds : bond 0.04620 / 3.08 ( 917) hydrogen bonds : angle 4.33526 / 3.03 ( 2487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4984.01 seconds wall clock time: 86 minutes 44.24 seconds (5204.24 seconds total)