Starting phenix.real_space_refine on Mon Apr 6 18:07:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lvv_23543/04_2026/7lvv_23543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lvv_23543/04_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_23543/04_2026/7lvv_23543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lvv_23543/04_2026/7lvv_23543.map" model { file = "/net/cci-nas-00/data/ceres_data/7lvv_23543/04_2026/7lvv_23543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lvv_23543/04_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-2.1rc1-6017/lib/python3.9/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: 5.44, per 1000 atoms: 0.26 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: 1.76 Conformation dependent library (CDL) restraints added in 982.1 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: 3.11 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: 5.12 Time building geometry restraints manager: 2.43 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: 25140 2.43 - 4.85: 4075 4.85 - 7.28: 466 7.28 - 9.71: 70 9.71 - 12.13: 20 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: 11273 32.96 - 65.91: 1469 65.91 - 98.87: 60 98.87 - 131.83: 1 131.83 - 164.78: 2 Dihedral angle restraints: 12805 sinusoidal: 6033 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 12802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2554 0.149 - 0.298: 629 0.298 - 0.448: 31 0.448 - 0.597: 0 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=" CA ASP A 88 " pdb=" N ASP A 88 " pdb=" C ASP A 88 " pdb=" CB ASP A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA THR C 49 " pdb=" N THR C 49 " pdb=" C THR C 49 " pdb=" CB THR C 49 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.70e+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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.410 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 : 0.013 0.085 21681 Z= 0.921 Angle : 1.795 12.133 29771 Z= 1.309 Chirality : 0.119 0.746 3215 Planarity : 0.007 0.080 3504 Dihedral : 23.618 164.782 8433 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 covalent geometry : bond 0.01254 (21681) covalent geometry : angle 1.79546 (29771) hydrogen bonds : bond 0.20943 ( 917) hydrogen bonds : angle 9.21543 ( 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 : 0.677 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: 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: 0.8126 (t) REVERT: A 185 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8446 (tmm-80) REVERT: A 237 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8177 (tp-100) REVERT: A 366 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6971 (pp20) REVERT: A 451 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: A 629 TRP cc_start: 0.8505 (m-10) cc_final: 0.8172 (m-10) REVERT: A 641 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.4809 (mm-30) REVERT: A 1024 MET cc_start: 0.8023 (mtt) cc_final: 0.7526 (mtm) REVERT: B 188 PHE cc_start: 0.7504 (t80) cc_final: 0.7285 (t80) REVERT: B 246 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: B 319 ASP cc_start: 0.8007 (t0) cc_final: 0.7370 (t0) REVERT: B 328 LYS cc_start: 0.8652 (mttt) cc_final: 0.7481 (mmtm) REVERT: B 472 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7578 (tmm160) REVERT: B 512 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8222 (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 831 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8832 (tt) REVERT: B 857 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8384 (m90) REVERT: B 876 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8836 (mp) REVERT: B 897 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7821 (mm) REVERT: B 983 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9091 (mmtm) REVERT: B 986 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9253 (p) REVERT: C 25 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8118 (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: 0.8138 (t70) REVERT: D 94 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5437 (mmtm) REVERT: D 132 LEU cc_start: 0.7770 (tp) cc_final: 0.7562 (tp) outliers start: 274 outliers final: 33 residues processed: 713 average time/residue: 0.2022 time to fit residues: 203.1580 Evaluate side-chains 294 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 158 LYS 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 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 897 ILE 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: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 212 HIS A 232 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 233 ASN B 288 ASN B 448 ASN B 537 HIS B 620 HIS B 763 GLN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 72 GLN D 10 GLN D 24 ASN 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 = 0.3687 r_free = 0.3687 target = 0.093089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074779 restraints weight = 65996.008| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.87 r_work: 0.3160 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21681 Z= 0.185 Angle : 0.705 8.889 29771 Z= 0.386 Chirality : 0.043 0.187 3215 Planarity : 0.005 0.063 3504 Dihedral : 22.976 172.589 3905 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 4.23 % Allowed : 21.57 % Favored : 74.20 % 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: -2.83 (0.16), residues: 2296 helix: -1.04 (0.15), residues: 1064 sheet: -2.54 (0.35), residues: 180 loop : -2.64 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 46 TYR 0.023 0.002 TYR A 814 PHE 0.031 0.002 PHE B 882 TRP 0.013 0.001 TRP A 677 HIS 0.010 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00411 (21681) covalent geometry : angle 0.70466 (29771) hydrogen bonds : bond 0.05387 ( 917) hydrogen bonds : angle 5.14081 ( 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 343 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8348 (tmm-80) REVERT: A 291 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.7923 (mtt-85) REVERT: A 451 TYR cc_start: 0.9004 (m-10) cc_final: 0.8719 (m-80) REVERT: A 488 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7722 (mtpt) REVERT: A 606 GLU cc_start: 0.8712 (pp20) cc_final: 0.8353 (pp20) REVERT: A 719 MET cc_start: 0.9221 (mmm) cc_final: 0.8898 (mmm) REVERT: A 766 MET cc_start: 0.9117 (tpp) cc_final: 0.8717 (tpp) REVERT: A 1029 MET cc_start: 0.6699 (tpt) cc_final: 0.6491 (tpt) REVERT: B 158 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8667 (ptpp) REVERT: B 232 ASN cc_start: 0.8335 (t0) cc_final: 0.8086 (t0) REVERT: B 245 PHE cc_start: 0.7798 (p90) cc_final: 0.7502 (p90) REVERT: B 246 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: B 259 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7837 (pttm) REVERT: B 570 VAL cc_start: 0.8472 (t) cc_final: 0.8202 (m) REVERT: B 648 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8887 (ptmt) REVERT: B 649 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: B 664 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7973 (tptp) REVERT: B 719 MET cc_start: 0.9234 (mtp) cc_final: 0.8467 (mmm) REVERT: B 912 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6120 (mp0) REVERT: B 986 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8575 (p) REVERT: C 69 ASP cc_start: 0.7261 (t0) cc_final: 0.6963 (t70) REVERT: C 86 THR cc_start: 0.8835 (m) cc_final: 0.8630 (t) REVERT: C 90 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9098 (mm-30) REVERT: C 93 LYS cc_start: 0.9165 (mttt) cc_final: 0.8861 (mtmm) REVERT: C 102 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8328 (p0) REVERT: C 103 ASN cc_start: 0.7988 (t0) cc_final: 0.7341 (p0) REVERT: C 123 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7990 (ttm-80) REVERT: C 143 GLU cc_start: 0.7888 (pm20) cc_final: 0.7581 (pp20) REVERT: D 90 GLU cc_start: 0.4979 (mm-30) cc_final: 0.4760 (mm-30) REVERT: D 136 LEU cc_start: 0.6758 (mt) cc_final: 0.6498 (pp) outliers start: 83 outliers final: 34 residues processed: 331 average time/residue: 0.1770 time to fit residues: 87.0109 Evaluate side-chains 225 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 488 LYS 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 611 THR 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 810 CYS Chi-restraints excluded: chain B residue 109 SER 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 310 ILE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 491 ASP 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 694 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 986 THR 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 45 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP 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: 0.8980 chunk 99 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 220 optimal weight: 0.0000 chunk 29 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 227 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** 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 227 GLN B 229 HIS B 438 ASN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN B 620 HIS B 628 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3657 r_free = 0.3657 target = 0.091801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073499 restraints weight = 66408.639| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.89 r_work: 0.3118 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21681 Z= 0.150 Angle : 0.616 9.564 29771 Z= 0.335 Chirality : 0.041 0.170 3215 Planarity : 0.005 0.046 3504 Dihedral : 22.206 177.560 3824 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 3.16 % Allowed : 21.88 % 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: -1.93 (0.17), residues: 2296 helix: -0.22 (0.16), residues: 1059 sheet: -1.88 (0.36), residues: 179 loop : -2.30 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 75 TYR 0.019 0.001 TYR B 262 PHE 0.023 0.002 PHE D 140 TRP 0.017 0.001 TRP B 713 HIS 0.009 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00332 (21681) covalent geometry : angle 0.61629 (29771) hydrogen bonds : bond 0.04534 ( 917) hydrogen bonds : angle 4.62805 ( 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 273 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 0.733 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: A 185 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8269 (tmm-80) REVERT: A 266 GLN cc_start: 0.9328 (pt0) cc_final: 0.9082 (pt0) REVERT: A 451 TYR cc_start: 0.8940 (m-10) cc_final: 0.8656 (m-80) REVERT: A 606 GLU cc_start: 0.8680 (pp20) cc_final: 0.8331 (pp20) REVERT: A 719 MET cc_start: 0.9272 (mmm) cc_final: 0.8854 (mmm) REVERT: A 766 MET cc_start: 0.9085 (tpp) cc_final: 0.8690 (tpp) REVERT: A 1029 MET cc_start: 0.6919 (tpt) cc_final: 0.6645 (tpt) REVERT: B 11 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8609 (ttpp) REVERT: B 69 ASP cc_start: 0.7622 (p0) cc_final: 0.7412 (p0) REVERT: B 178 LYS cc_start: 0.6482 (mttt) cc_final: 0.6235 (mtmt) REVERT: B 246 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7392 (m-10) REVERT: B 282 LEU cc_start: 0.9487 (mt) cc_final: 0.9254 (mt) REVERT: B 314 MET cc_start: 0.8835 (mtp) cc_final: 0.8612 (mtp) REVERT: B 570 VAL cc_start: 0.8621 (t) cc_final: 0.8383 (m) REVERT: B 628 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8265 (p0) REVERT: B 649 ASP cc_start: 0.9273 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: B 664 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8064 (tptp) REVERT: B 719 MET cc_start: 0.9124 (mtp) cc_final: 0.8472 (mmm) REVERT: B 762 MET cc_start: 0.9204 (mmm) cc_final: 0.8866 (mmt) REVERT: B 806 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: B 912 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6041 (mp0) REVERT: B 986 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8686 (p) REVERT: C 8 LYS cc_start: 0.8393 (mmmm) cc_final: 0.8130 (ttmm) REVERT: C 51 VAL cc_start: 0.9256 (t) cc_final: 0.9049 (p) REVERT: C 102 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8353 (p0) REVERT: C 123 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7834 (ttm-80) REVERT: C 141 GLU cc_start: 0.8347 (pp20) cc_final: 0.8008 (pp20) REVERT: D 136 LEU cc_start: 0.7015 (mt) cc_final: 0.6650 (pp) outliers start: 62 outliers final: 29 residues processed: 261 average time/residue: 0.1547 time to fit residues: 62.2351 Evaluate side-chains 218 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 694 ILE Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 5 LEU 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 115 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 652 GLN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072663 restraints weight = 66310.925| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.83 r_work: 0.3104 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21681 Z= 0.139 Angle : 0.573 8.139 29771 Z= 0.314 Chirality : 0.039 0.167 3215 Planarity : 0.004 0.048 3504 Dihedral : 21.685 178.454 3817 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 3.42 % Allowed : 21.77 % 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: -1.45 (0.17), residues: 2296 helix: 0.17 (0.16), residues: 1068 sheet: -1.75 (0.33), residues: 216 loop : -2.02 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 46 TYR 0.018 0.001 TYR B 262 PHE 0.022 0.001 PHE D 140 TRP 0.015 0.001 TRP B 629 HIS 0.009 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00299 (21681) covalent geometry : angle 0.57346 (29771) hydrogen bonds : bond 0.04014 ( 917) hydrogen bonds : angle 4.30379 ( 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 268 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7992 (ttm110) REVERT: A 316 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7790 (pp20) REVERT: A 326 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: A 339 ASP cc_start: 0.8902 (t0) cc_final: 0.8667 (t0) REVERT: A 393 MET cc_start: 0.8486 (tpp) cc_final: 0.7848 (tmm) REVERT: A 606 GLU cc_start: 0.8683 (pp20) cc_final: 0.8306 (pp20) REVERT: A 719 MET cc_start: 0.9275 (mmm) cc_final: 0.8741 (mmm) REVERT: A 766 MET cc_start: 0.9063 (tpp) cc_final: 0.8710 (tpp) REVERT: A 1029 MET cc_start: 0.7059 (tpt) cc_final: 0.6493 (tpt) REVERT: B 11 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8732 (ttpp) REVERT: B 158 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8558 (ptpt) REVERT: B 170 GLU cc_start: 0.9242 (tp30) cc_final: 0.8950 (tm-30) REVERT: B 246 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7646 (m-10) REVERT: B 266 GLN cc_start: 0.8676 (mt0) cc_final: 0.8378 (tp40) REVERT: B 628 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7942 (p0) REVERT: B 649 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: B 664 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8164 (tptp) REVERT: B 719 MET cc_start: 0.9155 (mtp) cc_final: 0.8357 (mmm) REVERT: B 912 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6082 (mp0) REVERT: C 102 ASP cc_start: 0.8750 (m-30) cc_final: 0.8420 (p0) REVERT: C 123 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7890 (ttm-80) REVERT: C 141 GLU cc_start: 0.8348 (pp20) cc_final: 0.7941 (pp20) REVERT: D 25 GLU cc_start: 0.7299 (tt0) cc_final: 0.5672 (pt0) REVERT: D 132 LEU cc_start: 0.6353 (tp) cc_final: 0.6135 (tp) REVERT: D 136 LEU cc_start: 0.6999 (mt) cc_final: 0.6672 (pp) outliers start: 67 outliers final: 33 residues processed: 253 average time/residue: 0.1581 time to fit residues: 61.6769 Evaluate side-chains 218 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR 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 158 LYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 649 ASP 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 817 THR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 115 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN B 758 ASN C 116 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 = 0.3588 r_free = 0.3588 target = 0.088231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069765 restraints weight = 66219.209| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.84 r_work: 0.3040 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21681 Z= 0.176 Angle : 0.582 8.079 29771 Z= 0.315 Chirality : 0.040 0.182 3215 Planarity : 0.004 0.043 3504 Dihedral : 21.567 177.977 3810 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.75 % Favored : 96.21 % Rotamer: Outliers : 3.11 % Allowed : 22.79 % Favored : 74.09 % 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: -1.23 (0.17), residues: 2296 helix: 0.32 (0.16), residues: 1078 sheet: -1.43 (0.34), residues: 213 loop : -1.94 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 46 TYR 0.012 0.001 TYR A 396 PHE 0.028 0.002 PHE B 223 TRP 0.008 0.001 TRP B 629 HIS 0.009 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00400 (21681) covalent geometry : angle 0.58176 (29771) hydrogen bonds : bond 0.04244 ( 917) hydrogen bonds : angle 4.26757 ( 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 249 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 188 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7918 (ttm110) REVERT: A 287 GLU cc_start: 0.8959 (tt0) cc_final: 0.8483 (tm-30) REVERT: A 291 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8366 (mtt-85) REVERT: A 326 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7087 (m-10) REVERT: A 372 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8820 (tp30) REVERT: A 393 MET cc_start: 0.8569 (tpp) cc_final: 0.7914 (tmm) REVERT: A 606 GLU cc_start: 0.8692 (pp20) cc_final: 0.8321 (pp20) REVERT: A 719 MET cc_start: 0.9284 (mmm) cc_final: 0.9069 (mmm) REVERT: A 766 MET cc_start: 0.9188 (tpp) cc_final: 0.8886 (tpp) REVERT: A 810 CYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 1029 MET cc_start: 0.7367 (tpt) cc_final: 0.7113 (tpp) REVERT: B 158 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8672 (ptpp) REVERT: B 170 GLU cc_start: 0.9271 (tp30) cc_final: 0.9014 (tm-30) REVERT: B 245 PHE cc_start: 0.7637 (p90) cc_final: 0.6914 (p90) REVERT: B 246 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7924 (m-10) REVERT: B 266 GLN cc_start: 0.8765 (mt0) cc_final: 0.8338 (mm-40) REVERT: B 649 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8702 (m-30) REVERT: B 664 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8246 (tptp) REVERT: B 719 MET cc_start: 0.9210 (mtp) cc_final: 0.8363 (mmm) REVERT: B 753 MET cc_start: 0.8813 (ppp) cc_final: 0.8286 (ppp) REVERT: B 762 MET cc_start: 0.9251 (mmm) cc_final: 0.8801 (mmt) REVERT: B 806 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: B 920 GLU cc_start: 0.7243 (mp0) cc_final: 0.6721 (mm-30) REVERT: C 102 ASP cc_start: 0.8800 (m-30) cc_final: 0.8404 (p0) REVERT: C 107 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7483 (pp20) REVERT: C 123 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7928 (ttm-80) REVERT: C 141 GLU cc_start: 0.8135 (pp20) cc_final: 0.7779 (pp20) REVERT: D 4 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7853 (pm20) outliers start: 61 outliers final: 34 residues processed: 231 average time/residue: 0.1676 time to fit residues: 58.9291 Evaluate side-chains 215 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 326 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 13 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 Chi-restraints excluded: chain D residue 115 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 223 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 189 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.089806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071572 restraints weight = 65704.285| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.83 r_work: 0.3078 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5892 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= 0.116 Angle : 0.543 7.085 29771 Z= 0.296 Chirality : 0.038 0.184 3215 Planarity : 0.004 0.042 3504 Dihedral : 21.369 177.902 3810 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 2.55 % Allowed : 22.90 % Favored : 74.55 % 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: -0.89 (0.17), residues: 2296 helix: 0.59 (0.16), residues: 1064 sheet: -1.22 (0.34), residues: 210 loop : -1.74 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 46 TYR 0.012 0.001 TYR A 305 PHE 0.016 0.001 PHE C 142 TRP 0.008 0.001 TRP B 960 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00252 (21681) covalent geometry : angle 0.54347 (29771) hydrogen bonds : bond 0.03648 ( 917) hydrogen bonds : angle 4.13597 ( 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 254 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7817 (ttm110) REVERT: A 287 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: A 291 ARG cc_start: 0.8519 (mtt-85) cc_final: 0.7488 (mtt-85) REVERT: A 326 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6398 (m-10) REVERT: A 393 MET cc_start: 0.8570 (tpp) cc_final: 0.7998 (tmm) REVERT: A 451 TYR cc_start: 0.8767 (m-10) cc_final: 0.8374 (m-80) REVERT: A 606 GLU cc_start: 0.8682 (pp20) cc_final: 0.8281 (pp20) REVERT: A 719 MET cc_start: 0.9225 (mmm) cc_final: 0.8620 (mmm) REVERT: A 762 MET cc_start: 0.9092 (mmm) cc_final: 0.8274 (mmt) REVERT: A 766 MET cc_start: 0.9042 (tpp) cc_final: 0.8763 (tpp) REVERT: A 810 CYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 1029 MET cc_start: 0.7541 (tpt) cc_final: 0.7319 (tpp) REVERT: B 158 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8587 (ptpp) REVERT: B 159 ASP cc_start: 0.8812 (m-30) cc_final: 0.8564 (m-30) REVERT: B 245 PHE cc_start: 0.7149 (p90) cc_final: 0.6920 (p90) REVERT: B 246 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.8012 (m-10) REVERT: B 247 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8282 (mttp) REVERT: B 266 GLN cc_start: 0.8698 (mt0) cc_final: 0.8384 (mm-40) REVERT: B 323 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8435 (mm-30) REVERT: B 509 ILE cc_start: 0.9140 (pt) cc_final: 0.8929 (mt) REVERT: B 714 GLU cc_start: 0.8842 (mp0) cc_final: 0.8611 (mp0) REVERT: B 753 MET cc_start: 0.8768 (ppp) cc_final: 0.8239 (ppp) REVERT: B 762 MET cc_start: 0.9282 (mmm) cc_final: 0.8847 (mmt) REVERT: C 69 ASP cc_start: 0.7409 (t0) cc_final: 0.6587 (t0) REVERT: C 73 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 85 ASP cc_start: 0.7417 (t0) cc_final: 0.7160 (t0) REVERT: C 102 ASP cc_start: 0.8886 (m-30) cc_final: 0.8432 (p0) REVERT: C 107 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7707 (pp20) REVERT: C 116 GLN cc_start: 0.8462 (mt0) cc_final: 0.8170 (mm-40) REVERT: C 123 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8137 (ttm-80) REVERT: C 126 MET cc_start: 0.7351 (mtp) cc_final: 0.7101 (mtt) REVERT: C 128 ASP cc_start: 0.8398 (t0) cc_final: 0.8175 (t0) REVERT: C 141 GLU cc_start: 0.8162 (pp20) cc_final: 0.7778 (pp20) REVERT: D 25 GLU cc_start: 0.7105 (tt0) cc_final: 0.5394 (pt0) REVERT: D 83 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6778 (mm-30) REVERT: D 120 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7526 (tm-30) outliers start: 50 outliers final: 29 residues processed: 242 average time/residue: 0.1606 time to fit residues: 58.7811 Evaluate side-chains 218 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 241 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 247 LYS 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 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 17 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 62 optimal weight: 0.0040 chunk 63 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS ** B 858 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 = 0.3616 r_free = 0.3616 target = 0.089674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.071491 restraints weight = 66723.330| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.81 r_work: 0.3068 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6137 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= 0.127 Angle : 0.557 13.620 29771 Z= 0.300 Chirality : 0.039 0.168 3215 Planarity : 0.004 0.041 3504 Dihedral : 21.242 177.261 3808 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 2.50 % Allowed : 23.10 % Favored : 74.40 % 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: -0.75 (0.17), residues: 2296 helix: 0.70 (0.16), residues: 1076 sheet: -1.25 (0.33), residues: 233 loop : -1.65 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 75 TYR 0.012 0.001 TYR A 305 PHE 0.015 0.001 PHE C 142 TRP 0.019 0.001 TRP B 888 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00282 (21681) covalent geometry : angle 0.55696 (29771) hydrogen bonds : bond 0.03647 ( 917) hydrogen bonds : angle 4.07574 ( 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 235 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.661 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 279 GLN cc_start: 0.8548 (pt0) cc_final: 0.8291 (pt0) REVERT: A 287 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: A 291 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.7546 (mtt-85) REVERT: A 299 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8379 (mt-10) REVERT: A 326 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: A 372 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8873 (tp30) REVERT: A 393 MET cc_start: 0.8562 (tpp) cc_final: 0.8004 (tmm) REVERT: A 606 GLU cc_start: 0.8715 (pp20) cc_final: 0.8311 (pp20) REVERT: A 719 MET cc_start: 0.9215 (mmm) cc_final: 0.8996 (mmm) REVERT: A 762 MET cc_start: 0.9067 (mmm) cc_final: 0.8272 (mmt) REVERT: A 766 MET cc_start: 0.9071 (tpp) cc_final: 0.8736 (tpp) REVERT: A 810 CYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8963 (p) REVERT: A 1029 MET cc_start: 0.7656 (tpt) cc_final: 0.7437 (tpp) REVERT: B 126 MET cc_start: 0.8523 (mmm) cc_final: 0.8314 (mmm) REVERT: B 158 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8655 (ptpp) REVERT: B 246 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: B 247 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: B 266 GLN cc_start: 0.8712 (mt0) cc_final: 0.8375 (mm-40) REVERT: B 323 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8499 (mm-30) REVERT: B 509 ILE cc_start: 0.9159 (pt) cc_final: 0.8946 (mt) REVERT: B 512 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8301 (m-10) REVERT: B 642 PHE cc_start: 0.7744 (t80) cc_final: 0.7527 (t80) REVERT: B 643 LEU cc_start: 0.9202 (mt) cc_final: 0.8614 (mp) REVERT: B 714 GLU cc_start: 0.8866 (mp0) cc_final: 0.8637 (mp0) REVERT: B 719 MET cc_start: 0.9637 (mmm) cc_final: 0.9406 (mmm) REVERT: B 753 MET cc_start: 0.8816 (ppp) cc_final: 0.8291 (ppp) REVERT: C 69 ASP cc_start: 0.7727 (t0) cc_final: 0.6885 (t0) REVERT: C 73 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7918 (tm-30) REVERT: C 102 ASP cc_start: 0.8885 (m-30) cc_final: 0.8463 (p0) REVERT: C 107 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7688 (pp20) REVERT: C 116 GLN cc_start: 0.8444 (mt0) cc_final: 0.8197 (mm-40) REVERT: C 123 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8134 (ttm-80) REVERT: C 141 GLU cc_start: 0.8160 (pp20) cc_final: 0.7881 (pp20) REVERT: D 83 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6812 (mm-30) REVERT: D 120 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7370 (tm-30) outliers start: 49 outliers final: 29 residues processed: 226 average time/residue: 0.1659 time to fit residues: 56.8298 Evaluate side-chains 215 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 315 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 442 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 247 LYS 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 512 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 537 HIS Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 175 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.088664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070574 restraints weight = 65690.003| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.78 r_work: 0.3047 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21681 Z= 0.136 Angle : 0.564 9.498 29771 Z= 0.304 Chirality : 0.039 0.195 3215 Planarity : 0.004 0.042 3504 Dihedral : 21.172 176.947 3804 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 2.40 % Allowed : 23.36 % Favored : 74.25 % 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: -0.64 (0.17), residues: 2296 helix: 0.75 (0.16), residues: 1084 sheet: -1.10 (0.33), residues: 233 loop : -1.59 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 75 TYR 0.017 0.001 TYR A 814 PHE 0.016 0.001 PHE A 813 TRP 0.007 0.001 TRP B 960 HIS 0.018 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00306 (21681) covalent geometry : angle 0.56370 (29771) hydrogen bonds : bond 0.03670 ( 917) hydrogen bonds : angle 4.05458 ( 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 228 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 GLN cc_start: 0.8578 (pt0) cc_final: 0.8328 (pt0) REVERT: A 287 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: A 291 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.7615 (mtt-85) REVERT: A 299 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8378 (mt-10) REVERT: A 326 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: A 366 GLU cc_start: 0.8653 (pp20) cc_final: 0.8076 (tm-30) REVERT: A 393 MET cc_start: 0.8547 (tpp) cc_final: 0.7991 (tmm) REVERT: A 606 GLU cc_start: 0.8724 (pp20) cc_final: 0.8317 (pp20) REVERT: A 719 MET cc_start: 0.9234 (mmm) cc_final: 0.9004 (mmm) REVERT: A 762 MET cc_start: 0.9069 (mmm) cc_final: 0.8289 (mmt) REVERT: A 766 MET cc_start: 0.9128 (tpp) cc_final: 0.8791 (tpp) REVERT: A 810 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8942 (p) REVERT: B 246 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: B 247 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8336 (mttp) REVERT: B 266 GLN cc_start: 0.8738 (mt0) cc_final: 0.8448 (mm-40) REVERT: B 323 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 643 LEU cc_start: 0.9277 (mt) cc_final: 0.8818 (mp) REVERT: B 714 GLU cc_start: 0.8891 (mp0) cc_final: 0.8664 (mp0) REVERT: B 753 MET cc_start: 0.8841 (ppp) cc_final: 0.8322 (ppp) REVERT: B 762 MET cc_start: 0.9254 (mmm) cc_final: 0.8527 (mmt) REVERT: B 920 GLU cc_start: 0.7527 (pm20) cc_final: 0.7271 (pm20) REVERT: C 69 ASP cc_start: 0.7912 (t0) cc_final: 0.7141 (t0) REVERT: C 73 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7990 (tm-30) REVERT: C 99 TYR cc_start: 0.8562 (m-80) cc_final: 0.8273 (m-10) REVERT: C 102 ASP cc_start: 0.8879 (m-30) cc_final: 0.8395 (p0) REVERT: D 83 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6687 (mm-30) REVERT: D 120 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7408 (tm-30) outliers start: 47 outliers final: 32 residues processed: 218 average time/residue: 0.1644 time to fit residues: 54.8087 Evaluate side-chains 206 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 247 LYS 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 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 999 HIS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 102 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 156 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS B 819 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 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 = 0.3612 r_free = 0.3612 target = 0.089031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.070679 restraints weight = 66169.988| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.90 r_work: 0.3052 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.6524 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= 0.144 Angle : 0.581 11.229 29771 Z= 0.310 Chirality : 0.039 0.226 3215 Planarity : 0.004 0.041 3504 Dihedral : 21.174 176.792 3804 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.55 % Allowed : 23.05 % Favored : 74.40 % 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: -0.58 (0.17), residues: 2296 helix: 0.77 (0.16), residues: 1085 sheet: -0.96 (0.33), residues: 235 loop : -1.55 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 75 TYR 0.013 0.001 TYR A 305 PHE 0.021 0.001 PHE B 642 TRP 0.008 0.001 TRP A 888 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00326 (21681) covalent geometry : angle 0.58115 (29771) hydrogen bonds : bond 0.03804 ( 917) hydrogen bonds : angle 4.09957 ( 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 225 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: A 291 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.7592 (mtt-85) REVERT: A 299 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 326 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6757 (m-10) REVERT: A 366 GLU cc_start: 0.8667 (pp20) cc_final: 0.8133 (tm-30) REVERT: A 393 MET cc_start: 0.8550 (tpp) cc_final: 0.7965 (tmm) REVERT: A 606 GLU cc_start: 0.8703 (pp20) cc_final: 0.8254 (pp20) REVERT: A 762 MET cc_start: 0.9093 (mmm) cc_final: 0.8296 (mmt) REVERT: A 766 MET cc_start: 0.9102 (tpp) cc_final: 0.8753 (tpp) REVERT: A 1029 MET cc_start: 0.7774 (tpp) cc_final: 0.7288 (ttt) REVERT: B 158 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8572 (ptpt) REVERT: B 246 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: B 247 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8203 (mttp) REVERT: B 266 GLN cc_start: 0.8698 (mt0) cc_final: 0.8464 (mm110) REVERT: B 323 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8498 (mm-30) REVERT: B 509 ILE cc_start: 0.9150 (pt) cc_final: 0.8886 (mt) REVERT: B 543 MET cc_start: 0.9003 (mmp) cc_final: 0.8795 (mmp) REVERT: B 642 PHE cc_start: 0.7740 (t80) cc_final: 0.7283 (t80) REVERT: B 643 LEU cc_start: 0.9033 (mt) cc_final: 0.8515 (mp) REVERT: B 714 GLU cc_start: 0.8863 (mp0) cc_final: 0.8599 (mp0) REVERT: B 753 MET cc_start: 0.8846 (ppp) cc_final: 0.8278 (ppp) REVERT: B 762 MET cc_start: 0.9233 (mmm) cc_final: 0.8578 (mmt) REVERT: C 41 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8654 (mm-30) REVERT: C 69 ASP cc_start: 0.7994 (t0) cc_final: 0.7357 (t0) REVERT: C 73 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 99 TYR cc_start: 0.8502 (m-80) cc_final: 0.8206 (m-10) REVERT: C 102 ASP cc_start: 0.8696 (m-30) cc_final: 0.8447 (p0) REVERT: C 107 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7634 (pp20) REVERT: C 128 ASP cc_start: 0.8426 (t0) cc_final: 0.8191 (t0) REVERT: C 141 GLU cc_start: 0.8326 (pp20) cc_final: 0.7916 (pp20) REVERT: D 120 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7184 (tm-30) outliers start: 50 outliers final: 37 residues processed: 212 average time/residue: 0.1609 time to fit residues: 52.4308 Evaluate side-chains 210 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 247 LYS 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 537 HIS Chi-restraints excluded: chain B residue 621 ILE 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 817 THR Chi-restraints excluded: chain B residue 999 HIS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 6.9990 chunk 72 optimal weight: 0.0770 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 152 optimal weight: 0.1980 chunk 230 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 199 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.090258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071950 restraints weight = 66339.569| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.94 r_work: 0.3081 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6657 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= 0.119 Angle : 0.571 8.848 29771 Z= 0.306 Chirality : 0.039 0.211 3215 Planarity : 0.004 0.041 3504 Dihedral : 21.107 176.982 3804 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 1.89 % Allowed : 23.66 % Favored : 74.45 % 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: -0.46 (0.17), residues: 2296 helix: 0.89 (0.16), residues: 1074 sheet: -0.86 (0.33), residues: 233 loop : -1.51 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 75 TYR 0.014 0.001 TYR B 539 PHE 0.023 0.001 PHE B 535 TRP 0.012 0.001 TRP A 888 HIS 0.009 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00263 (21681) covalent geometry : angle 0.57084 (29771) hydrogen bonds : bond 0.03477 ( 917) hydrogen bonds : angle 4.05120 ( 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 210 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8241 (tp30) REVERT: A 291 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.7576 (mtt-85) REVERT: A 299 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 326 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: A 366 GLU cc_start: 0.8612 (pp20) cc_final: 0.8096 (tm-30) REVERT: A 393 MET cc_start: 0.8545 (tpp) cc_final: 0.7983 (tmm) REVERT: A 606 GLU cc_start: 0.8711 (pp20) cc_final: 0.8279 (pp20) REVERT: A 719 MET cc_start: 0.9221 (mmm) cc_final: 0.8985 (mmm) REVERT: A 762 MET cc_start: 0.9059 (mmm) cc_final: 0.8223 (mmt) REVERT: A 766 MET cc_start: 0.8991 (tpp) cc_final: 0.8661 (tpp) REVERT: A 1029 MET cc_start: 0.7819 (tpp) cc_final: 0.7282 (ttt) REVERT: B 246 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: B 247 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8313 (mttp) REVERT: B 266 GLN cc_start: 0.8726 (mt0) cc_final: 0.8509 (mm110) REVERT: B 323 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8500 (mm-30) REVERT: B 664 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8252 (tptp) REVERT: B 753 MET cc_start: 0.8831 (ppp) cc_final: 0.8265 (ppp) REVERT: B 762 MET cc_start: 0.9244 (mmm) cc_final: 0.8579 (mmt) REVERT: B 920 GLU cc_start: 0.7538 (pm20) cc_final: 0.7094 (pm20) REVERT: C 69 ASP cc_start: 0.7962 (t0) cc_final: 0.7287 (t0) REVERT: C 73 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7896 (tm-30) REVERT: C 99 TYR cc_start: 0.8453 (m-80) cc_final: 0.8082 (m-10) REVERT: C 141 GLU cc_start: 0.8315 (pp20) cc_final: 0.7909 (pp20) REVERT: D 25 GLU cc_start: 0.6848 (tt0) cc_final: 0.6387 (pt0) outliers start: 37 outliers final: 28 residues processed: 201 average time/residue: 0.1613 time to fit residues: 49.7073 Evaluate side-chains 208 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 208 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 247 LYS 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 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 999 HIS 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 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: 0.0030 chunk 219 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS B 239 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 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 = 0.3588 r_free = 0.3588 target = 0.088051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.069666 restraints weight = 66741.761| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.87 r_work: 0.3029 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21681 Z= 0.157 Angle : 0.602 9.197 29771 Z= 0.320 Chirality : 0.039 0.214 3215 Planarity : 0.004 0.066 3504 Dihedral : 21.119 176.040 3804 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 2.19 % Allowed : 23.56 % Favored : 74.25 % 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: -0.45 (0.17), residues: 2296 helix: 0.90 (0.16), residues: 1081 sheet: -0.75 (0.35), residues: 225 loop : -1.54 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 123 TYR 0.014 0.001 TYR A 305 PHE 0.019 0.001 PHE C 142 TRP 0.026 0.001 TRP B 713 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00358 (21681) covalent geometry : angle 0.60207 (29771) hydrogen bonds : bond 0.03983 ( 917) hydrogen bonds : angle 4.11559 ( 2487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5428.39 seconds wall clock time: 93 minutes 46.78 seconds (5626.78 seconds total)