Starting phenix.real_space_refine on Wed Nov 19 10:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6csx_7609/11_2025/6csx_7609.cif Found real_map, /net/cci-nas-00/data/ceres_data/6csx_7609/11_2025/6csx_7609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6csx_7609/11_2025/6csx_7609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6csx_7609/11_2025/6csx_7609.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6csx_7609/11_2025/6csx_7609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6csx_7609/11_2025/6csx_7609.map" } resolution = 3.0 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= 0.008 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 129 5.16 5 C 15009 2.51 5 N 3748 2.21 5 O 4334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23232 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7735 Classifications: {'peptide': 1019} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 973} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7685 Classifications: {'peptide': 1015} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 968} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 7305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7305 Classifications: {'peptide': 965} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 919} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 216 Unusual residues: {'D12': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 1, 'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {'PTY': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 2, 'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 6.18, per 1000 atoms: 0.27 Number of scatterers: 23232 At special positions: 0 Unit cell: (117.852, 116.144, 144.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 P 12 15.00 O 4334 8.00 N 3748 7.00 C 15009 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: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5504 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 25 sheets defined 52.9% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 3 through 7 removed outlier: 4.180A pdb=" N ASP B 7 " --> pdb=" O PHE B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.528A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.576A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.646A pdb=" N LEU B 118 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.583A pdb=" N VAL B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 4.040A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 242 through 248' Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.864A pdb=" N THR B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 removed outlier: 3.648A pdb=" N ILE B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.865A pdb=" N THR B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 366' Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.545A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 402 removed outlier: 3.793A pdb=" N MET B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.676A pdb=" N VAL B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 removed outlier: 3.587A pdb=" N ALA B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.561A pdb=" N THR B 431 " --> pdb=" O PRO B 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.696A pdb=" N SER B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 463 through 487 removed outlier: 3.778A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.671A pdb=" N GLY B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.870A pdb=" N TYR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 599 removed outlier: 4.037A pdb=" N VAL B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 4.224A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 707 removed outlier: 3.521A pdb=" N GLN B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 removed outlier: 3.503A pdb=" N LEU B 739 " --> pdb=" O LYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.833A pdb=" N THR B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 780 removed outlier: 3.699A pdb=" N ARG B 780 " --> pdb=" O ALA B 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 777 through 780' Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.573A pdb=" N GLY B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 848 removed outlier: 3.687A pdb=" N GLU B 845 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 851 No H-bonds generated for 'chain 'B' and resid 849 through 851' Processing helix chain 'B' and resid 861 through 869 removed outlier: 4.057A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 892 removed outlier: 3.630A pdb=" N TYR B 877 " --> pdb=" O ALA B 873 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 903 Processing helix chain 'B' and resid 904 through 918 removed outlier: 3.706A pdb=" N GLY B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 910 " --> pdb=" O PRO B 906 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 917 " --> pdb=" O LEU B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 955 removed outlier: 3.549A pdb=" N VAL B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 953 " --> pdb=" O ALA B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 984 removed outlier: 3.542A pdb=" N ARG B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix removed outlier: 3.828A pdb=" N SER B 979 " --> pdb=" O ILE B 975 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 992 removed outlier: 3.618A pdb=" N ILE B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1013 removed outlier: 4.239A pdb=" N GLN B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B1002 " --> pdb=" O GLY B 998 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B1005 " --> pdb=" O ASN B1001 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1033 Proline residue: B1023 - end of helix removed outlier: 3.774A pdb=" N VAL B1027 " --> pdb=" O PRO B1023 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B1030 " --> pdb=" O PHE B1026 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B1032 " --> pdb=" O VAL B1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.682A pdb=" N ILE C 6 " --> pdb=" O PRO C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 8 through 22 Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.621A pdb=" N LEU C 30 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.811A pdb=" N GLN C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.665A pdb=" N VAL C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.618A pdb=" N PHE C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.598A pdb=" N VAL C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.628A pdb=" N GLY C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.619A pdb=" N ALA C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 337 through 360 removed outlier: 3.717A pdb=" N VAL C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 386 removed outlier: 3.603A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.621A pdb=" N VAL C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.634A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 422 removed outlier: 3.921A pdb=" N VAL C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 433 Processing helix chain 'C' and resid 444 through 452 removed outlier: 4.660A pdb=" N SER C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 3.670A pdb=" N PHE C 458 " --> pdb=" O PRO C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 478 through 486 removed outlier: 3.626A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 removed outlier: 3.592A pdb=" N THR C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 558 removed outlier: 3.529A pdb=" N TYR C 545 " --> pdb=" O TYR C 541 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 600 removed outlier: 3.617A pdb=" N LYS C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 599 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 655 removed outlier: 3.690A pdb=" N MET C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 653 " --> pdb=" O MET C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 690 through 706 removed outlier: 3.801A pdb=" N LYS C 694 " --> pdb=" O LEU C 690 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 695 " --> pdb=" O GLY C 691 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.895A pdb=" N ALA C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 755 removed outlier: 3.645A pdb=" N ALA C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 788 removed outlier: 3.516A pdb=" N ILE C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 848 removed outlier: 3.899A pdb=" N GLU C 845 " --> pdb=" O MET C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 890 removed outlier: 3.662A pdb=" N GLN C 865 " --> pdb=" O GLY C 861 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 866 " --> pdb=" O MET C 862 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 895 through 902 removed outlier: 3.716A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 920 removed outlier: 3.592A pdb=" N ILE C 910 " --> pdb=" O PRO C 906 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 919 " --> pdb=" O ALA C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 937 removed outlier: 3.560A pdb=" N LEU C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 942 removed outlier: 3.677A pdb=" N ASN C 941 " --> pdb=" O LEU C 937 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA C 942 " --> pdb=" O SER C 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 937 through 942' Processing helix chain 'C' and resid 945 through 953 Processing helix chain 'C' and resid 959 through 971 removed outlier: 4.381A pdb=" N ARG C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 991 removed outlier: 3.804A pdb=" N LEU C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 1001 through 1013 removed outlier: 4.407A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C1011 " --> pdb=" O VAL C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1020 removed outlier: 4.041A pdb=" N ILE C1019 " --> pdb=" O VAL C1016 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE C1020 " --> pdb=" O LEU C1017 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1016 through 1020' Processing helix chain 'C' and resid 1021 through 1031 removed outlier: 3.535A pdb=" N ARG C1030 " --> pdb=" O PHE C1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 7 removed outlier: 4.367A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.702A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.754A pdb=" N VAL A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.601A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.552A pdb=" N ILE A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.514A pdb=" N PHE A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.584A pdb=" N ALA A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 358 removed outlier: 3.939A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 366 through 386 removed outlier: 3.615A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix removed outlier: 3.610A pdb=" N PHE A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 401 through 423 removed outlier: 3.900A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 449 removed outlier: 3.619A pdb=" N THR A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.691A pdb=" N PHE A 458 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.775A pdb=" N ALA A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.895A pdb=" N ALA A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.553A pdb=" N TYR A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 599 removed outlier: 3.581A pdb=" N VAL A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.741A pdb=" N MET A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 708 removed outlier: 4.012A pdb=" N LYS A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.506A pdb=" N ASN A 747 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 780 removed outlier: 3.565A pdb=" N ARG A 780 " --> pdb=" O ALA A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 780' Processing helix chain 'A' and resid 782 through 788 removed outlier: 3.546A pdb=" N ILE A 786 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 787 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 788 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.810A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 861 through 867 removed outlier: 3.771A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 893 removed outlier: 3.864A pdb=" N TYR A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 883 " --> pdb=" O ILE A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 removed outlier: 3.543A pdb=" N LEU A 903 " --> pdb=" O PHE A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 919 removed outlier: 3.894A pdb=" N ILE A 910 " --> pdb=" O PRO A 906 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 912 " --> pdb=" O GLY A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.561A pdb=" N LEU A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 984 removed outlier: 3.789A pdb=" N LEU A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 984 " --> pdb=" O LEU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 3.565A pdb=" N VAL A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1013 removed outlier: 3.525A pdb=" N GLN A1000 " --> pdb=" O GLY A 996 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.327A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 89 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 77 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 177 removed outlier: 5.748A pdb=" N LYS B 292 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 175 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY B 290 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 177 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 288 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 142 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 291 " --> pdb=" O MET B 138 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR B 327 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY B 141 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR B 325 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B 143 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE B 323 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 177 removed outlier: 5.748A pdb=" N LYS B 292 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 175 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY B 290 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 177 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 288 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.036A pdb=" N TYR B 182 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS B 770 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.594A pdb=" N SER B 233 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.594A pdb=" N SER B 233 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 254 removed outlier: 7.222A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 253 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER B 258 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 713 through 718 removed outlier: 4.257A pdb=" N VAL B 716 " --> pdb=" O LEU B 828 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 828 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY B 829 " --> pdb=" O PHE B 680 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 858 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 805 through 812 removed outlier: 5.070A pdb=" N SER A 233 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.589A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 89 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.601A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.601A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 573 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.624A pdb=" N TYR C 182 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS C 770 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG C 767 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE C 763 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS C 769 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP C 761 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 771 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 217 through 219 removed outlier: 4.215A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER C 233 " --> pdb=" O PHE A 727 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A 729 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 235 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 731 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 250 through 253 Processing sheet with id=AB8, first strand: chain 'C' and resid 826 through 828 Processing sheet with id=AB9, first strand: chain 'C' and resid 790 through 791 Processing sheet with id=AC1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.070A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU A 826 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 828 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 716 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.070A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY A 829 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.709A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.709A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 286 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.613A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.880A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 790 through 792 1116 hydrogen bonds defined for protein. 3189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3810 1.30 - 1.43: 5777 1.43 - 1.56: 13770 1.56 - 1.68: 24 1.68 - 1.81: 252 Bond restraints: 23633 Sorted by residual: bond pdb=" N PRO C 852 " pdb=" CD PRO C 852 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C8 PTY B1105 " pdb=" O7 PTY B1105 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C8 PTY B1104 " pdb=" O7 PTY B1104 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C8 PTY A1105 " pdb=" O7 PTY A1105 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C30 PTY A1103 " pdb=" O4 PTY A1103 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 23628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 31441 3.78 - 7.56: 458 7.56 - 11.35: 84 11.35 - 15.13: 3 15.13 - 18.91: 11 Bond angle restraints: 31997 Sorted by residual: angle pdb=" N VAL B 413 " pdb=" CA VAL B 413 " pdb=" C VAL B 413 " ideal model delta sigma weight residual 110.62 101.18 9.44 1.02e+00 9.61e-01 8.57e+01 angle pdb=" N GLN C 588 " pdb=" CA GLN C 588 " pdb=" C GLN C 588 " ideal model delta sigma weight residual 111.69 103.41 8.28 1.23e+00 6.61e-01 4.53e+01 angle pdb=" N VAL C 416 " pdb=" CA VAL C 416 " pdb=" C VAL C 416 " ideal model delta sigma weight residual 110.72 104.12 6.60 1.01e+00 9.80e-01 4.27e+01 angle pdb=" O11 PTY B1106 " pdb=" P1 PTY B1106 " pdb=" O14 PTY B1106 " ideal model delta sigma weight residual 92.90 111.81 -18.91 3.00e+00 1.11e-01 3.97e+01 angle pdb=" C VAL B 904 " pdb=" N VAL B 905 " pdb=" CA VAL B 905 " ideal model delta sigma weight residual 120.24 124.07 -3.83 6.30e-01 2.52e+00 3.70e+01 ... (remaining 31992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 13750 28.00 - 56.00: 425 56.00 - 83.99: 49 83.99 - 111.99: 6 111.99 - 139.99: 6 Dihedral angle restraints: 14236 sinusoidal: 5660 harmonic: 8576 Sorted by residual: dihedral pdb=" CA LYS C 131 " pdb=" C LYS C 131 " pdb=" N SER C 132 " pdb=" CA SER C 132 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALA C 446 " pdb=" C ALA C 446 " pdb=" N MET C 447 " pdb=" CA MET C 447 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" N ASN C 415 " pdb=" C ASN C 415 " pdb=" CA ASN C 415 " pdb=" CB ASN C 415 " ideal model delta harmonic sigma weight residual 122.80 136.99 -14.19 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 14233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3358 0.096 - 0.192: 358 0.192 - 0.287: 30 0.287 - 0.383: 5 0.383 - 0.479: 2 Chirality restraints: 3753 Sorted by residual: chirality pdb=" CA LEU C 488 " pdb=" N LEU C 488 " pdb=" C LEU C 488 " pdb=" CB LEU C 488 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA ASN C 415 " pdb=" N ASN C 415 " pdb=" C ASN C 415 " pdb=" CB ASN C 415 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA VAL B 412 " pdb=" N VAL B 412 " pdb=" C VAL B 412 " pdb=" CB VAL B 412 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3750 not shown) Planarity restraints: 4046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 717 " -0.080 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO C 718 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO C 718 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 718 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 317 " 0.073 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO C 318 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO C 318 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 318 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 451 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA C 451 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA C 451 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL C 452 " 0.022 2.00e-02 2.50e+03 ... (remaining 4043 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 52 2.43 - 3.05: 12960 3.05 - 3.67: 34503 3.67 - 4.28: 53965 4.28 - 4.90: 88602 Nonbonded interactions: 190082 Sorted by model distance: nonbonded pdb=" O VAL C 452 " pdb=" CD2 PHE C 453 " model vdw 1.815 3.340 nonbonded pdb=" O PRO C 427 " pdb=" OG1 THR C 431 " model vdw 2.222 3.040 nonbonded pdb=" CE2 PHE C 317 " pdb=" CD2 LEU C 321 " model vdw 2.232 3.760 nonbonded pdb=" O SER C 319 " pdb=" N LEU C 321 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP C 153 " pdb=" OH TYR C 182 " model vdw 2.244 3.040 ... (remaining 190077 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 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 413 or (resid 414 and (name N or name CA or name C o \ r name O or name CB )) or resid 415 through 602 or (resid 603 and (name N or nam \ e CA or name C or name O or name CB )) or resid 604 through 644 or (resid 645 th \ rough 646 and (name N or name CA or name C or name O or name CB )) or resid 647 \ through 1026 or (resid 1104 and (name C1 or name C11 or name C12 or name C13 or \ name C14 or name C8 or name O4 or name O7 )) or (resid 1105 and (name C11 or nam \ e C12 or name C13 or name C14 or name C5 or name C6 or name C8 or name O14 or na \ me O7 )) or (resid 1106 and (name C1 or name C30 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O30 or name O4 or n \ ame O7 )))) selection = (chain 'B' and (resid 1 through 413 or (resid 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 449 or (resid 450 and (name N or \ name CA or name C or name CB or name OG )) or resid 451 through 499 or resid 54 \ 0 through 602 or (resid 603 and (name N or name CA or name C or name O or name C \ B )) or resid 604 through 644 or (resid 645 through 646 and (name N or name CA o \ r name C or name O or name CB )) or resid 647 through 949 or resid 971 through 1 \ 026 or (resid 1105 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C8 or name O4 or name O7 )) or (resid 1106 and (name C11 or name C12 or \ name C13 or name C14 or name C5 or name C6 or name C8 or name O14 or name O7 )) \ or (resid 1107 and (name C1 or name C30 or name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name O30 or name O4 or name O7 )) \ )) selection = (chain 'C' and (resid 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 449 or (resid 450 and (name N or name CA or name C o \ r name CB or name OG )) or resid 451 through 499 or resid 540 through 949 or res \ id 971 through 1026 or (resid 1101 and (name C1 or name C11 or name C12 or name \ C13 or name C14 or name C8 or name O4 or name O7 )) or (resid 1102 and (name C11 \ or name C12 or name C13 or name C14 or name C5 or name C6 or name C8 or name O1 \ 4 or name O7 )) or (resid 1103 and (name C1 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name O30 or name \ O4 or name O7 )))) } 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: 3.040 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: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.850 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.009 0.087 23633 Z= 0.384 Angle : 1.209 18.910 31997 Z= 0.603 Chirality : 0.062 0.479 3753 Planarity : 0.008 0.123 4046 Dihedral : 13.610 139.990 8732 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.80 % Favored : 93.67 % Rotamer: Outliers : 2.42 % Allowed : 4.07 % Favored : 93.51 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -5.28 (0.11), residues: 2985 helix: -4.39 (0.06), residues: 1492 sheet: -2.36 (0.22), residues: 425 loop : -2.16 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 8 TYR 0.058 0.004 TYR B 49 PHE 0.052 0.003 PHE B 5 TRP 0.021 0.003 TRP B 754 HIS 0.009 0.002 HIS C 692 Details of bonding type rmsd covalent geometry : bond 0.00902 (23633) covalent geometry : angle 1.20929 (31997) hydrogen bonds : bond 0.29024 ( 1082) hydrogen bonds : angle 10.39268 ( 3189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 524 time to evaluate : 0.765 Fit side-chains REVERT: B 28 LEU cc_start: 0.7933 (mp) cc_final: 0.7608 (pp) REVERT: B 176 GLN cc_start: 0.7216 (tp40) cc_final: 0.6828 (tm-30) REVERT: B 218 GLN cc_start: 0.8811 (mt0) cc_final: 0.8268 (mt0) REVERT: B 435 MET cc_start: 0.6948 (mmp) cc_final: 0.5932 (ptm) REVERT: B 558 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7250 (ptt90) REVERT: B 953 MET cc_start: 0.7117 (mtt) cc_final: 0.6914 (mtm) REVERT: C 29 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7663 (mtmt) REVERT: C 184 MET cc_start: 0.8956 (tpp) cc_final: 0.8244 (tpt) REVERT: C 413 VAL cc_start: 0.8890 (p) cc_final: 0.8606 (t) REVERT: C 519 MET cc_start: 0.5812 (pp-130) cc_final: 0.5491 (pp-130) REVERT: C 868 LEU cc_start: 0.8841 (tm) cc_final: 0.8498 (mm) REVERT: C 958 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6862 (pttt) REVERT: A 366 LEU cc_start: 0.8950 (tt) cc_final: 0.8618 (tt) outliers start: 59 outliers final: 19 residues processed: 574 average time/residue: 0.6642 time to fit residues: 434.9704 Evaluate side-chains 330 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 472 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 112 GLN B 211 ASN B 747 ASN C 63 GLN C 74 ASN C 213 GLN C 228 GLN C 231 ASN C 282 ASN C 298 ASN C 361 ASN C 469 GLN C 596 HIS ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS C 871 ASN A 58 GLN A 68 ASN A 229 GLN A 231 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 439 GLN A 469 GLN A 737 GLN A 928 GLN A 941 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108798 restraints weight = 35444.312| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.71 r_work: 0.3207 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23633 Z= 0.126 Angle : 0.653 10.477 31997 Z= 0.336 Chirality : 0.044 0.215 3753 Planarity : 0.005 0.072 4046 Dihedral : 11.804 156.316 3591 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 4.27 % Allowed : 11.84 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.13), residues: 2985 helix: -2.48 (0.11), residues: 1520 sheet: -1.61 (0.23), residues: 416 loop : -1.63 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 653 TYR 0.019 0.001 TYR A 49 PHE 0.023 0.001 PHE B 5 TRP 0.007 0.001 TRP A 754 HIS 0.004 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00273 (23633) covalent geometry : angle 0.65344 (31997) hydrogen bonds : bond 0.04572 ( 1082) hydrogen bonds : angle 5.60296 ( 3189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 393 time to evaluate : 0.987 Fit side-chains REVERT: B 28 LEU cc_start: 0.8394 (mp) cc_final: 0.7802 (pp) REVERT: B 138 MET cc_start: 0.8418 (ptm) cc_final: 0.8192 (ptm) REVERT: B 176 GLN cc_start: 0.7249 (tp40) cc_final: 0.6663 (tm-30) REVERT: B 196 PHE cc_start: 0.7962 (m-80) cc_final: 0.7332 (m-10) REVERT: B 408 ASP cc_start: 0.8213 (m-30) cc_final: 0.8003 (m-30) REVERT: B 435 MET cc_start: 0.7699 (mmp) cc_final: 0.6087 (ttp) REVERT: C 29 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7962 (mtmt) REVERT: C 69 MET cc_start: 0.9133 (mmt) cc_final: 0.8920 (mmt) REVERT: C 117 LEU cc_start: 0.8543 (mt) cc_final: 0.7631 (tp) REVERT: C 184 MET cc_start: 0.9148 (tpp) cc_final: 0.8707 (tpt) REVERT: C 519 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.5344 (pp-130) REVERT: C 566 ASP cc_start: 0.8238 (m-30) cc_final: 0.7974 (m-30) REVERT: C 744 ASN cc_start: 0.7877 (t0) cc_final: 0.7527 (m-40) REVERT: C 826 GLU cc_start: 0.8602 (tt0) cc_final: 0.8325 (tt0) REVERT: C 958 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6844 (pttt) REVERT: C 977 MET cc_start: 0.8704 (mmm) cc_final: 0.8319 (mmm) REVERT: C 1031 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7676 (ptt180) REVERT: A 174 ASP cc_start: 0.8341 (p0) cc_final: 0.7524 (t0) REVERT: A 363 ARG cc_start: 0.7585 (ttm110) cc_final: 0.7140 (ttp-110) REVERT: A 447 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7587 (mpp) REVERT: A 640 GLU cc_start: 0.8099 (tp30) cc_final: 0.7737 (pm20) REVERT: A 681 ASP cc_start: 0.8486 (t0) cc_final: 0.8201 (t0) REVERT: A 858 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7913 (t0) outliers start: 104 outliers final: 23 residues processed: 458 average time/residue: 0.5619 time to fit residues: 301.0965 Evaluate side-chains 331 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 902 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 117 optimal weight: 6.9990 chunk 297 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 67 optimal weight: 0.0060 chunk 135 optimal weight: 3.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN B 846 GLN C 63 GLN C 68 ASN C 237 GLN ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN A 237 GLN A 391 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107144 restraints weight = 35359.146| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.69 r_work: 0.3178 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23633 Z= 0.125 Angle : 0.611 9.670 31997 Z= 0.310 Chirality : 0.044 0.202 3753 Planarity : 0.004 0.051 4046 Dihedral : 10.434 151.205 3569 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 4.73 % Allowed : 14.10 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -2.11 (0.15), residues: 2985 helix: -1.33 (0.13), residues: 1513 sheet: -1.24 (0.24), residues: 424 loop : -1.23 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 558 TYR 0.017 0.001 TYR C 49 PHE 0.023 0.001 PHE B 5 TRP 0.010 0.001 TRP B 895 HIS 0.002 0.001 HIS C 692 Details of bonding type rmsd covalent geometry : bond 0.00286 (23633) covalent geometry : angle 0.61065 (31997) hydrogen bonds : bond 0.03842 ( 1082) hydrogen bonds : angle 4.96694 ( 3189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 353 time to evaluate : 0.932 Fit side-chains TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. REVERT: B 28 LEU cc_start: 0.8373 (mp) cc_final: 0.7786 (pp) REVERT: B 176 GLN cc_start: 0.7190 (tp40) cc_final: 0.6677 (tm-30) REVERT: B 196 PHE cc_start: 0.7935 (m-80) cc_final: 0.7427 (m-10) REVERT: B 408 ASP cc_start: 0.8246 (m-30) cc_final: 0.7981 (m-30) REVERT: B 435 MET cc_start: 0.7652 (mmp) cc_final: 0.6211 (ptt) REVERT: B 628 PHE cc_start: 0.8311 (m-10) cc_final: 0.8089 (m-10) REVERT: B 825 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8621 (mtt) REVERT: B 969 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7587 (ptm-80) REVERT: B 987 MET cc_start: 0.8155 (tpt) cc_final: 0.7638 (mmm) REVERT: B 1008 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8201 (ttt) REVERT: B 1011 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7603 (ttm) REVERT: C 29 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7935 (mtmt) REVERT: C 117 LEU cc_start: 0.8439 (mt) cc_final: 0.7552 (tp) REVERT: C 184 MET cc_start: 0.9174 (tpp) cc_final: 0.8672 (tpt) REVERT: C 334 LYS cc_start: 0.8775 (ttmp) cc_final: 0.8203 (tptt) REVERT: C 415 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6493 (p0) REVERT: C 519 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5600 (pp-130) REVERT: C 542 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 547 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8756 (mp) REVERT: C 744 ASN cc_start: 0.7873 (t0) cc_final: 0.7559 (m-40) REVERT: C 919 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7628 (ttm110) REVERT: C 1031 ARG cc_start: 0.8058 (ptm160) cc_final: 0.7679 (ptt180) REVERT: A 95 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: A 115 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7985 (ttt) REVERT: A 174 ASP cc_start: 0.8412 (p0) cc_final: 0.7545 (t0) REVERT: A 335 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 363 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7379 (ttp-110) REVERT: A 447 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7566 (mpp) REVERT: A 640 GLU cc_start: 0.8024 (tp30) cc_final: 0.7710 (pm20) REVERT: A 825 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8192 (mtt) REVERT: A 858 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7795 (t0) REVERT: A 924 ASP cc_start: 0.7042 (p0) cc_final: 0.6776 (p0) REVERT: A 928 GLN cc_start: 0.8567 (mt0) cc_final: 0.8364 (mt0) outliers start: 115 outliers final: 36 residues processed: 424 average time/residue: 0.5881 time to fit residues: 290.3190 Evaluate side-chains 356 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 984 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 170 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 687 GLN B1001 ASN C 237 GLN C 391 ASN C 923 ASN A 144 ASN A 391 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103902 restraints weight = 35439.885| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.68 r_work: 0.3123 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23633 Z= 0.164 Angle : 0.637 10.721 31997 Z= 0.320 Chirality : 0.046 0.235 3753 Planarity : 0.004 0.046 4046 Dihedral : 10.019 138.221 3563 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 5.22 % Allowed : 15.33 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -1.59 (0.15), residues: 2985 helix: -0.83 (0.13), residues: 1519 sheet: -1.11 (0.25), residues: 407 loop : -1.08 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 558 TYR 0.020 0.002 TYR C 49 PHE 0.026 0.002 PHE B 5 TRP 0.007 0.001 TRP B 789 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00392 (23633) covalent geometry : angle 0.63701 (31997) hydrogen bonds : bond 0.03794 ( 1082) hydrogen bonds : angle 4.79166 ( 3189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 311 time to evaluate : 0.856 Fit side-chains REVERT: B 1 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6972 (tpp) REVERT: B 28 LEU cc_start: 0.8337 (mp) cc_final: 0.7748 (pp) REVERT: B 176 GLN cc_start: 0.7070 (tp40) cc_final: 0.6573 (tm-30) REVERT: B 408 ASP cc_start: 0.8366 (m-30) cc_final: 0.8091 (m-30) REVERT: B 435 MET cc_start: 0.7826 (mmp) cc_final: 0.6257 (ptm) REVERT: B 685 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9034 (mm) REVERT: B 825 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8502 (mtt) REVERT: B 960 LEU cc_start: 0.6917 (tp) cc_final: 0.6700 (tt) REVERT: B 969 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7665 (ptm-80) REVERT: B 987 MET cc_start: 0.8189 (tpt) cc_final: 0.7700 (mmm) REVERT: B 1008 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8248 (ttt) REVERT: C 29 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7971 (mtmt) REVERT: C 184 MET cc_start: 0.9163 (tpp) cc_final: 0.8664 (tpt) REVERT: C 229 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: C 439 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: C 519 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5640 (pp-130) REVERT: C 542 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8503 (tp) REVERT: C 546 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 547 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8764 (mp) REVERT: C 744 ASN cc_start: 0.7895 (t0) cc_final: 0.7590 (m-40) REVERT: C 919 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7669 (ttm110) REVERT: A 115 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7970 (ttt) REVERT: A 174 ASP cc_start: 0.8460 (p0) cc_final: 0.7676 (t0) REVERT: A 363 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7426 (ttp-110) REVERT: A 447 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7595 (mpp) REVERT: A 542 LEU cc_start: 0.6472 (pt) cc_final: 0.6188 (pt) REVERT: A 569 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8167 (mt0) REVERT: A 640 GLU cc_start: 0.8071 (tp30) cc_final: 0.7743 (pm20) REVERT: A 825 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8222 (mtt) REVERT: A 858 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: A 924 ASP cc_start: 0.7196 (p0) cc_final: 0.6924 (p0) REVERT: A 928 GLN cc_start: 0.8535 (mt0) cc_final: 0.8322 (mt0) outliers start: 127 outliers final: 49 residues processed: 396 average time/residue: 0.5764 time to fit residues: 266.6861 Evaluate side-chains 359 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 984 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN C 237 GLN A 58 GLN A 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103552 restraints weight = 35160.861| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.67 r_work: 0.3120 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23633 Z= 0.161 Angle : 0.630 10.486 31997 Z= 0.315 Chirality : 0.046 0.282 3753 Planarity : 0.004 0.048 4046 Dihedral : 9.668 122.886 3563 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 4.81 % Allowed : 16.19 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -1.29 (0.15), residues: 2985 helix: -0.55 (0.13), residues: 1536 sheet: -0.93 (0.25), residues: 414 loop : -1.01 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 558 TYR 0.017 0.001 TYR C 49 PHE 0.022 0.001 PHE B 5 TRP 0.008 0.001 TRP B 789 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00385 (23633) covalent geometry : angle 0.62986 (31997) hydrogen bonds : bond 0.03670 ( 1082) hydrogen bonds : angle 4.71995 ( 3189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 302 time to evaluate : 1.010 Fit side-chains REVERT: B 1 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.6976 (tpp) REVERT: B 28 LEU cc_start: 0.8357 (mp) cc_final: 0.7784 (pp) REVERT: B 176 GLN cc_start: 0.7081 (tp40) cc_final: 0.6560 (tm-30) REVERT: B 408 ASP cc_start: 0.8349 (m-30) cc_final: 0.8090 (m-30) REVERT: B 435 MET cc_start: 0.7893 (mmp) cc_final: 0.6391 (ptt) REVERT: B 825 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8481 (mtt) REVERT: B 969 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7709 (ptm-80) REVERT: B 987 MET cc_start: 0.8191 (tpt) cc_final: 0.7758 (mmm) REVERT: C 29 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8005 (mtmt) REVERT: C 184 MET cc_start: 0.9155 (tpp) cc_final: 0.8622 (tpt) REVERT: C 229 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: C 237 GLN cc_start: 0.8548 (tt0) cc_final: 0.8171 (tt0) REVERT: C 439 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: C 519 MET cc_start: 0.6119 (pp-130) cc_final: 0.5761 (pp-130) REVERT: C 542 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8510 (tp) REVERT: C 546 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8390 (tp) REVERT: C 682 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7816 (p90) REVERT: C 744 ASN cc_start: 0.7922 (t0) cc_final: 0.7642 (m110) REVERT: C 919 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7719 (ttm110) REVERT: A 95 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: A 115 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7946 (ttt) REVERT: A 174 ASP cc_start: 0.8467 (p0) cc_final: 0.7699 (t0) REVERT: A 363 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7368 (ttp-110) REVERT: A 447 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7509 (mpp) REVERT: A 569 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: A 640 GLU cc_start: 0.8052 (tp30) cc_final: 0.7748 (pm20) REVERT: A 825 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: A 858 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: A 924 ASP cc_start: 0.7195 (p0) cc_final: 0.6948 (p0) outliers start: 117 outliers final: 47 residues processed: 386 average time/residue: 0.5787 time to fit residues: 261.1547 Evaluate side-chains 349 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 66 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 279 optimal weight: 0.0570 chunk 254 optimal weight: 0.2980 chunk 22 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 697 GLN A 58 GLN A 237 GLN A 391 ASN A 928 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102299 restraints weight = 35481.398| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.68 r_work: 0.3104 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23633 Z= 0.183 Angle : 0.644 10.824 31997 Z= 0.323 Chirality : 0.046 0.278 3753 Planarity : 0.004 0.049 4046 Dihedral : 9.466 99.032 3563 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 4.64 % Allowed : 16.89 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -1.13 (0.15), residues: 2985 helix: -0.39 (0.13), residues: 1533 sheet: -0.95 (0.25), residues: 403 loop : -0.96 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 558 TYR 0.018 0.002 TYR C 49 PHE 0.027 0.002 PHE C 948 TRP 0.008 0.001 TRP B 789 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00440 (23633) covalent geometry : angle 0.64392 (31997) hydrogen bonds : bond 0.03781 ( 1082) hydrogen bonds : angle 4.72327 ( 3189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 288 time to evaluate : 0.929 Fit side-chains REVERT: B 1 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.6960 (tpp) REVERT: B 28 LEU cc_start: 0.8409 (mp) cc_final: 0.7813 (pp) REVERT: B 176 GLN cc_start: 0.7044 (tp40) cc_final: 0.6537 (tm-30) REVERT: B 362 PHE cc_start: 0.8288 (t80) cc_final: 0.7971 (t80) REVERT: B 408 ASP cc_start: 0.8391 (m-30) cc_final: 0.8118 (m-30) REVERT: B 435 MET cc_start: 0.8042 (mmp) cc_final: 0.6362 (ptt) REVERT: B 439 GLN cc_start: 0.7961 (tt0) cc_final: 0.7612 (pt0) REVERT: B 825 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8420 (mtt) REVERT: B 960 LEU cc_start: 0.7059 (tp) cc_final: 0.6627 (tp) REVERT: B 969 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7720 (ptm-80) REVERT: B 987 MET cc_start: 0.8262 (tpt) cc_final: 0.7841 (mmm) REVERT: C 29 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8034 (mtmt) REVERT: C 184 MET cc_start: 0.9148 (tpp) cc_final: 0.8638 (tpt) REVERT: C 229 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: C 334 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8474 (tptt) REVERT: C 439 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: C 542 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8521 (tp) REVERT: C 546 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8420 (tp) REVERT: C 682 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7848 (p90) REVERT: C 744 ASN cc_start: 0.7926 (t0) cc_final: 0.7641 (m110) REVERT: C 919 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7741 (ttm110) REVERT: A 95 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8326 (mt-10) REVERT: A 115 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7955 (ttt) REVERT: A 174 ASP cc_start: 0.8502 (p0) cc_final: 0.7746 (t0) REVERT: A 363 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7091 (ttm170) REVERT: A 447 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7551 (mpp) REVERT: A 496 MET cc_start: 0.8234 (ptp) cc_final: 0.7986 (ptt) REVERT: A 569 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: A 640 GLU cc_start: 0.8087 (tp30) cc_final: 0.7767 (pm20) REVERT: A 825 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8356 (mtt) REVERT: A 858 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8036 (m-30) outliers start: 113 outliers final: 56 residues processed: 370 average time/residue: 0.5988 time to fit residues: 258.7329 Evaluate side-chains 352 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 280 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 207 optimal weight: 2.9990 chunk 279 optimal weight: 0.0170 chunk 202 optimal weight: 0.1980 chunk 160 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 294 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN C 692 HIS C 923 ASN A 58 GLN A 237 GLN A 391 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106717 restraints weight = 35164.598| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.67 r_work: 0.3171 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23633 Z= 0.106 Angle : 0.583 11.744 31997 Z= 0.290 Chirality : 0.043 0.274 3753 Planarity : 0.004 0.050 4046 Dihedral : 8.671 77.941 3563 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 3.29 % Allowed : 18.45 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -0.66 (0.16), residues: 2985 helix: 0.02 (0.14), residues: 1535 sheet: -0.63 (0.25), residues: 407 loop : -0.83 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 558 TYR 0.011 0.001 TYR C 545 PHE 0.020 0.001 PHE C 948 TRP 0.009 0.001 TRP A 754 HIS 0.002 0.000 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00238 (23633) covalent geometry : angle 0.58330 (31997) hydrogen bonds : bond 0.03051 ( 1082) hydrogen bonds : angle 4.47021 ( 3189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 322 time to evaluate : 0.947 Fit side-chains REVERT: B 28 LEU cc_start: 0.8379 (mp) cc_final: 0.7798 (pp) REVERT: B 176 GLN cc_start: 0.6994 (tp40) cc_final: 0.6500 (tm-30) REVERT: B 278 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8131 (pt) REVERT: B 362 PHE cc_start: 0.8320 (t80) cc_final: 0.8025 (t80) REVERT: B 408 ASP cc_start: 0.8307 (m-30) cc_final: 0.8038 (m-30) REVERT: B 435 MET cc_start: 0.7826 (mmp) cc_final: 0.6243 (ptm) REVERT: B 588 GLN cc_start: 0.8389 (tp40) cc_final: 0.8162 (tp-100) REVERT: B 987 MET cc_start: 0.8298 (tpt) cc_final: 0.7922 (mmm) REVERT: C 29 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7975 (mtmt) REVERT: C 104 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8975 (tm-30) REVERT: C 117 LEU cc_start: 0.8373 (mt) cc_final: 0.7544 (tp) REVERT: C 184 MET cc_start: 0.9100 (tpp) cc_final: 0.8620 (tpt) REVERT: C 237 GLN cc_start: 0.8464 (tt0) cc_final: 0.8143 (tt0) REVERT: C 334 LYS cc_start: 0.8869 (ttmp) cc_final: 0.8448 (tptt) REVERT: C 439 GLN cc_start: 0.8065 (tm130) cc_final: 0.7609 (tm-30) REVERT: C 682 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7481 (p90) REVERT: C 744 ASN cc_start: 0.7859 (t0) cc_final: 0.7634 (m110) REVERT: C 919 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7751 (ttm110) REVERT: A 95 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: A 174 ASP cc_start: 0.8375 (p0) cc_final: 0.7554 (t0) REVERT: A 259 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6581 (mtm-85) REVERT: A 363 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7396 (ttp-110) REVERT: A 447 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7376 (mpp) REVERT: A 496 MET cc_start: 0.8135 (ptp) cc_final: 0.7826 (ptt) REVERT: A 640 GLU cc_start: 0.8028 (tp30) cc_final: 0.7739 (pm20) REVERT: A 666 PHE cc_start: 0.8360 (p90) cc_final: 0.7398 (m-80) REVERT: A 719 ASN cc_start: 0.8011 (t0) cc_final: 0.7623 (t0) outliers start: 80 outliers final: 34 residues processed: 374 average time/residue: 0.5900 time to fit residues: 257.1477 Evaluate side-chains 330 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 100 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 284 optimal weight: 0.4980 chunk 185 optimal weight: 0.9980 chunk 72 optimal weight: 0.0050 chunk 232 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 231 ASN C 3 ASN A 58 GLN A 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107253 restraints weight = 35075.137| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.67 r_work: 0.3177 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23633 Z= 0.105 Angle : 0.591 12.177 31997 Z= 0.292 Chirality : 0.043 0.307 3753 Planarity : 0.004 0.052 4046 Dihedral : 8.281 77.262 3561 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 20.30 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -0.35 (0.16), residues: 2985 helix: 0.30 (0.14), residues: 1533 sheet: -0.51 (0.25), residues: 402 loop : -0.72 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 558 TYR 0.022 0.001 TYR C 545 PHE 0.033 0.001 PHE C 948 TRP 0.009 0.001 TRP A 754 HIS 0.002 0.000 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00236 (23633) covalent geometry : angle 0.59086 (31997) hydrogen bonds : bond 0.02974 ( 1082) hydrogen bonds : angle 4.34944 ( 3189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.969 Fit side-chains TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. REVERT: B 28 LEU cc_start: 0.8379 (mp) cc_final: 0.7805 (pp) REVERT: B 176 GLN cc_start: 0.6921 (tp40) cc_final: 0.6535 (tm-30) REVERT: B 278 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8128 (pt) REVERT: B 362 PHE cc_start: 0.8311 (t80) cc_final: 0.8009 (t80) REVERT: B 408 ASP cc_start: 0.8327 (m-30) cc_final: 0.8016 (m-30) REVERT: B 435 MET cc_start: 0.7831 (mmp) cc_final: 0.6221 (ptm) REVERT: B 987 MET cc_start: 0.8299 (tpt) cc_final: 0.7941 (mmm) REVERT: C 29 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7993 (mtmt) REVERT: C 104 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8990 (tm-30) REVERT: C 117 LEU cc_start: 0.8353 (mt) cc_final: 0.7534 (tp) REVERT: C 184 MET cc_start: 0.9079 (tpp) cc_final: 0.8637 (tpt) REVERT: C 312 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8190 (mtpt) REVERT: C 334 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8446 (tptt) REVERT: C 429 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7260 (mt-10) REVERT: C 439 GLN cc_start: 0.7985 (tm130) cc_final: 0.7551 (tm-30) REVERT: C 682 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7515 (p90) REVERT: C 744 ASN cc_start: 0.7805 (t0) cc_final: 0.7591 (m110) REVERT: C 919 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7715 (ttm110) REVERT: C 958 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7209 (pttt) REVERT: A 174 ASP cc_start: 0.8354 (p0) cc_final: 0.7479 (t0) REVERT: A 259 ARG cc_start: 0.7347 (mtm180) cc_final: 0.6518 (mtm-85) REVERT: A 363 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7384 (ttp-110) REVERT: A 496 MET cc_start: 0.8077 (ptp) cc_final: 0.7719 (ptt) REVERT: A 640 GLU cc_start: 0.8059 (tp30) cc_final: 0.7763 (pm20) REVERT: A 666 PHE cc_start: 0.8334 (p90) cc_final: 0.7316 (m-80) outliers start: 60 outliers final: 31 residues processed: 353 average time/residue: 0.5926 time to fit residues: 243.9547 Evaluate side-chains 322 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 226 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 846 GLN A 58 GLN A 89 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106163 restraints weight = 35391.089| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.68 r_work: 0.3163 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23633 Z= 0.119 Angle : 0.601 12.251 31997 Z= 0.297 Chirality : 0.044 0.301 3753 Planarity : 0.004 0.058 4046 Dihedral : 8.208 76.591 3561 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 2.47 % Allowed : 20.55 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -0.22 (0.16), residues: 2985 helix: 0.44 (0.14), residues: 1533 sheet: -0.49 (0.25), residues: 406 loop : -0.69 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 558 TYR 0.024 0.001 TYR C 545 PHE 0.027 0.001 PHE C 948 TRP 0.008 0.001 TRP A 754 HIS 0.002 0.000 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00279 (23633) covalent geometry : angle 0.60067 (31997) hydrogen bonds : bond 0.03091 ( 1082) hydrogen bonds : angle 4.35256 ( 3189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 0.832 Fit side-chains TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. REVERT: B 28 LEU cc_start: 0.8390 (mp) cc_final: 0.7818 (pp) REVERT: B 176 GLN cc_start: 0.6949 (tp40) cc_final: 0.6574 (tm-30) REVERT: B 278 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8187 (pt) REVERT: B 362 PHE cc_start: 0.8311 (t80) cc_final: 0.7996 (t80) REVERT: B 408 ASP cc_start: 0.8390 (m-30) cc_final: 0.8076 (m-30) REVERT: B 435 MET cc_start: 0.7855 (mmp) cc_final: 0.6249 (ptt) REVERT: B 953 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7857 (mtt) REVERT: B 987 MET cc_start: 0.8354 (tpt) cc_final: 0.7994 (mmm) REVERT: C 29 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8010 (mtmt) REVERT: C 104 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8985 (tm-30) REVERT: C 117 LEU cc_start: 0.8358 (mt) cc_final: 0.7532 (tp) REVERT: C 184 MET cc_start: 0.9087 (tpp) cc_final: 0.8633 (tpt) REVERT: C 312 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8239 (mtpt) REVERT: C 334 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8453 (tptt) REVERT: C 429 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7303 (mt-10) REVERT: C 439 GLN cc_start: 0.7972 (tm130) cc_final: 0.7543 (tm-30) REVERT: C 682 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7561 (p90) REVERT: C 744 ASN cc_start: 0.7886 (t0) cc_final: 0.7552 (m-40) REVERT: C 919 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7763 (ttm110) REVERT: C 958 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7275 (pttt) REVERT: A 174 ASP cc_start: 0.8442 (p0) cc_final: 0.7623 (t0) REVERT: A 363 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7356 (ttp-110) REVERT: A 496 MET cc_start: 0.8077 (ptp) cc_final: 0.7643 (ptt) REVERT: A 640 GLU cc_start: 0.8037 (tp30) cc_final: 0.7779 (pm20) REVERT: A 666 PHE cc_start: 0.8322 (p90) cc_final: 0.7301 (m-80) REVERT: A 858 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (m-30) outliers start: 60 outliers final: 38 residues processed: 330 average time/residue: 0.5718 time to fit residues: 221.8150 Evaluate side-chains 322 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 228 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 50 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 268 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 overall best weight: 2.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN C 697 GLN A 58 GLN A 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103786 restraints weight = 35301.085| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.66 r_work: 0.3127 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23633 Z= 0.151 Angle : 0.636 12.176 31997 Z= 0.316 Chirality : 0.046 0.345 3753 Planarity : 0.004 0.061 4046 Dihedral : 8.412 75.521 3561 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 2.34 % Allowed : 20.84 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -0.26 (0.16), residues: 2985 helix: 0.39 (0.14), residues: 1543 sheet: -0.58 (0.25), residues: 401 loop : -0.65 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 558 TYR 0.027 0.001 TYR C 545 PHE 0.023 0.001 PHE C 948 TRP 0.006 0.001 TRP B 789 HIS 0.002 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00361 (23633) covalent geometry : angle 0.63631 (31997) hydrogen bonds : bond 0.03408 ( 1082) hydrogen bonds : angle 4.47574 ( 3189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 0.956 Fit side-chains TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. REVERT: B 28 LEU cc_start: 0.8412 (mp) cc_final: 0.7830 (pp) REVERT: B 176 GLN cc_start: 0.6911 (tp40) cc_final: 0.6519 (tm-30) REVERT: B 278 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8212 (pt) REVERT: B 362 PHE cc_start: 0.8322 (t80) cc_final: 0.7985 (t80) REVERT: B 408 ASP cc_start: 0.8456 (m-30) cc_final: 0.8153 (m-30) REVERT: B 435 MET cc_start: 0.8029 (mmp) cc_final: 0.6372 (ptt) REVERT: B 953 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7873 (mtt) REVERT: B 987 MET cc_start: 0.8354 (tpt) cc_final: 0.7976 (mmm) REVERT: B 1008 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8292 (ttp) REVERT: C 29 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8011 (mtmt) REVERT: C 117 LEU cc_start: 0.8372 (mt) cc_final: 0.7502 (tp) REVERT: C 184 MET cc_start: 0.9113 (tpp) cc_final: 0.8592 (tpt) REVERT: C 312 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8266 (mtpt) REVERT: C 334 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8483 (tptt) REVERT: C 439 GLN cc_start: 0.8051 (tm130) cc_final: 0.7685 (tm-30) REVERT: C 519 MET cc_start: 0.6564 (pp-130) cc_final: 0.6187 (tmt) REVERT: C 682 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7773 (p90) REVERT: C 744 ASN cc_start: 0.7865 (t0) cc_final: 0.7522 (m-40) REVERT: C 919 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7798 (ttm110) REVERT: A 174 ASP cc_start: 0.8470 (p0) cc_final: 0.7726 (t0) REVERT: A 363 ARG cc_start: 0.7736 (ttm110) cc_final: 0.7392 (ttp-110) REVERT: A 496 MET cc_start: 0.8148 (ptp) cc_final: 0.7740 (ptt) REVERT: A 558 ARG cc_start: 0.6786 (tpp-160) cc_final: 0.6533 (mpp-170) REVERT: A 640 GLU cc_start: 0.8018 (tp30) cc_final: 0.7766 (pm20) REVERT: A 666 PHE cc_start: 0.8231 (p90) cc_final: 0.7203 (m-80) REVERT: A 858 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8064 (m-30) outliers start: 57 outliers final: 40 residues processed: 329 average time/residue: 0.5785 time to fit residues: 223.5629 Evaluate side-chains 326 residues out of total 2439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 279 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 145 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN A 58 GLN A 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102455 restraints weight = 35337.388| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.65 r_work: 0.3103 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23633 Z= 0.181 Angle : 0.665 12.018 31997 Z= 0.331 Chirality : 0.047 0.343 3753 Planarity : 0.004 0.062 4046 Dihedral : 8.695 75.229 3559 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 2.26 % Allowed : 21.00 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.16), residues: 2985 helix: 0.33 (0.14), residues: 1533 sheet: -0.60 (0.25), residues: 402 loop : -0.69 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 558 TYR 0.028 0.001 TYR C 545 PHE 0.023 0.002 PHE C 682 TRP 0.007 0.001 TRP B 634 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00436 (23633) covalent geometry : angle 0.66515 (31997) hydrogen bonds : bond 0.03635 ( 1082) hydrogen bonds : angle 4.58262 ( 3189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7823.77 seconds wall clock time: 134 minutes 0.39 seconds (8040.39 seconds total)