Starting phenix.real_space_refine on Sat Mar 7 03:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lo5_23461/03_2026/7lo5_23461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo5_23461/03_2026/7lo5_23461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lo5_23461/03_2026/7lo5_23461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo5_23461/03_2026/7lo5_23461.map" model { file = "/net/cci-nas-00/data/ceres_data/7lo5_23461/03_2026/7lo5_23461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo5_23461/03_2026/7lo5_23461.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 108 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 215 5.49 5 S 82 5.16 5 C 23071 2.51 5 N 6614 2.21 5 O 7463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 169 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37449 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 8249 Classifications: {'peptide': 1016} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 974} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 8230 Classifications: {'peptide': 1013} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 971} Chain breaks: 2 Chain: "C" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8234 Classifications: {'peptide': 1014} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 2 Chain: "D" Number of atoms: 8221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8221 Classifications: {'peptide': 1012} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 970} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "K" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "L" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 521 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 7.62, per 1000 atoms: 0.20 Number of scatterers: 37449 At special positions: 0 Unit cell: (113.025, 193.17, 221.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 82 16.00 P 215 15.00 O 7463 8.00 N 6614 7.00 C 23071 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: 2.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 33 sheets defined 52.6% alpha, 10.5% beta 87 base pairs and 180 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.519A pdb=" N ASP A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.560A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 175 removed outlier: 3.626A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.706A pdb=" N ILE A 167 " --> pdb=" O HIS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 201 through 222 removed outlier: 4.765A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.664A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.619A pdb=" N GLN A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 270 removed outlier: 5.042A pdb=" N ARG A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 293 removed outlier: 4.509A pdb=" N ARG A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.668A pdb=" N GLU A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 removed outlier: 3.501A pdb=" N VAL A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.332A pdb=" N GLU A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 394 Processing helix chain 'A' and resid 427 through 440 removed outlier: 3.731A pdb=" N LEU A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.636A pdb=" N ASN A 461 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.469A pdb=" N VAL A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 558 Processing helix chain 'A' and resid 600 through 611 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 682 through 701 Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 765 through 770 removed outlier: 3.503A pdb=" N ILE A 769 " --> pdb=" O GLN A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 838 Processing helix chain 'A' and resid 844 through 858 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 870 Processing helix chain 'A' and resid 882 through 898 Processing helix chain 'A' and resid 918 through 926 removed outlier: 3.553A pdb=" N LEU A 922 " --> pdb=" O THR A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 4.028A pdb=" N TYR A 962 " --> pdb=" O ALA A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 976 Processing helix chain 'A' and resid 984 through 991 Processing helix chain 'A' and resid 995 through 1023 removed outlier: 3.873A pdb=" N HIS A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU A1001 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG A1002 " --> pdb=" O ASP A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 20 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.624A pdb=" N GLY B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 144 through 175 removed outlier: 3.513A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Proline residue: B 162 - end of helix removed outlier: 3.727A pdb=" N ILE B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.787A pdb=" N GLU B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 222 Processing helix chain 'B' and resid 226 through 232 removed outlier: 4.302A pdb=" N GLU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.614A pdb=" N GLN B 240 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 270 removed outlier: 4.633A pdb=" N ARG B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 removed outlier: 5.179A pdb=" N ARG B 280 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 307 through 326 Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.200A pdb=" N GLU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 394 Processing helix chain 'B' and resid 427 through 438 Processing helix chain 'B' and resid 457 through 461 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 491 through 504 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.970A pdb=" N ASP B 525 " --> pdb=" O ARG B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 4.744A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 removed outlier: 3.526A pdb=" N LYS B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 611 Processing helix chain 'B' and resid 646 through 652 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 682 through 701 Processing helix chain 'B' and resid 704 through 710 Processing helix chain 'B' and resid 720 through 729 Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 765 through 769 Processing helix chain 'B' and resid 827 through 838 Processing helix chain 'B' and resid 844 through 856 removed outlier: 5.034A pdb=" N HIS B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'B' and resid 882 through 898 Processing helix chain 'B' and resid 918 through 924 Processing helix chain 'B' and resid 957 through 961 Processing helix chain 'B' and resid 969 through 976 Processing helix chain 'B' and resid 984 through 991 Processing helix chain 'B' and resid 995 through 1023 removed outlier: 3.752A pdb=" N HIS B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU B1001 " --> pdb=" O ALA B 997 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG B1002 " --> pdb=" O ASP B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.586A pdb=" N GLY C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.510A pdb=" N GLN C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.687A pdb=" N ASP C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.751A pdb=" N ILE C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 196 removed outlier: 3.597A pdb=" N GLU C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 222 Processing helix chain 'C' and resid 226 through 232 removed outlier: 4.033A pdb=" N GLU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 244 removed outlier: 3.542A pdb=" N LEU C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 260 through 270 removed outlier: 4.051A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 290 removed outlier: 4.963A pdb=" N ARG C 280 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 removed outlier: 3.628A pdb=" N ARG C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 326 Processing helix chain 'C' and resid 345 through 355 removed outlier: 3.852A pdb=" N LEU C 351 " --> pdb=" O PHE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 374 through 394 removed outlier: 3.600A pdb=" N TYR C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 4.061A pdb=" N THR C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 439 Processing helix chain 'C' and resid 457 through 461 Processing helix chain 'C' and resid 467 through 477 Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 491 through 504 Processing helix chain 'C' and resid 516 through 521 removed outlier: 4.145A pdb=" N ASP C 520 " --> pdb=" O SER C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.307A pdb=" N VAL C 532 " --> pdb=" O ARG C 528 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.503A pdb=" N ARG C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 Processing helix chain 'C' and resid 611 through 616 removed outlier: 6.350A pdb=" N GLU C 614 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 616 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.591A pdb=" N THR C 650 " --> pdb=" O ALA C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 678 Processing helix chain 'C' and resid 683 through 702 removed outlier: 3.620A pdb=" N LYS C 702 " --> pdb=" O ASN C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 710 Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 765 through 770 Processing helix chain 'C' and resid 771 through 774 Processing helix chain 'C' and resid 827 through 838 Processing helix chain 'C' and resid 844 through 857 removed outlier: 3.534A pdb=" N ALA C 854 " --> pdb=" O HIS C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 865 through 870 Processing helix chain 'C' and resid 881 through 898 Processing helix chain 'C' and resid 918 through 925 Processing helix chain 'C' and resid 956 through 961 Processing helix chain 'C' and resid 969 through 977 Processing helix chain 'C' and resid 984 through 991 Processing helix chain 'C' and resid 995 through 1023 removed outlier: 3.703A pdb=" N HIS C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU C1001 " --> pdb=" O ALA C 997 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ARG C1002 " --> pdb=" O ASP C 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 21 Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.687A pdb=" N GLN D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.501A pdb=" N GLN D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 142 Processing helix chain 'D' and resid 144 through 175 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.893A pdb=" N ARG D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 219 removed outlier: 3.575A pdb=" N ALA D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 232 through 246 removed outlier: 4.016A pdb=" N PHE D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 260 through 270 removed outlier: 4.175A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE D 265 " --> pdb=" O TYR D 261 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 292 removed outlier: 4.590A pdb=" N ARG D 280 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 307 through 325 Processing helix chain 'D' and resid 348 through 355 Processing helix chain 'D' and resid 356 through 367 removed outlier: 4.380A pdb=" N GLU D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLN D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 393 Processing helix chain 'D' and resid 427 through 440 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'D' and resid 477 through 482 Processing helix chain 'D' and resid 491 through 504 Processing helix chain 'D' and resid 517 through 520 Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'D' and resid 532 through 534 No H-bonds generated for 'chain 'D' and resid 532 through 534' Processing helix chain 'D' and resid 551 through 558 removed outlier: 3.587A pdb=" N LYS D 555 " --> pdb=" O GLY D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 611 Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 646 through 651 Processing helix chain 'D' and resid 674 through 678 Processing helix chain 'D' and resid 682 through 701 removed outlier: 3.536A pdb=" N LEU D 686 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 710 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 770 through 774 Processing helix chain 'D' and resid 827 through 838 removed outlier: 4.006A pdb=" N LEU D 831 " --> pdb=" O THR D 827 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR D 836 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS D 837 " --> pdb=" O ALA D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 857 removed outlier: 3.698A pdb=" N HIS D 850 " --> pdb=" O GLU D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 865 through 870 Processing helix chain 'D' and resid 882 through 898 Processing helix chain 'D' and resid 899 through 902 removed outlier: 3.519A pdb=" N VAL D 902 " --> pdb=" O PHE D 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 899 through 902' Processing helix chain 'D' and resid 918 through 925 Processing helix chain 'D' and resid 956 through 962 removed outlier: 3.956A pdb=" N TRP D 960 " --> pdb=" O PRO D 956 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 978 removed outlier: 3.547A pdb=" N VAL D 973 " --> pdb=" O ALA D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 989 Processing helix chain 'D' and resid 999 through 1023 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.677A pdb=" N GLY A 65 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR A 77 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 67 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN A 103 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 112 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG A 123 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 114 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 404 removed outlier: 6.348A pdb=" N ILE A 337 " --> pdb=" O HIS A 369 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASN A 371 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP A 339 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU A 336 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE A 445 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 338 " --> pdb=" O ILE A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 508 through 515 removed outlier: 6.255A pdb=" N ILE A 538 " --> pdb=" O TRP A 591 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N HIS A 593 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 540 " --> pdb=" O HIS A 593 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 590 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 667 through 668 Processing sheet with id=AA6, first strand: chain 'A' and resid 679 through 680 Processing sheet with id=AA7, first strand: chain 'A' and resid 814 through 816 Processing sheet with id=AA8, first strand: chain 'A' and resid 908 through 911 removed outlier: 6.847A pdb=" N THR A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLY A 942 " --> pdb=" O ARG A 934 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N ARG A 934 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 944 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 932 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 946 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.693A pdb=" N GLY B 65 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR B 77 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 67 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN B 103 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 104 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 122 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 116 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLU B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 402 through 404 removed outlier: 6.203A pdb=" N ILE B 337 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASN B 371 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP B 339 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU B 336 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 538 " --> pdb=" O TRP B 591 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS B 593 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 540 " --> pdb=" O HIS B 593 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 590 " --> pdb=" O ILE B 621 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 667 through 668 Processing sheet with id=AB4, first strand: chain 'B' and resid 679 through 680 removed outlier: 4.109A pdb=" N LEU B 799 " --> pdb=" O PRO B 742 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 814 through 816 Processing sheet with id=AB6, first strand: chain 'B' and resid 908 through 911 removed outlier: 4.673A pdb=" N ALA B 943 " --> pdb=" O GLN B 933 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 963 through 964 removed outlier: 4.112A pdb=" N ARG B 967 " --> pdb=" O LEU B 964 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 46 through 49 removed outlier: 3.786A pdb=" N GLY C 76 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG C 75 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N ILE C 105 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR C 77 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU C 107 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU C 79 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN C 116 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 402 through 403 removed outlier: 8.456A pdb=" N VAL C 403 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS C 370 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 337 " --> pdb=" O HIS C 369 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN C 371 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP C 339 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU C 336 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE C 446 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU C 338 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 508 " --> pdb=" O ARG C 577 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 538 " --> pdb=" O TRP C 591 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N HIS C 593 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 540 " --> pdb=" O HIS C 593 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE C 590 " --> pdb=" O ILE C 621 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 668 Processing sheet with id=AC3, first strand: chain 'C' and resid 679 through 680 removed outlier: 6.793A pdb=" N ASP C 749 " --> pdb=" O TYR C 745 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 814 through 815 Processing sheet with id=AC5, first strand: chain 'C' and resid 928 through 935 removed outlier: 4.442A pdb=" N ARG C 929 " --> pdb=" O GLU C 945 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU C 945 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 931 " --> pdb=" O ALA C 943 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA C 943 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN C 933 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 963 through 964 removed outlier: 4.163A pdb=" N ARG C 967 " --> pdb=" O LEU C 964 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.607A pdb=" N GLY D 65 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR D 77 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASN D 103 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG D 123 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 114 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'D' and resid 402 through 404 removed outlier: 8.463A pdb=" N VAL D 403 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS D 370 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE D 337 " --> pdb=" O HIS D 369 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN D 371 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP D 339 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU D 336 " --> pdb=" O ARG D 443 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE D 445 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU D 338 " --> pdb=" O ILE D 445 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 508 through 515 removed outlier: 6.329A pdb=" N ILE D 538 " --> pdb=" O TRP D 591 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE D 590 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 667 through 668 Processing sheet with id=AD3, first strand: chain 'D' and resid 679 through 680 removed outlier: 7.644A pdb=" N ASP D 749 " --> pdb=" O TYR D 745 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR D 745 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 779 through 782 Processing sheet with id=AD5, first strand: chain 'D' and resid 814 through 816 Processing sheet with id=AD6, first strand: chain 'D' and resid 909 through 910 removed outlier: 7.498A pdb=" N GLN D 933 " --> pdb=" O THR D 941 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA D 943 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS D 931 " --> pdb=" O ALA D 943 " (cutoff:3.500A) 1568 hydrogen bonds defined for protein. 4482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 236 hydrogen bonds 472 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 180 stacking parallelities Total time for adding SS restraints: 8.95 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5945 1.31 - 1.44: 11195 1.44 - 1.56: 20977 1.56 - 1.69: 425 1.69 - 1.81: 160 Bond restraints: 38702 Sorted by residual: bond pdb=" C ILE C 987 " pdb=" N ARG C 988 " ideal model delta sigma weight residual 1.335 1.439 -0.104 1.31e-02 5.83e+03 6.36e+01 bond pdb=" C SER A 2 " pdb=" N LEU A 3 " ideal model delta sigma weight residual 1.335 1.423 -0.088 1.31e-02 5.83e+03 4.49e+01 bond pdb=" C PRO A 449 " pdb=" O PRO A 449 " ideal model delta sigma weight residual 1.246 1.192 0.054 8.50e-03 1.38e+04 3.98e+01 bond pdb=" C SER C 74 " pdb=" N ARG C 75 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.58e-02 4.01e+03 3.72e+01 bond pdb=" C VAL B 442 " pdb=" N ARG B 443 " ideal model delta sigma weight residual 1.332 1.414 -0.082 1.35e-02 5.49e+03 3.69e+01 ... (remaining 38697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 45790 2.36 - 4.72: 6924 4.72 - 7.08: 469 7.08 - 9.45: 52 9.45 - 11.81: 8 Bond angle restraints: 53243 Sorted by residual: angle pdb=" N ASN B 548 " pdb=" CA ASN B 548 " pdb=" C ASN B 548 " ideal model delta sigma weight residual 112.97 104.15 8.82 1.06e+00 8.90e-01 6.92e+01 angle pdb=" N ARG C 522 " pdb=" CA ARG C 522 " pdb=" C ARG C 522 " ideal model delta sigma weight residual 114.04 104.09 9.95 1.24e+00 6.50e-01 6.44e+01 angle pdb=" O3' DC G 23 " pdb=" C3' DC G 23 " pdb=" C2' DC G 23 " ideal model delta sigma weight residual 111.50 99.69 11.81 1.50e+00 4.44e-01 6.20e+01 angle pdb=" N ASN C 548 " pdb=" CA ASN C 548 " pdb=" C ASN C 548 " ideal model delta sigma weight residual 112.97 104.89 8.08 1.06e+00 8.90e-01 5.81e+01 angle pdb=" N ASP B 638 " pdb=" CA ASP B 638 " pdb=" C ASP B 638 " ideal model delta sigma weight residual 112.57 104.25 8.32 1.13e+00 7.83e-01 5.43e+01 ... (remaining 53238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 20292 35.94 - 71.87: 2405 71.87 - 107.81: 74 107.81 - 143.74: 4 143.74 - 179.68: 6 Dihedral angle restraints: 22781 sinusoidal: 10863 harmonic: 11918 Sorted by residual: dihedral pdb=" C GLU C 506 " pdb=" N GLU C 506 " pdb=" CA GLU C 506 " pdb=" CB GLU C 506 " ideal model delta harmonic sigma weight residual -122.60 -136.40 13.80 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" C CYS A 370 " pdb=" N CYS A 370 " pdb=" CA CYS A 370 " pdb=" CB CYS A 370 " ideal model delta harmonic sigma weight residual -122.60 -110.02 -12.58 0 2.50e+00 1.60e-01 2.53e+01 dihedral pdb=" C THR A 318 " pdb=" N THR A 318 " pdb=" CA THR A 318 " pdb=" CB THR A 318 " ideal model delta harmonic sigma weight residual -122.00 -134.15 12.15 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 22778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3249 0.094 - 0.188: 1991 0.188 - 0.282: 439 0.282 - 0.376: 52 0.376 - 0.470: 8 Chirality restraints: 5739 Sorted by residual: chirality pdb=" C3' DT L 27 " pdb=" C4' DT L 27 " pdb=" O3' DT L 27 " pdb=" C2' DT L 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.19 -0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CA GLU C 506 " pdb=" N GLU C 506 " pdb=" C GLU C 506 " pdb=" CB GLU C 506 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" C3' DT J 27 " pdb=" C4' DT J 27 " pdb=" O3' DT J 27 " pdb=" C2' DT J 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.24 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 5736 not shown) Planarity restraints: 6185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 925 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.42e+01 pdb=" C ALA B 925 " -0.085 2.00e-02 2.50e+03 pdb=" O ALA B 925 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS B 926 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 756 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C SER D 756 " 0.078 2.00e-02 2.50e+03 pdb=" O SER D 756 " -0.029 2.00e-02 2.50e+03 pdb=" N LYS D 757 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 937 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ALA C 937 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA C 937 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 938 " -0.022 2.00e-02 2.50e+03 ... (remaining 6182 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 66 2.43 - 3.05: 22349 3.05 - 3.67: 57853 3.67 - 4.28: 98572 4.28 - 4.90: 148896 Nonbonded interactions: 327736 Sorted by model distance: nonbonded pdb=" OD2 ASP B 64 " pdb="CA CA B1102 " model vdw 1.819 2.510 nonbonded pdb=" OE2 GLU A 79 " pdb="CA CA A1102 " model vdw 1.832 2.510 nonbonded pdb=" OE2 GLU D 25 " pdb="CA CA D1101 " model vdw 1.916 2.510 nonbonded pdb=" OE2 GLU B 25 " pdb="CA CA B1102 " model vdw 1.941 2.510 nonbonded pdb=" OE2 GLU B 79 " pdb="CA CA B1102 " model vdw 2.007 2.510 ... (remaining 327731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 411 or resid 421 through 578 or resid 587 throug \ h 839 or resid 843 through 1029)) selection = (chain 'B' and (resid 2 through 411 or resid 421 through 839 or resid 843 throug \ h 1029)) selection = (chain 'C' and (resid 2 through 411 or resid 421 through 578 or resid 587 throug \ h 839 or resid 843 through 1029)) selection = (chain 'D' and (resid 2 through 411 or resid 421 through 578 or resid 587 throug \ h 1029)) } ncs_group { reference = (chain 'E' and resid 1 through 25) selection = (chain 'G' and resid 1 through 25) selection = (chain 'I' and resid 1 through 25) selection = chain 'K' } ncs_group { reference = (chain 'F' and resid 4 through 28) selection = (chain 'H' and resid 4 through 28) selection = (chain 'J' and resid 4 through 28) selection = chain 'L' } 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: 12.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.470 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.070 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:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.011 0.104 38702 Z= 0.834 Angle : 1.602 11.807 53243 Z= 1.190 Chirality : 0.113 0.470 5739 Planarity : 0.005 0.128 6185 Dihedral : 24.100 179.676 15085 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 12.88 % Allowed : 16.74 % Favored : 70.37 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.11), residues: 4029 helix: -2.59 (0.09), residues: 1937 sheet: -2.04 (0.24), residues: 364 loop : -2.51 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 151 TYR 0.033 0.003 TYR C 286 PHE 0.020 0.003 PHE D 770 TRP 0.017 0.002 TRP C 960 HIS 0.006 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.01141 (38702) covalent geometry : angle 1.60193 (53243) hydrogen bonds : bond 0.20724 ( 1804) hydrogen bonds : angle 8.70579 ( 4954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 444 poor density : 587 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7595 (p0) REVERT: A 126 MET cc_start: 0.8717 (mmm) cc_final: 0.8192 (mtm) REVERT: A 208 MET cc_start: 0.9095 (mtt) cc_final: 0.8840 (mtt) REVERT: A 318 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8872 (t) REVERT: A 329 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: A 560 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8873 (t0) REVERT: A 651 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8480 (mmtt) REVERT: A 709 MET cc_start: 0.9329 (mmt) cc_final: 0.9033 (mmm) REVERT: A 719 MET cc_start: 0.9176 (mmm) cc_final: 0.8942 (mmp) REVERT: A 893 MET cc_start: 0.8030 (ttm) cc_final: 0.7696 (ttp) REVERT: B 3 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8528 (tt) REVERT: B 73 GLN cc_start: 0.8292 (mt0) cc_final: 0.7907 (mt0) REVERT: B 215 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 367 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 633 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.7959 (m) REVERT: B 719 MET cc_start: 0.9134 (mmm) cc_final: 0.8794 (mmm) REVERT: B 881 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 534 ASP cc_start: 0.8148 (m-30) cc_final: 0.7703 (m-30) REVERT: C 654 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7759 (mtmm) REVERT: C 696 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8409 (mmm160) REVERT: C 864 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8791 (tptt) REVERT: C 1024 MET cc_start: 0.7762 (mtt) cc_final: 0.7354 (mtt) REVERT: D 14 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7294 (mp0) REVERT: D 69 ASP cc_start: 0.7084 (t0) cc_final: 0.6441 (p0) REVERT: D 83 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6667 (mm-30) REVERT: D 167 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6672 (mm) REVERT: D 191 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7099 (tp) REVERT: D 200 PHE cc_start: 0.7255 (t80) cc_final: 0.7037 (t80) REVERT: D 234 ILE cc_start: 0.5497 (mm) cc_final: 0.5257 (mp) REVERT: D 333 LYS cc_start: 0.7778 (mttt) cc_final: 0.7333 (mppt) REVERT: D 335 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7601 (p) REVERT: D 370 CYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5470 (p) REVERT: D 422 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6569 (mt) REVERT: D 433 ARG cc_start: 0.3662 (OUTLIER) cc_final: 0.2611 (mtm180) REVERT: D 451 TYR cc_start: 0.1545 (OUTLIER) cc_final: 0.1335 (m-80) REVERT: D 473 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5639 (mtp180) REVERT: D 505 LYS cc_start: 0.8852 (tttt) cc_final: 0.8512 (mmtm) REVERT: D 534 ASP cc_start: 0.6753 (m-30) cc_final: 0.6548 (m-30) REVERT: D 543 MET cc_start: 0.6727 (mmm) cc_final: 0.6521 (mmm) REVERT: D 544 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5620 (mttt) REVERT: D 693 PHE cc_start: 0.8505 (t80) cc_final: 0.8096 (t80) REVERT: D 700 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 835 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6182 (tm-30) REVERT: D 843 ILE cc_start: 0.2708 (OUTLIER) cc_final: 0.2049 (mp) REVERT: D 892 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5456 (mt) REVERT: D 944 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8054 (t) REVERT: D 986 THR cc_start: 0.6397 (OUTLIER) cc_final: 0.5856 (p) REVERT: D 1016 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8310 (tm-30) outliers start: 444 outliers final: 41 residues processed: 923 average time/residue: 0.8895 time to fit residues: 949.7962 Evaluate side-chains 289 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 950 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 950 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 ARG Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 544 LYS Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 835 GLN Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 844 SER Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 944 VAL Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 116 GLN A 122 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 279 GLN A 410 ASN A 448 ASN A 537 HIS A 628 ASN A 673 ASN A 728 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 HIS B 10 GLN B 116 GLN B 122 GLN B 371 ASN B 437 GLN B 448 ASN B 457 ASN B 565 GLN B 628 ASN B 857 HIS B 896 HIS C 33 GLN C 59 ASN C 146 GLN C 163 HIS C 212 HIS C 236 GLN C 325 HIS C 448 ASN C 560 ASN C 565 GLN C 728 GLN C 792 GLN C 858 HIS D 10 GLN D 211 GLN ** D 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 266 GLN D 294 ASN D 325 HIS D 371 ASN D 410 ASN D 437 GLN D 438 ASN D 448 ASN D 620 HIS D 628 ASN D 652 GLN D 760 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 GLN ** D 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.071844 restraints weight = 80111.634| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.37 r_work: 0.2996 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 38702 Z= 0.167 Angle : 0.669 11.718 53243 Z= 0.366 Chirality : 0.042 0.383 5739 Planarity : 0.005 0.058 6185 Dihedral : 24.019 179.452 7051 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.67 % Allowed : 24.29 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.12), residues: 4029 helix: -0.35 (0.11), residues: 1942 sheet: -1.45 (0.23), residues: 410 loop : -1.88 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 822 TYR 0.020 0.002 TYR D 246 PHE 0.015 0.001 PHE D 882 TRP 0.027 0.001 TRP C 885 HIS 0.005 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00366 (38702) covalent geometry : angle 0.66894 (53243) hydrogen bonds : bond 0.05485 ( 1804) hydrogen bonds : angle 5.18354 ( 4954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 254 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7581 (p0) REVERT: A 110 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7921 (mpp80) REVERT: A 119 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: A 126 MET cc_start: 0.8960 (mmm) cc_final: 0.8587 (mtm) REVERT: A 224 ASP cc_start: 0.8789 (t0) cc_final: 0.8502 (t0) REVERT: A 259 LYS cc_start: 0.9286 (tppt) cc_final: 0.9000 (tppp) REVERT: A 318 THR cc_start: 0.9420 (t) cc_final: 0.9179 (t) REVERT: A 329 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: A 656 LEU cc_start: 0.8828 (tt) cc_final: 0.8608 (tm) REVERT: B 86 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7981 (t) REVERT: B 152 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8913 (ttmm) REVERT: B 215 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8719 (p) REVERT: B 230 GLU cc_start: 0.8444 (mp0) cc_final: 0.8163 (mp0) REVERT: B 277 GLU cc_start: 0.8992 (tp30) cc_final: 0.8193 (tp30) REVERT: B 291 ARG cc_start: 0.8951 (mpt-90) cc_final: 0.8673 (mpt-90) REVERT: B 367 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: B 652 GLN cc_start: 0.7737 (pp30) cc_final: 0.7535 (pp30) REVERT: B 719 MET cc_start: 0.9243 (mmm) cc_final: 0.8994 (mmm) REVERT: B 749 ASP cc_start: 0.8641 (t0) cc_final: 0.8439 (t0) REVERT: B 804 LEU cc_start: 0.9044 (tt) cc_final: 0.8842 (tp) REVERT: B 881 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: B 1029 MET cc_start: 0.7453 (mtp) cc_final: 0.7177 (mtp) REVERT: C 1 MET cc_start: 0.7927 (mtt) cc_final: 0.7614 (mpp) REVERT: C 203 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7811 (ttp80) REVERT: C 245 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7950 (p90) REVERT: C 316 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 612 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.7957 (mmmt) REVERT: C 654 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7891 (mtmm) REVERT: C 709 MET cc_start: 0.8391 (mpp) cc_final: 0.8115 (mpp) REVERT: C 753 MET cc_start: 0.8153 (ttp) cc_final: 0.7660 (tmm) REVERT: D 1 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7281 (mtm) REVERT: D 14 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8045 (mp0) REVERT: D 178 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6897 (tmmm) REVERT: D 207 GLU cc_start: 0.7594 (tt0) cc_final: 0.7042 (tm-30) REVERT: D 324 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8564 (tttm) REVERT: D 333 LYS cc_start: 0.8402 (mttt) cc_final: 0.7750 (mppt) REVERT: D 475 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7869 (mmtt) REVERT: D 642 PHE cc_start: 0.7940 (m-80) cc_final: 0.7704 (m-10) REVERT: D 693 PHE cc_start: 0.8926 (t80) cc_final: 0.8572 (t80) REVERT: D 700 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8708 (tp) REVERT: D 765 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: D 905 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: D 1016 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8335 (tm-30) outliers start: 161 outliers final: 47 residues processed: 389 average time/residue: 0.7369 time to fit residues: 342.7548 Evaluate side-chains 242 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 176 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 TRP Chi-restraints excluded: chain C residue 612 LYS Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 796 THR Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 324 LYS Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 GLN Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 236 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 163 HIS A 227 GLN A 239 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 33 GLN B 73 GLN B 229 HIS B 632 GLN C 53 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 939 GLN D 24 ASN D 53 GLN D 163 HIS ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066960 restraints weight = 80408.026| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.35 r_work: 0.2900 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 38702 Z= 0.265 Angle : 0.652 10.588 53243 Z= 0.356 Chirality : 0.044 0.360 5739 Planarity : 0.005 0.062 6185 Dihedral : 23.747 179.506 6955 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.38 % Allowed : 24.26 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 4029 helix: 0.29 (0.12), residues: 1927 sheet: -1.06 (0.23), residues: 425 loop : -1.71 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 875 TYR 0.021 0.002 TYR C 879 PHE 0.028 0.002 PHE D 200 TRP 0.010 0.001 TRP D 607 HIS 0.009 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00614 (38702) covalent geometry : angle 0.65185 (53243) hydrogen bonds : bond 0.05516 ( 1804) hydrogen bonds : angle 4.84738 ( 4954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 205 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: A 126 MET cc_start: 0.9233 (mmm) cc_final: 0.8446 (mtm) REVERT: A 224 ASP cc_start: 0.8710 (t0) cc_final: 0.8405 (t0) REVERT: A 259 LYS cc_start: 0.9299 (tppt) cc_final: 0.8954 (tppp) REVERT: A 642 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: A 656 LEU cc_start: 0.8809 (tt) cc_final: 0.8579 (tm) REVERT: A 708 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 23 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7974 (mtp180) REVERT: B 86 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7893 (t) REVERT: B 230 GLU cc_start: 0.8775 (mp0) cc_final: 0.8418 (mp0) REVERT: B 277 GLU cc_start: 0.9235 (tp30) cc_final: 0.8413 (tp30) REVERT: B 291 ARG cc_start: 0.8981 (mpt-90) cc_final: 0.8761 (mpt-90) REVERT: B 367 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: B 602 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8353 (ptp-170) REVERT: B 719 MET cc_start: 0.9238 (mmm) cc_final: 0.8995 (mmm) REVERT: B 749 ASP cc_start: 0.8838 (t0) cc_final: 0.8634 (t0) REVERT: B 881 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: C 1 MET cc_start: 0.7994 (mtt) cc_final: 0.7704 (mpp) REVERT: C 203 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7854 (ttp80) REVERT: C 245 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8045 (p90) REVERT: C 260 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8077 (mtp-110) REVERT: C 316 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 465 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8119 (ttt180) REVERT: C 602 ARG cc_start: 0.8511 (ptp90) cc_final: 0.8274 (ptp90) REVERT: C 641 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: C 705 LEU cc_start: 0.8345 (tp) cc_final: 0.7982 (tm) REVERT: C 709 MET cc_start: 0.8540 (tpp) cc_final: 0.7997 (mpp) REVERT: C 737 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8501 (tptp) REVERT: C 753 MET cc_start: 0.8170 (ttp) cc_final: 0.7744 (tmm) REVERT: C 1002 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8497 (pmm-80) REVERT: D 1 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7359 (mtm) REVERT: D 14 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8142 (mp0) REVERT: D 178 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6951 (tmmm) REVERT: D 207 GLU cc_start: 0.7240 (tt0) cc_final: 0.6780 (tm-30) REVERT: D 333 LYS cc_start: 0.8430 (mttt) cc_final: 0.7809 (mppt) REVERT: D 642 PHE cc_start: 0.8021 (m-80) cc_final: 0.7802 (m-10) REVERT: D 713 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7867 (p90) REVERT: D 728 GLN cc_start: 0.7582 (mt0) cc_final: 0.7192 (mm-40) REVERT: D 762 MET cc_start: 0.6565 (mmt) cc_final: 0.6206 (mmt) REVERT: D 765 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: D 782 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7697 (tm) REVERT: D 905 TYR cc_start: 0.7224 (t80) cc_final: 0.6708 (m-80) REVERT: D 1016 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8268 (tm-30) REVERT: D 1024 MET cc_start: 0.6466 (mtt) cc_final: 0.6202 (mtp) outliers start: 151 outliers final: 59 residues processed: 329 average time/residue: 0.7427 time to fit residues: 291.4656 Evaluate side-chains 247 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 168 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 457 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 LYS Chi-restraints excluded: chain C residue 792 GLN Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 796 THR Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 713 TRP Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 765 GLN Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 333 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 308 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 328 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 387 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 73 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN C 437 GLN C 966 ASN ** D 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.101517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069023 restraints weight = 80036.831| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.35 r_work: 0.2962 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38702 Z= 0.142 Angle : 0.566 13.205 53243 Z= 0.305 Chirality : 0.040 0.194 5739 Planarity : 0.005 0.050 6185 Dihedral : 23.358 179.448 6942 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.42 % Allowed : 25.25 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4029 helix: 0.72 (0.12), residues: 1927 sheet: -0.74 (0.24), residues: 416 loop : -1.47 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 472 TYR 0.018 0.001 TYR D 745 PHE 0.019 0.001 PHE D 200 TRP 0.009 0.001 TRP C 499 HIS 0.007 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00318 (38702) covalent geometry : angle 0.56632 (53243) hydrogen bonds : bond 0.04236 ( 1804) hydrogen bonds : angle 4.58032 ( 4954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 210 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 110 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8330 (mmt-90) REVERT: A 119 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: A 126 MET cc_start: 0.9243 (mmm) cc_final: 0.8245 (mtm) REVERT: A 224 ASP cc_start: 0.8642 (t0) cc_final: 0.8255 (t0) REVERT: A 259 LYS cc_start: 0.9292 (tppt) cc_final: 0.8897 (tppp) REVERT: A 329 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: A 642 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: A 908 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8365 (tmmt) REVERT: B 86 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7923 (t) REVERT: B 109 SER cc_start: 0.8878 (m) cc_final: 0.8518 (t) REVERT: B 128 ASP cc_start: 0.8818 (t70) cc_final: 0.8113 (t0) REVERT: B 230 GLU cc_start: 0.8821 (mp0) cc_final: 0.8452 (mp0) REVERT: B 277 GLU cc_start: 0.9144 (tp30) cc_final: 0.8358 (tp30) REVERT: B 291 ARG cc_start: 0.9055 (mpt-90) cc_final: 0.8798 (mpt-90) REVERT: B 367 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: B 719 MET cc_start: 0.9221 (mmm) cc_final: 0.9013 (mmm) REVERT: B 881 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 1029 MET cc_start: 0.7007 (mtp) cc_final: 0.6776 (mtm) REVERT: C 203 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: C 245 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8278 (p90) REVERT: C 316 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 602 ARG cc_start: 0.8370 (ptp90) cc_final: 0.7926 (ptp90) REVERT: C 705 LEU cc_start: 0.8352 (tp) cc_final: 0.7947 (tm) REVERT: C 709 MET cc_start: 0.8648 (tpp) cc_final: 0.8118 (mpp) REVERT: C 753 MET cc_start: 0.8223 (ttp) cc_final: 0.7756 (tmm) REVERT: C 931 LYS cc_start: 0.8413 (mptt) cc_final: 0.8197 (ptpp) REVERT: C 952 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6629 (tt) REVERT: C 1002 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8610 (pmm-80) REVERT: D 14 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8214 (mp0) REVERT: D 59 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7934 (p0) REVERT: D 207 GLU cc_start: 0.7335 (tt0) cc_final: 0.6860 (tm-30) REVERT: D 333 LYS cc_start: 0.8447 (mttt) cc_final: 0.7831 (mppt) REVERT: D 451 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: D 709 MET cc_start: 0.7188 (mmt) cc_final: 0.6941 (mmm) REVERT: D 719 MET cc_start: 0.7708 (mmp) cc_final: 0.7355 (mmm) REVERT: D 754 TYR cc_start: 0.7478 (t80) cc_final: 0.7032 (t80) REVERT: D 762 MET cc_start: 0.6446 (mmt) cc_final: 0.6060 (mmt) REVERT: D 765 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6678 (mp10) REVERT: D 782 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7899 (tm) REVERT: D 905 TYR cc_start: 0.7387 (t80) cc_final: 0.6837 (m-80) REVERT: D 1016 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8270 (tm-30) outliers start: 118 outliers final: 50 residues processed: 307 average time/residue: 0.7099 time to fit residues: 260.9414 Evaluate side-chains 236 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 GLN Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 208 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 390 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 137 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 381 optimal weight: 10.0000 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.100299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067763 restraints weight = 80256.587| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.33 r_work: 0.2924 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38702 Z= 0.184 Angle : 0.570 10.839 53243 Z= 0.308 Chirality : 0.041 0.183 5739 Planarity : 0.005 0.050 6185 Dihedral : 23.166 179.089 6940 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.80 % Allowed : 25.33 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 4029 helix: 0.85 (0.12), residues: 1938 sheet: -0.49 (0.24), residues: 408 loop : -1.41 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 110 TYR 0.017 0.001 TYR D 745 PHE 0.020 0.001 PHE C 882 TRP 0.013 0.001 TRP C 885 HIS 0.006 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00424 (38702) covalent geometry : angle 0.56954 (53243) hydrogen bonds : bond 0.04441 ( 1804) hydrogen bonds : angle 4.51667 ( 4954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 181 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 110 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8379 (mmt-90) REVERT: A 119 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: A 126 MET cc_start: 0.9272 (mmm) cc_final: 0.8168 (mtm) REVERT: A 224 ASP cc_start: 0.8590 (t0) cc_final: 0.8334 (t0) REVERT: A 259 LYS cc_start: 0.9324 (tppt) cc_final: 0.8916 (tppp) REVERT: A 329 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 642 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: A 648 LYS cc_start: 0.9177 (mptt) cc_final: 0.8934 (pptt) REVERT: A 708 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8687 (mp) REVERT: A 908 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8394 (tmmt) REVERT: A 1029 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7466 (mtp) REVERT: B 23 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7899 (mtp180) REVERT: B 86 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7899 (t) REVERT: B 109 SER cc_start: 0.8810 (m) cc_final: 0.8488 (t) REVERT: B 128 ASP cc_start: 0.8827 (t70) cc_final: 0.8134 (t0) REVERT: B 230 GLU cc_start: 0.8854 (mp0) cc_final: 0.8423 (mp0) REVERT: B 277 GLU cc_start: 0.9189 (tp30) cc_final: 0.8388 (tp30) REVERT: B 367 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: B 602 ARG cc_start: 0.8722 (ttp-110) cc_final: 0.8420 (ttp80) REVERT: B 832 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8705 (mppt) REVERT: B 881 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: C 1 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7307 (mpp) REVERT: C 203 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7924 (ttp80) REVERT: C 245 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8367 (p90) REVERT: C 260 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8272 (mtp-110) REVERT: C 316 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 465 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8283 (ttt180) REVERT: C 472 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7948 (ptm-80) REVERT: C 602 ARG cc_start: 0.8364 (ptp90) cc_final: 0.7921 (ptp90) REVERT: C 705 LEU cc_start: 0.8393 (tp) cc_final: 0.7958 (tm) REVERT: C 709 MET cc_start: 0.8620 (tpp) cc_final: 0.8055 (mpp) REVERT: C 753 MET cc_start: 0.8226 (ttp) cc_final: 0.7761 (tmm) REVERT: C 952 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6636 (tt) REVERT: C 1002 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8643 (pmm-80) REVERT: D 14 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8221 (mp0) REVERT: D 207 GLU cc_start: 0.7545 (tt0) cc_final: 0.7025 (tm-30) REVERT: D 333 LYS cc_start: 0.8417 (mttt) cc_final: 0.7777 (mppt) REVERT: D 451 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: D 709 MET cc_start: 0.7222 (mmt) cc_final: 0.6979 (mmm) REVERT: D 762 MET cc_start: 0.6439 (mmt) cc_final: 0.6015 (mmt) REVERT: D 765 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: D 780 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7547 (pp) REVERT: D 782 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7902 (tm) REVERT: D 905 TYR cc_start: 0.7374 (t80) cc_final: 0.6845 (m-80) REVERT: D 1016 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8211 (tm-30) outliers start: 131 outliers final: 61 residues processed: 295 average time/residue: 0.7090 time to fit residues: 249.7990 Evaluate side-chains 245 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 162 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 765 GLN Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 225 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 394 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 255 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 371 optimal weight: 0.0980 chunk 305 optimal weight: 7.9990 chunk 277 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN D 212 HIS ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN D 792 GLN D 999 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.069400 restraints weight = 80189.058| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.34 r_work: 0.2955 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38702 Z= 0.125 Angle : 0.535 12.593 53243 Z= 0.288 Chirality : 0.039 0.161 5739 Planarity : 0.004 0.049 6185 Dihedral : 22.905 179.089 6939 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.11 % Allowed : 25.62 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4029 helix: 1.02 (0.12), residues: 1937 sheet: -0.42 (0.24), residues: 424 loop : -1.27 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 110 TYR 0.017 0.001 TYR D 745 PHE 0.020 0.001 PHE D 878 TRP 0.011 0.001 TRP B 885 HIS 0.007 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00279 (38702) covalent geometry : angle 0.53511 (53243) hydrogen bonds : bond 0.03791 ( 1804) hydrogen bonds : angle 4.39735 ( 4954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 198 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 110 ARG cc_start: 0.8594 (tpp80) cc_final: 0.8381 (mmt-90) REVERT: A 119 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: A 126 MET cc_start: 0.9199 (mmm) cc_final: 0.8067 (mtm) REVERT: A 224 ASP cc_start: 0.8609 (t0) cc_final: 0.8349 (t0) REVERT: A 259 LYS cc_start: 0.9245 (tppt) cc_final: 0.8831 (tppp) REVERT: A 329 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: A 642 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 648 LYS cc_start: 0.9124 (mptt) cc_final: 0.8865 (pptt) REVERT: A 908 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8328 (tmmt) REVERT: A 1029 MET cc_start: 0.7822 (mtp) cc_final: 0.7395 (mtp) REVERT: B 23 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7924 (mtp180) REVERT: B 86 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7754 (t) REVERT: B 109 SER cc_start: 0.8594 (m) cc_final: 0.8322 (t) REVERT: B 128 ASP cc_start: 0.8759 (t70) cc_final: 0.8041 (t0) REVERT: B 277 GLU cc_start: 0.9149 (tp30) cc_final: 0.8346 (tp30) REVERT: B 367 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: B 602 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8393 (ttp80) REVERT: B 881 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: B 1029 MET cc_start: 0.6991 (mtp) cc_final: 0.6695 (mtm) REVERT: C 1 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7325 (mpp) REVERT: C 203 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7856 (ttp80) REVERT: C 316 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8043 (tm-30) REVERT: C 327 GLN cc_start: 0.8878 (mp10) cc_final: 0.8617 (mp10) REVERT: C 465 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8152 (ttt180) REVERT: C 472 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7896 (ptm-80) REVERT: C 602 ARG cc_start: 0.8313 (ptp90) cc_final: 0.7878 (ptp90) REVERT: C 652 GLN cc_start: 0.8534 (mm-40) cc_final: 0.7814 (tm-30) REVERT: C 705 LEU cc_start: 0.8375 (tp) cc_final: 0.7932 (tm) REVERT: C 709 MET cc_start: 0.8558 (tpp) cc_final: 0.8009 (mpp) REVERT: C 753 MET cc_start: 0.8192 (ttp) cc_final: 0.7616 (tmm) REVERT: C 818 MET cc_start: 0.8820 (mpp) cc_final: 0.8499 (pmm) REVERT: C 933 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7655 (mp10) REVERT: C 1002 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8646 (pmm-80) REVERT: D 14 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8080 (mp0) REVERT: D 59 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7764 (p0) REVERT: D 207 GLU cc_start: 0.7619 (tt0) cc_final: 0.7109 (tm-30) REVERT: D 208 MET cc_start: 0.7364 (mtp) cc_final: 0.6671 (tmm) REVERT: D 333 LYS cc_start: 0.8443 (mttt) cc_final: 0.8131 (mmmt) REVERT: D 451 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: D 709 MET cc_start: 0.7206 (mmt) cc_final: 0.6962 (mmm) REVERT: D 751 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8086 (tp) REVERT: D 762 MET cc_start: 0.6279 (mmt) cc_final: 0.5889 (mmt) REVERT: D 765 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6772 (mp10) REVERT: D 780 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7421 (pp) REVERT: D 782 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7957 (tm) REVERT: D 905 TYR cc_start: 0.7430 (t80) cc_final: 0.6929 (m-80) REVERT: D 1016 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8198 (tm-30) outliers start: 107 outliers final: 47 residues processed: 290 average time/residue: 0.7284 time to fit residues: 252.9045 Evaluate side-chains 235 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 765 GLN Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 419 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 264 optimal weight: 0.7980 chunk 378 optimal weight: 0.5980 chunk 339 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 270 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 406 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069186 restraints weight = 80416.851| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.34 r_work: 0.2940 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38702 Z= 0.137 Angle : 0.539 11.965 53243 Z= 0.289 Chirality : 0.039 0.160 5739 Planarity : 0.004 0.050 6185 Dihedral : 22.738 178.466 6938 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.96 % Allowed : 25.80 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.13), residues: 4029 helix: 1.08 (0.12), residues: 1951 sheet: -0.29 (0.24), residues: 426 loop : -1.23 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 203 TYR 0.017 0.001 TYR D 181 PHE 0.017 0.001 PHE D 878 TRP 0.008 0.001 TRP B 885 HIS 0.006 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00310 (38702) covalent geometry : angle 0.53915 (53243) hydrogen bonds : bond 0.03838 ( 1804) hydrogen bonds : angle 4.32745 ( 4954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 184 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7411 (tm-30) REVERT: A 110 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8424 (mmt-90) REVERT: A 119 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: A 126 MET cc_start: 0.9216 (mmm) cc_final: 0.8011 (mtm) REVERT: A 149 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8381 (mm-30) REVERT: A 224 ASP cc_start: 0.8581 (t0) cc_final: 0.8313 (t0) REVERT: A 259 LYS cc_start: 0.9255 (tppt) cc_final: 0.8847 (tppp) REVERT: A 329 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: A 642 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 648 LYS cc_start: 0.9165 (mptt) cc_final: 0.8928 (pptt) REVERT: A 908 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8376 (tmmt) REVERT: A 1029 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7496 (mtp) REVERT: B 23 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7930 (mtp180) REVERT: B 126 MET cc_start: 0.8972 (mtm) cc_final: 0.8575 (mtm) REVERT: B 128 ASP cc_start: 0.8785 (t70) cc_final: 0.8095 (t0) REVERT: B 277 GLU cc_start: 0.9140 (tp30) cc_final: 0.8355 (tp30) REVERT: B 316 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8589 (mm-30) REVERT: B 367 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8511 (mt-10) REVERT: B 602 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.8442 (ttp80) REVERT: B 1029 MET cc_start: 0.6991 (mtp) cc_final: 0.6683 (mtm) REVERT: C 125 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8155 (p0) REVERT: C 245 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8414 (p90) REVERT: C 316 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8068 (tm-30) REVERT: C 327 GLN cc_start: 0.8961 (mp10) cc_final: 0.8528 (mp10) REVERT: C 465 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8244 (ttt180) REVERT: C 472 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7937 (ptm-80) REVERT: C 602 ARG cc_start: 0.8354 (ptp90) cc_final: 0.7924 (ptp90) REVERT: C 652 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7828 (tm-30) REVERT: C 705 LEU cc_start: 0.8430 (tp) cc_final: 0.7997 (tm) REVERT: C 709 MET cc_start: 0.8576 (tpp) cc_final: 0.8015 (mpp) REVERT: C 753 MET cc_start: 0.8241 (ttp) cc_final: 0.7724 (tmm) REVERT: C 933 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: C 952 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6513 (tt) REVERT: C 1002 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8673 (pmm-80) REVERT: D 1 MET cc_start: 0.7512 (mpp) cc_final: 0.6933 (mtm) REVERT: D 14 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8156 (mp0) REVERT: D 207 GLU cc_start: 0.7657 (tt0) cc_final: 0.7112 (tm-30) REVERT: D 208 MET cc_start: 0.7448 (mtp) cc_final: 0.6704 (tmm) REVERT: D 333 LYS cc_start: 0.8442 (mttt) cc_final: 0.7853 (mppt) REVERT: D 451 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: D 709 MET cc_start: 0.7240 (mmt) cc_final: 0.7000 (mmm) REVERT: D 751 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8088 (tp) REVERT: D 762 MET cc_start: 0.6315 (mmt) cc_final: 0.5918 (mmp) REVERT: D 765 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6826 (mp10) REVERT: D 780 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7422 (pp) REVERT: D 782 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7909 (tm) REVERT: D 905 TYR cc_start: 0.7367 (t80) cc_final: 0.6900 (m-80) REVERT: D 1016 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8182 (tm-30) outliers start: 102 outliers final: 47 residues processed: 274 average time/residue: 0.7158 time to fit residues: 235.5693 Evaluate side-chains 231 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 765 GLN Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 946 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 414 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 333 optimal weight: 0.8980 chunk 317 optimal weight: 0.5980 chunk 213 optimal weight: 0.7980 chunk 375 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 ASN B 73 GLN B 266 GLN B 325 HIS ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN D 430 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.101911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069506 restraints weight = 80099.018| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.35 r_work: 0.2952 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38702 Z= 0.131 Angle : 0.538 12.201 53243 Z= 0.288 Chirality : 0.039 0.166 5739 Planarity : 0.004 0.050 6185 Dihedral : 22.610 179.166 6933 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 2.64 % Allowed : 26.18 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 4029 helix: 1.16 (0.12), residues: 1948 sheet: -0.19 (0.24), residues: 426 loop : -1.19 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 110 TYR 0.020 0.001 TYR D 181 PHE 0.016 0.001 PHE D 878 TRP 0.009 0.001 TRP B 885 HIS 0.011 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00296 (38702) covalent geometry : angle 0.53839 (53243) hydrogen bonds : bond 0.03715 ( 1804) hydrogen bonds : angle 4.28130 ( 4954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 110 ARG cc_start: 0.8655 (tpp80) cc_final: 0.8440 (mmt-90) REVERT: A 119 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: A 126 MET cc_start: 0.9155 (mmm) cc_final: 0.7944 (mtm) REVERT: A 149 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8336 (mm-30) REVERT: A 224 ASP cc_start: 0.8553 (t0) cc_final: 0.8275 (t0) REVERT: A 259 LYS cc_start: 0.9234 (tppt) cc_final: 0.8822 (tppp) REVERT: A 329 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 642 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: A 648 LYS cc_start: 0.9133 (mptt) cc_final: 0.8906 (pptt) REVERT: A 666 TYR cc_start: 0.8672 (p90) cc_final: 0.8419 (p90) REVERT: A 708 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 908 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8383 (tmmt) REVERT: A 1029 MET cc_start: 0.7812 (mtp) cc_final: 0.7470 (mtp) REVERT: B 23 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7925 (mtp180) REVERT: B 126 MET cc_start: 0.8955 (mtm) cc_final: 0.8595 (mtm) REVERT: B 128 ASP cc_start: 0.8764 (t70) cc_final: 0.8067 (t0) REVERT: B 277 GLU cc_start: 0.9126 (tp30) cc_final: 0.8317 (tp30) REVERT: B 316 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8572 (mm-30) REVERT: B 367 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: B 602 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8424 (ttp80) REVERT: B 893 MET cc_start: 0.7519 (ttp) cc_final: 0.7294 (ttp) REVERT: B 1029 MET cc_start: 0.6997 (mtp) cc_final: 0.6646 (mtm) REVERT: C 125 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8009 (p0) REVERT: C 316 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 362 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8395 (tp40) REVERT: C 465 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8238 (ttt180) REVERT: C 472 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7918 (ptm-80) REVERT: C 602 ARG cc_start: 0.8317 (ptp90) cc_final: 0.7883 (ptp90) REVERT: C 652 GLN cc_start: 0.8551 (mm-40) cc_final: 0.7838 (tm-30) REVERT: C 705 LEU cc_start: 0.8424 (tp) cc_final: 0.7998 (tm) REVERT: C 709 MET cc_start: 0.8602 (tpp) cc_final: 0.8114 (mpp) REVERT: C 753 MET cc_start: 0.8215 (ttp) cc_final: 0.7687 (tmm) REVERT: C 933 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: C 952 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6488 (tt) REVERT: C 1002 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8642 (pmm-80) REVERT: D 14 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8086 (mp0) REVERT: D 207 GLU cc_start: 0.7552 (tt0) cc_final: 0.7114 (tm-30) REVERT: D 208 MET cc_start: 0.7445 (mtp) cc_final: 0.6705 (tmm) REVERT: D 293 TYR cc_start: 0.7485 (t80) cc_final: 0.7155 (t80) REVERT: D 333 LYS cc_start: 0.8487 (mttt) cc_final: 0.8158 (mmmt) REVERT: D 451 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: D 709 MET cc_start: 0.7256 (mmt) cc_final: 0.7032 (mmm) REVERT: D 751 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8241 (tp) REVERT: D 762 MET cc_start: 0.6231 (mmt) cc_final: 0.5828 (mmp) REVERT: D 782 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7884 (tm) REVERT: D 818 MET cc_start: 0.7943 (mtp) cc_final: 0.7559 (ttm) REVERT: D 905 TYR cc_start: 0.7397 (t80) cc_final: 0.6929 (m-80) REVERT: D 967 ARG cc_start: 0.6323 (mtt90) cc_final: 0.6049 (mtm-85) REVERT: D 1016 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8175 (tm-30) REVERT: D 1029 MET cc_start: 0.7330 (mpm) cc_final: 0.6712 (mpt) outliers start: 91 outliers final: 54 residues processed: 261 average time/residue: 0.7121 time to fit residues: 222.4643 Evaluate side-chains 241 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 171 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 999 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 267 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 410 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 294 optimal weight: 0.0070 chunk 407 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 537 HIS ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067323 restraints weight = 80674.425| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.33 r_work: 0.2903 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 38702 Z= 0.218 Angle : 0.594 12.443 53243 Z= 0.317 Chirality : 0.041 0.229 5739 Planarity : 0.004 0.050 6185 Dihedral : 22.702 178.472 6933 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 2.70 % Allowed : 26.00 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4029 helix: 1.05 (0.12), residues: 1947 sheet: -0.12 (0.25), residues: 419 loop : -1.25 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 110 TYR 0.030 0.002 TYR D 666 PHE 0.017 0.001 PHE B 849 TRP 0.012 0.001 TRP C 639 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00503 (38702) covalent geometry : angle 0.59354 (53243) hydrogen bonds : bond 0.04507 ( 1804) hydrogen bonds : angle 4.40268 ( 4954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 168 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 110 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8420 (mmt-90) REVERT: A 119 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: A 149 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8372 (mm-30) REVERT: A 224 ASP cc_start: 0.8589 (t0) cc_final: 0.8325 (t0) REVERT: A 259 LYS cc_start: 0.9297 (tppt) cc_final: 0.8878 (tppp) REVERT: A 329 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: A 642 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: A 648 LYS cc_start: 0.9165 (mptt) cc_final: 0.8944 (pptt) REVERT: A 708 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8687 (mp) REVERT: A 908 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8398 (tmmt) REVERT: A 1029 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: B 23 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7950 (mtp180) REVERT: B 126 MET cc_start: 0.9125 (mtm) cc_final: 0.8801 (mtm) REVERT: B 128 ASP cc_start: 0.8745 (t70) cc_final: 0.8029 (t0) REVERT: B 277 GLU cc_start: 0.9206 (tp30) cc_final: 0.8350 (tp30) REVERT: B 367 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: B 429 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: C 316 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 362 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8393 (tp40) REVERT: C 465 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8328 (ttt180) REVERT: C 472 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7992 (ptm-80) REVERT: C 602 ARG cc_start: 0.8360 (ptp90) cc_final: 0.7962 (ptp90) REVERT: C 652 GLN cc_start: 0.8530 (mm-40) cc_final: 0.7803 (tm-30) REVERT: C 705 LEU cc_start: 0.8426 (tp) cc_final: 0.8107 (tm) REVERT: C 709 MET cc_start: 0.8608 (tpp) cc_final: 0.8141 (mpp) REVERT: C 753 MET cc_start: 0.8137 (ttp) cc_final: 0.7629 (tmm) REVERT: C 933 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: C 952 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6490 (tt) REVERT: C 1002 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8657 (pmm-80) REVERT: D 14 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8131 (mp0) REVERT: D 115 MET cc_start: 0.8504 (mtp) cc_final: 0.8155 (ttm) REVERT: D 207 GLU cc_start: 0.7685 (tt0) cc_final: 0.7232 (tm-30) REVERT: D 208 MET cc_start: 0.7406 (mtp) cc_final: 0.6813 (tmm) REVERT: D 293 TYR cc_start: 0.7645 (t80) cc_final: 0.7231 (t80) REVERT: D 333 LYS cc_start: 0.8468 (mttt) cc_final: 0.7844 (mppt) REVERT: D 451 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: D 709 MET cc_start: 0.7285 (mmt) cc_final: 0.7047 (mmm) REVERT: D 751 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8282 (tp) REVERT: D 782 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7850 (tm) REVERT: D 818 MET cc_start: 0.7950 (mtp) cc_final: 0.7522 (ttm) REVERT: D 905 TYR cc_start: 0.7485 (t80) cc_final: 0.6930 (m-80) REVERT: D 1016 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8165 (tm-30) REVERT: D 1029 MET cc_start: 0.7308 (mpm) cc_final: 0.6750 (mpt) outliers start: 93 outliers final: 55 residues processed: 250 average time/residue: 0.7355 time to fit residues: 220.3359 Evaluate side-chains 235 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 0.0050 chunk 414 optimal weight: 10.0000 chunk 301 optimal weight: 0.9980 chunk 297 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.069562 restraints weight = 80241.931| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.34 r_work: 0.2968 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38702 Z= 0.126 Angle : 0.548 12.570 53243 Z= 0.292 Chirality : 0.039 0.213 5739 Planarity : 0.004 0.051 6185 Dihedral : 22.524 179.922 6933 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 2.21 % Allowed : 26.52 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4029 helix: 1.20 (0.12), residues: 1940 sheet: -0.13 (0.24), residues: 432 loop : -1.12 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 602 TYR 0.021 0.001 TYR D 181 PHE 0.017 0.001 PHE D 878 TRP 0.008 0.001 TRP D 607 HIS 0.007 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00283 (38702) covalent geometry : angle 0.54820 (53243) hydrogen bonds : bond 0.03701 ( 1804) hydrogen bonds : angle 4.28728 ( 4954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 183 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 110 ARG cc_start: 0.8694 (tpp80) cc_final: 0.8478 (mmt-90) REVERT: A 119 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: A 126 MET cc_start: 0.8967 (mmm) cc_final: 0.8296 (mtm) REVERT: A 149 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8360 (mm-30) REVERT: A 224 ASP cc_start: 0.8534 (t0) cc_final: 0.8261 (t0) REVERT: A 259 LYS cc_start: 0.9249 (tppt) cc_final: 0.8839 (tppp) REVERT: A 329 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: A 642 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: A 648 LYS cc_start: 0.9150 (mptt) cc_final: 0.8911 (pptt) REVERT: A 685 GLU cc_start: 0.8592 (tt0) cc_final: 0.8315 (tp30) REVERT: A 708 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8701 (mp) REVERT: A 908 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8435 (tmmt) REVERT: A 1029 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7457 (mtp) REVERT: B 23 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7938 (mtp180) REVERT: B 126 MET cc_start: 0.9002 (mtm) cc_final: 0.8679 (mtm) REVERT: B 128 ASP cc_start: 0.8750 (t70) cc_final: 0.8047 (t0) REVERT: B 277 GLU cc_start: 0.9132 (tp30) cc_final: 0.8242 (OUTLIER) REVERT: B 652 GLN cc_start: 0.8096 (pp30) cc_final: 0.7810 (pp30) REVERT: B 1029 MET cc_start: 0.6915 (mtp) cc_final: 0.6567 (mtm) REVERT: C 125 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8028 (p0) REVERT: C 316 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8107 (tm-30) REVERT: C 465 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8291 (ttt180) REVERT: C 472 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7945 (ptm-80) REVERT: C 602 ARG cc_start: 0.8396 (ptp90) cc_final: 0.7994 (ptp90) REVERT: C 652 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7906 (tm-30) REVERT: C 705 LEU cc_start: 0.8438 (tp) cc_final: 0.8109 (tm) REVERT: C 709 MET cc_start: 0.8649 (tpp) cc_final: 0.8258 (mpp) REVERT: C 753 MET cc_start: 0.8149 (ttp) cc_final: 0.7611 (tmm) REVERT: C 818 MET cc_start: 0.8808 (mpp) cc_final: 0.8514 (pmm) REVERT: C 933 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: C 952 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6499 (tt) REVERT: C 1002 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8640 (pmm-80) REVERT: D 14 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8128 (mp0) REVERT: D 207 GLU cc_start: 0.7625 (tt0) cc_final: 0.7228 (tm-30) REVERT: D 208 MET cc_start: 0.7437 (mtp) cc_final: 0.6847 (tmm) REVERT: D 293 TYR cc_start: 0.7706 (t80) cc_final: 0.7333 (t80) REVERT: D 333 LYS cc_start: 0.8471 (mttt) cc_final: 0.8139 (mmmt) REVERT: D 451 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: D 709 MET cc_start: 0.7307 (mmt) cc_final: 0.7059 (mmm) REVERT: D 751 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8300 (tp) REVERT: D 818 MET cc_start: 0.7897 (mtp) cc_final: 0.7441 (ttm) REVERT: D 905 TYR cc_start: 0.7466 (t80) cc_final: 0.6945 (m-80) REVERT: D 967 ARG cc_start: 0.5812 (mpt-90) cc_final: 0.5589 (mtm-85) REVERT: D 1016 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8171 (tm-30) REVERT: D 1029 MET cc_start: 0.7450 (mpm) cc_final: 0.6794 (mpt) outliers start: 76 outliers final: 51 residues processed: 250 average time/residue: 0.7169 time to fit residues: 213.8314 Evaluate side-chains 236 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 910 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 15 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 322 optimal weight: 0.7980 chunk 393 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 652 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068756 restraints weight = 80505.200| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.35 r_work: 0.2939 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 38702 Z= 0.155 Angle : 0.563 12.871 53243 Z= 0.299 Chirality : 0.039 0.195 5739 Planarity : 0.004 0.052 6185 Dihedral : 22.465 179.898 6930 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.23 % Allowed : 26.55 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4029 helix: 1.21 (0.12), residues: 1937 sheet: -0.07 (0.25), residues: 433 loop : -1.12 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 602 TYR 0.034 0.001 TYR D 666 PHE 0.018 0.001 PHE D 878 TRP 0.009 0.001 TRP B 885 HIS 0.008 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00357 (38702) covalent geometry : angle 0.56319 (53243) hydrogen bonds : bond 0.03905 ( 1804) hydrogen bonds : angle 4.30687 ( 4954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14903.40 seconds wall clock time: 253 minutes 54.56 seconds (15234.56 seconds total)