Starting phenix.real_space_refine on Tue Sep 15 08:28:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lo5_23461/09_2026/7lo5_23461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo5_23461/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lo5_23461/09_2026/7lo5_23461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo5_23461/09_2026/7lo5_23461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lo5_23461/09_2026/7lo5_23461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo5_23461/09_2026/7lo5_23461.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lo5_23461/09_2026/7lo5_23461.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lo5_23461/09_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-2.2.1-6174/lib/python3.11/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: 7.88, per 1000 atoms: 0.21 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 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: 4.64 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: 10.02 Time building geometry restraints manager: 4.05 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 - 2.39: 46109 2.39 - 4.78: 6645 4.78 - 7.18: 434 7.18 - 9.57: 45 9.57 - 11.96: 10 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=" 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 angle pdb=" N LEU B 804 " pdb=" CA LEU B 804 " pdb=" C LEU B 804 " ideal model delta sigma weight residual 111.07 103.45 7.62 1.07e+00 8.73e-01 5.07e+01 ... (remaining 53238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 20220 35.94 - 71.87: 2349 71.87 - 107.81: 74 107.81 - 143.74: 4 143.74 - 179.68: 6 Dihedral angle restraints: 22653 sinusoidal: 10735 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 22650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3686 0.108 - 0.216: 1798 0.216 - 0.324: 231 0.324 - 0.432: 16 0.432 - 0.540: 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 -2.73 -2.19 -0.54 2.00e-01 2.50e+01 7.30e+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 -2.73 -2.24 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C3' DG J 3 " pdb=" C4' DG J 3 " pdb=" O3' DG J 3 " pdb=" C2' DG J 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.48e+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: 12.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.050 Extract box with map and model: 1.010 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 38.410 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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= 0.840 Angle : 1.590 11.959 53243 Z= 1.189 Chirality : 0.112 0.540 5739 Planarity : 0.005 0.128 6185 Dihedral : 23.924 179.676 14957 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/Z covalent geometry : bond 0.01129 / 0.84 (38702) covalent geometry : angle 1.59025 / 1.19 (53243) hydrogen bonds : bond 0.20724 / 13.87 ( 1804) hydrogen bonds : angle 8.70579 / 6.16 ( 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 : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.8874 (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: 0.8943 (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: 0.7908 (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: 0.7711 (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: 0.7352 (mtt) REVERT: D 14 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7295 (mp0) REVERT: D 69 ASP cc_start: 0.7084 (t0) cc_final: 0.6447 (p0) REVERT: D 83 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: D 167 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6673 (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: 0.6570 (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: 0.6519 (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: 0.8093 (t80) REVERT: D 700 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8558 (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: 0.8055 (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: 42 residues processed: 923 average time/residue: 0.9194 time to fit residues: 989.5069 Evaluate side-chains 293 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 222 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 643 LEU 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: 0.9980 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... A 24 ASN A 33 GLN A 116 GLN A 122 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 33 GLN B 116 GLN B 122 GLN B 371 ASN B 437 GLN B 448 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 233 ASN 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 233 ASN D 239 GLN D 266 GLN D 294 ASN D 371 ASN D 410 ASN D 437 GLN D 438 ASN D 448 ASN D 620 HIS D 628 ASN 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 = 0.3710 r_free = 0.3710 target = 0.104187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071945 restraints weight = 79964.703| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.36 r_work: 0.3011 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 38702 Z= 0.169 Angle : 0.737 10.969 53243 Z= 0.395 Chirality : 0.049 0.386 5739 Planarity : 0.006 0.060 6185 Dihedral : 24.108 179.977 6925 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.05 % Allowed : 24.43 % Favored : 70.52 % 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: -1.88 (0.12), residues: 4029 helix: -0.55 (0.11), residues: 1939 sheet: -1.44 (0.23), residues: 409 loop : -1.94 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 660 TYR 0.020 0.002 TYR C 838 PHE 0.028 0.002 PHE D 882 TRP 0.023 0.001 TRP C 885 HIS 0.005 0.001 HIS C 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (38702) covalent geometry : angle 0.73690 / 0.40 (53243) hydrogen bonds : bond 0.06288 / 4.19 ( 1804) hydrogen bonds : angle 5.33210 / 3.82 ( 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 429 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 255 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7609 (p0) REVERT: A 119 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: A 126 MET cc_start: 0.8969 (mmm) cc_final: 0.8576 (mtm) REVERT: A 224 ASP cc_start: 0.8764 (t0) cc_final: 0.8466 (t0) REVERT: A 259 LYS cc_start: 0.9333 (tppt) cc_final: 0.9073 (tppp) REVERT: A 318 THR cc_start: 0.9459 (t) cc_final: 0.9177 (t) REVERT: A 329 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A 656 LEU cc_start: 0.8891 (tt) cc_final: 0.8650 (tm) REVERT: A 709 MET cc_start: 0.9401 (mmt) cc_final: 0.9030 (mmm) REVERT: A 863 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8673 (pt0) REVERT: A 893 MET cc_start: 0.8666 (ttm) cc_final: 0.8297 (ttp) REVERT: B 86 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (t) REVERT: B 152 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8968 (ttmm) REVERT: B 215 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8791 (p) REVERT: B 230 GLU cc_start: 0.8374 (mp0) cc_final: 0.8096 (mp0) REVERT: B 266 GLN cc_start: 0.8876 (mt0) cc_final: 0.8487 (mt0) REVERT: B 277 GLU cc_start: 0.8974 (tp30) cc_final: 0.8117 (OUTLIER) REVERT: B 291 ARG cc_start: 0.8926 (mpt-90) cc_final: 0.8688 (mpt-90) REVERT: B 367 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8479 (mt-10) REVERT: B 652 GLN cc_start: 0.7732 (pp30) cc_final: 0.7512 (pp30) REVERT: B 719 MET cc_start: 0.9248 (mmm) cc_final: 0.8996 (mmm) REVERT: B 881 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: B 1029 MET cc_start: 0.7514 (mtp) cc_final: 0.7230 (mtp) REVERT: C 146 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: C 203 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7818 (ttp80) REVERT: C 316 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 602 ARG cc_start: 0.8395 (ptp90) cc_final: 0.7988 (ptp90) REVERT: C 612 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.7969 (mmmt) REVERT: C 654 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7831 (mtmm) REVERT: C 709 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: C 753 MET cc_start: 0.8119 (ttp) cc_final: 0.7578 (tmm) REVERT: D 1 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7491 (mtm) REVERT: D 14 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8142 (mp0) REVERT: D 324 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8647 (tttm) REVERT: D 642 PHE cc_start: 0.7920 (m-80) cc_final: 0.7529 (m-10) REVERT: D 693 PHE cc_start: 0.8917 (t80) cc_final: 0.8674 (t80) REVERT: D 700 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8746 (tp) REVERT: D 765 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: D 783 SER cc_start: 0.6939 (OUTLIER) cc_final: 0.6674 (m) REVERT: D 843 ILE cc_start: 0.3715 (OUTLIER) cc_final: 0.3514 (mp) REVERT: D 905 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: D 1016 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8351 (tm-30) outliers start: 174 outliers final: 51 residues processed: 401 average time/residue: 0.7473 time to fit residues: 362.0316 Evaluate side-chains 248 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 177 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 214 LEU Chi-restraints excluded: chain A residue 220 THR 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 672 THR 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 A residue 826 ILE Chi-restraints excluded: chain A residue 863 GLU 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 799 LEU Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain C residue 146 GLN 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 311 VAL Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 599 TRP Chi-restraints excluded: chain C residue 612 LYS 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 709 MET 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 D residue 1 MET Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 324 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 451 TYR 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 783 SER 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 827 THR Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 910 THR 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: 2.9990 chunk 269 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 88 optimal weight: 0.0970 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS A 227 GLN A 239 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 229 HIS B 632 GLN C 146 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 939 GLN D 53 GLN D 163 HIS D 288 ASN D 652 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067268 restraints weight = 80073.779| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.33 r_work: 0.2912 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 38702 Z= 0.269 Angle : 0.698 12.067 53243 Z= 0.375 Chirality : 0.049 0.364 5739 Planarity : 0.005 0.096 6185 Dihedral : 23.924 179.166 6832 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.64 % Allowed : 24.43 % Favored : 70.92 % 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: -1.20 (0.13), residues: 4029 helix: 0.12 (0.11), residues: 1936 sheet: -1.09 (0.24), residues: 417 loop : -1.77 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1002 TYR 0.023 0.002 TYR D 829 PHE 0.036 0.002 PHE D 200 TRP 0.011 0.002 TRP D 607 HIS 0.008 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (38702) covalent geometry : angle 0.69818 / 0.37 (53243) hydrogen bonds : bond 0.05972 / 3.94 ( 1804) hydrogen bonds : angle 4.95482 / 3.57 ( 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 351 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 191 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7196 (tm-30) REVERT: A 119 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: A 126 MET cc_start: 0.9204 (mmm) cc_final: 0.8498 (mtm) REVERT: A 224 ASP cc_start: 0.8706 (t0) cc_final: 0.8335 (t0) REVERT: A 259 LYS cc_start: 0.9351 (tppt) cc_final: 0.9111 (tppp) REVERT: A 329 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: A 642 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: B 86 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7983 (t) REVERT: B 152 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.9003 (ttmm) REVERT: B 230 GLU cc_start: 0.8702 (mp0) cc_final: 0.8382 (mp0) REVERT: B 277 GLU cc_start: 0.9178 (tp30) cc_final: 0.8353 (tp30) REVERT: B 291 ARG cc_start: 0.8977 (mpt-90) cc_final: 0.8714 (mpt-90) REVERT: B 367 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: B 719 MET cc_start: 0.9243 (mmm) cc_final: 0.8990 (mmm) REVERT: B 881 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B 1029 MET cc_start: 0.7518 (mtp) cc_final: 0.6762 (mtp) REVERT: C 1 MET cc_start: 0.8147 (mtt) cc_final: 0.7627 (mpp) REVERT: C 203 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7855 (ttp80) REVERT: C 245 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8031 (p90) REVERT: C 260 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8025 (mtp-110) REVERT: C 316 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8322 (tm-30) REVERT: C 602 ARG cc_start: 0.8465 (ptp90) cc_final: 0.8040 (ptp90) REVERT: C 641 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: C 654 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7986 (mtmm) REVERT: C 709 MET cc_start: 0.8432 (mpp) cc_final: 0.8136 (mpp) REVERT: C 737 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8523 (tptp) REVERT: C 753 MET cc_start: 0.8262 (ttp) cc_final: 0.7924 (OUTLIER) REVERT: D 1 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7533 (mtm) REVERT: D 14 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8146 (mp0) REVERT: D 642 PHE cc_start: 0.7904 (m-80) cc_final: 0.7600 (m-10) REVERT: D 782 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (tm) REVERT: D 829 TYR cc_start: 0.8050 (t80) cc_final: 0.7774 (t80) REVERT: D 905 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6621 (m-80) REVERT: D 1016 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8279 (tm-30) REVERT: D 1024 MET cc_start: 0.6293 (mtt) cc_final: 0.5939 (mtp) outliers start: 160 outliers final: 66 residues processed: 325 average time/residue: 0.7583 time to fit residues: 296.2108 Evaluate side-chains 247 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 166 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 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 240 GLN 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 782 LEU Chi-restraints excluded: chain A residue 783 SER 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 146 GLN 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 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 638 ASP 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 881 GLU 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 451 TYR 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 654 LYS 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 D residue 1 MET Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 34 GLN 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 220 THR Chi-restraints excluded: chain D residue 311 VAL 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 652 GLN Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 735 LEU 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 835 GLN Chi-restraints excluded: chain D residue 905 TYR 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: 0.0070 chunk 83 optimal weight: 0.8980 chunk 308 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 328 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 410 optimal weight: 10.0000 chunk 261 optimal weight: 0.5980 chunk 217 optimal weight: 2.9990 chunk 387 optimal weight: 9.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 4 GLN B 73 GLN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 ASN D 792 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069590 restraints weight = 79750.209| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.32 r_work: 0.2958 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38702 Z= 0.128 Angle : 0.597 11.061 53243 Z= 0.320 Chirality : 0.044 0.351 5739 Planarity : 0.005 0.051 6185 Dihedral : 23.731 179.768 6823 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.28 % Allowed : 25.65 % Favored : 71.07 % 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: -0.69 (0.13), residues: 4029 helix: 0.56 (0.12), residues: 1934 sheet: -0.83 (0.24), residues: 407 loop : -1.54 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.021 0.001 TYR D 293 PHE 0.015 0.001 PHE D 882 TRP 0.011 0.001 TRP C 499 HIS 0.007 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (38702) covalent geometry : angle 0.59682 / 0.32 (53243) hydrogen bonds : bond 0.04546 / 3.00 ( 1804) hydrogen bonds : angle 4.68938 / 3.38 ( 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 312 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 199 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 110 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8160 (mmt-90) REVERT: A 119 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7350 (pt0) REVERT: A 126 MET cc_start: 0.9177 (mmm) cc_final: 0.8503 (mtm) REVERT: A 224 ASP cc_start: 0.8677 (t0) cc_final: 0.8255 (t0) REVERT: A 259 LYS cc_start: 0.9292 (tppt) cc_final: 0.9019 (tppp) REVERT: A 642 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: B 86 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7749 (t) REVERT: B 109 SER cc_start: 0.8835 (m) cc_final: 0.8438 (t) REVERT: B 128 ASP cc_start: 0.8798 (t70) cc_final: 0.8107 (t0) REVERT: B 230 GLU cc_start: 0.8690 (mp0) cc_final: 0.8301 (mp0) REVERT: B 277 GLU cc_start: 0.9116 (tp30) cc_final: 0.8315 (tp30) REVERT: B 367 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: B 638 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: B 719 MET cc_start: 0.9212 (mmm) cc_final: 0.8975 (mmm) REVERT: B 818 MET cc_start: 0.8752 (mtm) cc_final: 0.8511 (tmm) REVERT: B 881 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: B 1029 MET cc_start: 0.7208 (mtp) cc_final: 0.6413 (mtp) REVERT: C 1 MET cc_start: 0.7946 (mtt) cc_final: 0.7360 (mpp) REVERT: C 110 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8653 (mtp-110) REVERT: C 203 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7782 (ttp80) REVERT: C 245 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8032 (p90) REVERT: C 316 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8066 (tm-30) REVERT: C 602 ARG cc_start: 0.8378 (ptp90) cc_final: 0.7852 (ptp90) REVERT: C 612 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8123 (mmmt) REVERT: C 705 LEU cc_start: 0.8307 (tp) cc_final: 0.7911 (tm) REVERT: C 709 MET cc_start: 0.8458 (mpp) cc_final: 0.7952 (mpp) REVERT: C 753 MET cc_start: 0.8201 (ttp) cc_final: 0.7733 (tmm) REVERT: C 818 MET cc_start: 0.8832 (mpp) cc_final: 0.8544 (pmm) REVERT: C 1002 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8555 (pmm-80) REVERT: D 1 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7193 (mtm) REVERT: D 14 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8107 (mp0) REVERT: D 208 MET cc_start: 0.7485 (mtp) cc_final: 0.7253 (mtt) REVERT: D 451 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: D 642 PHE cc_start: 0.7860 (m-80) cc_final: 0.7638 (m-10) REVERT: D 754 TYR cc_start: 0.7367 (t80) cc_final: 0.6999 (t80) REVERT: D 762 MET cc_start: 0.6427 (mmt) cc_final: 0.6059 (mmp) REVERT: D 782 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7792 (tm) REVERT: D 806 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5936 (tt0) REVERT: D 905 TYR cc_start: 0.7341 (t80) cc_final: 0.6815 (m-80) REVERT: D 1016 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8290 (tm-30) REVERT: D 1024 MET cc_start: 0.6150 (mtt) cc_final: 0.5867 (mtp) outliers start: 113 outliers final: 47 residues processed: 292 average time/residue: 0.7488 time to fit residues: 264.9379 Evaluate side-chains 228 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 VAL 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 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 863 GLU Chi-restraints excluded: chain A residue 922 LEU 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 287 GLU 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 638 ASP 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 B residue 951 THR 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 576 VAL Chi-restraints excluded: chain C residue 612 LYS Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 922 LEU 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 214 LEU Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 806 GLU 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 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: 5.9990 chunk 247 optimal weight: 4.9990 chunk 390 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 381 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 ASN C 53 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 410 ASN D 437 GLN D 438 ASN D 565 GLN D 628 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065450 restraints weight = 80534.903| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.33 r_work: 0.2865 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 38702 Z= 0.318 Angle : 0.706 10.033 53243 Z= 0.373 Chirality : 0.049 0.348 5739 Planarity : 0.005 0.057 6185 Dihedral : 23.647 179.715 6813 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.41 % Allowed : 24.87 % Favored : 70.72 % 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: -0.73 (0.13), residues: 4029 helix: 0.51 (0.12), residues: 1930 sheet: -0.67 (0.24), residues: 427 loop : -1.60 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 400 TYR 0.030 0.002 TYR D 829 PHE 0.022 0.002 PHE B 849 TRP 0.017 0.002 TRP B 885 HIS 0.009 0.002 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.32 (38702) covalent geometry : angle 0.70563 / 0.37 (53243) hydrogen bonds : bond 0.05913 / 3.90 ( 1804) hydrogen bonds : angle 4.78787 / 3.45 ( 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 324 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 172 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 119 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7490 (pt0) REVERT: A 126 MET cc_start: 0.9253 (mmm) cc_final: 0.8319 (mtm) REVERT: A 224 ASP cc_start: 0.8699 (t0) cc_final: 0.8308 (t0) REVERT: A 259 LYS cc_start: 0.9348 (tppt) cc_final: 0.9080 (tppp) REVERT: A 329 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: A 609 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8824 (ttpp) REVERT: A 642 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: A 708 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8568 (mp) REVERT: A 908 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8262 (tmmt) REVERT: B 86 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7936 (t) REVERT: B 109 SER cc_start: 0.8876 (m) cc_final: 0.8586 (t) REVERT: B 152 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9009 (ttmm) REVERT: B 230 GLU cc_start: 0.8849 (mp0) cc_final: 0.8361 (mp0) REVERT: B 277 GLU cc_start: 0.9280 (tp30) cc_final: 0.8430 (tp30) REVERT: B 367 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: B 429 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8107 (mm-30) REVERT: B 638 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: B 709 MET cc_start: 0.9462 (mmm) cc_final: 0.9215 (mmt) REVERT: B 719 MET cc_start: 0.9232 (mmm) cc_final: 0.9030 (mmm) REVERT: B 881 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: B 1029 MET cc_start: 0.7442 (mtp) cc_final: 0.6856 (mtp) REVERT: C 1 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7754 (mpp) REVERT: C 203 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7875 (ttp80) REVERT: C 245 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8394 (p90) REVERT: C 260 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8178 (mtp-110) REVERT: C 316 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 602 ARG cc_start: 0.8410 (ptp90) cc_final: 0.8004 (ptp90) REVERT: C 705 LEU cc_start: 0.8386 (tp) cc_final: 0.7746 (pt) REVERT: C 709 MET cc_start: 0.8614 (tpp) cc_final: 0.8340 (mpp) REVERT: C 753 MET cc_start: 0.8242 (ttp) cc_final: 0.7634 (tmm) REVERT: C 792 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: C 933 GLN cc_start: 0.7927 (mt0) cc_final: 0.7646 (mp10) REVERT: C 952 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6579 (tt) REVERT: C 1002 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8513 (pmm-80) REVERT: D 14 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8174 (mp0) REVERT: D 115 MET cc_start: 0.8586 (mtp) cc_final: 0.8272 (ttm) REVERT: D 642 PHE cc_start: 0.7868 (m-80) cc_final: 0.7599 (m-10) REVERT: D 762 MET cc_start: 0.6431 (mmt) cc_final: 0.6158 (mmt) REVERT: D 782 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7734 (tm) REVERT: D 905 TYR cc_start: 0.7384 (t80) cc_final: 0.6862 (m-80) REVERT: D 1016 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8212 (tm-30) REVERT: D 1024 MET cc_start: 0.6366 (mtt) cc_final: 0.6151 (mtp) outliers start: 152 outliers final: 69 residues processed: 302 average time/residue: 0.7123 time to fit residues: 263.5867 Evaluate side-chains 249 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 161 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 GLN 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 609 LYS 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 714 GLU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 GLN 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 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 633 VAL Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 642 PHE 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 796 THR Chi-restraints excluded: chain B residue 819 ASN 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 86 THR 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 238 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 792 GLN Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 803 ASP 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 3 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 411 THR 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 609 LYS Chi-restraints excluded: chain D residue 717 ILE 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 867 LEU 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: 0.8980 chunk 135 optimal weight: 1.9990 chunk 394 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 chunk 305 optimal weight: 6.9990 chunk 277 optimal weight: 0.0670 chunk 164 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN C 437 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN D 438 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067802 restraints weight = 80080.579| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.33 r_work: 0.2915 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38702 Z= 0.150 Angle : 0.592 10.722 53243 Z= 0.316 Chirality : 0.044 0.345 5739 Planarity : 0.004 0.049 6185 Dihedral : 23.495 178.782 6813 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.31 % Allowed : 25.68 % Favored : 71.01 % 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: -0.43 (0.13), residues: 4029 helix: 0.75 (0.12), residues: 1920 sheet: -0.39 (0.25), residues: 408 loop : -1.45 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 203 TYR 0.019 0.001 TYR D 181 PHE 0.027 0.001 PHE D 200 TRP 0.010 0.001 TRP C 499 HIS 0.006 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (38702) covalent geometry : angle 0.59190 / 0.32 (53243) hydrogen bonds : bond 0.04472 / 2.95 ( 1804) hydrogen bonds : angle 4.60322 / 3.32 ( 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 301 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 187 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 110 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8292 (mmt-90) REVERT: A 119 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: A 126 MET cc_start: 0.9227 (mmm) cc_final: 0.8308 (mtm) REVERT: A 224 ASP cc_start: 0.8673 (t0) cc_final: 0.8259 (t0) REVERT: A 259 LYS cc_start: 0.9306 (tppt) cc_final: 0.9021 (tppp) REVERT: A 329 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A 642 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: A 648 LYS cc_start: 0.9165 (mptt) cc_final: 0.8902 (pptt) REVERT: A 908 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8346 (tmmt) REVERT: A 1029 MET cc_start: 0.7856 (mtp) cc_final: 0.7443 (mtp) REVERT: B 86 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7822 (t) REVERT: B 277 GLU cc_start: 0.9222 (tp30) cc_final: 0.8416 (tp30) REVERT: B 367 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: B 638 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: B 881 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: B 1029 MET cc_start: 0.7409 (mtp) cc_final: 0.6865 (mtp) REVERT: C 1 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7337 (mpp) REVERT: C 107 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: C 203 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7851 (ttp80) REVERT: C 245 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8390 (p90) REVERT: C 316 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8193 (tm-30) REVERT: C 602 ARG cc_start: 0.8354 (ptp90) cc_final: 0.7918 (ptp90) REVERT: C 705 LEU cc_start: 0.8326 (tp) cc_final: 0.7912 (tm) REVERT: C 709 MET cc_start: 0.8613 (tpp) cc_final: 0.8054 (mpp) REVERT: C 753 MET cc_start: 0.8272 (ttp) cc_final: 0.7677 (tmm) REVERT: C 818 MET cc_start: 0.8825 (mpp) cc_final: 0.8549 (pmm) REVERT: C 933 GLN cc_start: 0.7928 (mt0) cc_final: 0.7667 (mp10) REVERT: C 952 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6617 (tt) REVERT: C 1002 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8541 (pmm-80) REVERT: D 1 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7135 (mtm) REVERT: D 14 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8141 (mp0) REVERT: D 115 MET cc_start: 0.8507 (mtp) cc_final: 0.8159 (ttm) REVERT: D 451 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: D 642 PHE cc_start: 0.7813 (m-80) cc_final: 0.7584 (m-10) REVERT: D 674 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5926 (ptp90) REVERT: D 728 GLN cc_start: 0.7534 (mt0) cc_final: 0.7302 (mm-40) REVERT: D 762 MET cc_start: 0.6453 (mmt) cc_final: 0.6168 (mmt) REVERT: D 782 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7731 (tm) REVERT: D 905 TYR cc_start: 0.7415 (t80) cc_final: 0.6859 (m-80) REVERT: D 1016 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8185 (tm-30) outliers start: 114 outliers final: 61 residues processed: 288 average time/residue: 0.7150 time to fit residues: 249.3372 Evaluate side-chains 242 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 164 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 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 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 863 GLU 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 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 638 ASP Chi-restraints excluded: chain B residue 642 PHE 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 796 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 107 GLU 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 245 PHE 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 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 803 ASP 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 975 GLU 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 59 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 674 ARG Chi-restraints excluded: chain D residue 717 ILE 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 931 LYS Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1028 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 419 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 378 optimal weight: 0.6980 chunk 339 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 406 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN D 438 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.099151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066671 restraints weight = 80707.075| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.28 r_work: 0.2884 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4135 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= 0.222 Angle : 0.619 10.957 53243 Z= 0.328 Chirality : 0.046 0.351 5739 Planarity : 0.005 0.053 6185 Dihedral : 23.395 179.250 6813 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.31 % Allowed : 25.80 % Favored : 70.89 % 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: -0.40 (0.13), residues: 4029 helix: 0.77 (0.12), residues: 1926 sheet: -0.35 (0.25), residues: 414 loop : -1.45 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 660 TYR 0.017 0.002 TYR D 745 PHE 0.017 0.001 PHE D 882 TRP 0.009 0.001 TRP B 885 HIS 0.006 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (38702) covalent geometry : angle 0.61929 / 0.33 (53243) hydrogen bonds : bond 0.04856 / 3.20 ( 1804) hydrogen bonds : angle 4.60728 / 3.32 ( 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 284 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 170 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 110 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8412 (mpp80) REVERT: A 119 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: A 126 MET cc_start: 0.9295 (mmm) cc_final: 0.8256 (mtm) REVERT: A 224 ASP cc_start: 0.8706 (t0) cc_final: 0.8303 (t0) REVERT: A 259 LYS cc_start: 0.9346 (tppt) cc_final: 0.9063 (tppp) REVERT: A 329 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: A 642 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: A 648 LYS cc_start: 0.9240 (mptt) cc_final: 0.8985 (pptt) REVERT: A 908 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8452 (tmmt) REVERT: A 1029 MET cc_start: 0.7894 (mtp) cc_final: 0.7435 (mtp) REVERT: B 86 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 277 GLU cc_start: 0.9234 (tp30) cc_final: 0.8434 (tp30) REVERT: B 367 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: B 638 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: B 881 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: B 1029 MET cc_start: 0.7407 (mtp) cc_final: 0.7001 (mtp) REVERT: C 1 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7458 (mpp) REVERT: C 203 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7927 (ttp80) REVERT: C 245 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8428 (p90) REVERT: C 316 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 362 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8445 (tp40) REVERT: C 602 ARG cc_start: 0.8388 (ptp90) cc_final: 0.7965 (ptp90) REVERT: C 652 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7811 (tm-30) REVERT: C 705 LEU cc_start: 0.8400 (tp) cc_final: 0.7982 (tm) REVERT: C 709 MET cc_start: 0.8676 (tpp) cc_final: 0.8092 (mpp) REVERT: C 753 MET cc_start: 0.8301 (ttp) cc_final: 0.7791 (tmm) REVERT: C 818 MET cc_start: 0.8811 (mpp) cc_final: 0.8580 (pmm) REVERT: C 933 GLN cc_start: 0.7968 (mt0) cc_final: 0.7734 (mp10) REVERT: C 952 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6624 (tt) REVERT: C 1002 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8578 (pmm-80) REVERT: D 14 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8226 (mp0) REVERT: D 115 MET cc_start: 0.8655 (mtp) cc_final: 0.8333 (ttm) REVERT: D 451 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: D 642 PHE cc_start: 0.7857 (m-80) cc_final: 0.7651 (m-10) REVERT: D 728 GLN cc_start: 0.7525 (mt0) cc_final: 0.7231 (mm-40) REVERT: D 762 MET cc_start: 0.6597 (mmt) cc_final: 0.6329 (mmt) REVERT: D 782 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7833 (tm) REVERT: D 829 TYR cc_start: 0.8101 (t80) cc_final: 0.7700 (t80) REVERT: D 905 TYR cc_start: 0.7455 (t80) cc_final: 0.6882 (m-80) REVERT: D 1016 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8159 (tm-30) outliers start: 114 outliers final: 68 residues processed: 268 average time/residue: 0.6932 time to fit residues: 227.3419 Evaluate side-chains 247 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 164 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 GLN 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 743 SER 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 86 THR Chi-restraints excluded: chain B residue 105 ILE 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 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 561 VAL 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 638 ASP 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 796 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 86 THR 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 362 GLN 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 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 803 ASP 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 975 GLU 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 121 VAL Chi-restraints excluded: chain D residue 214 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 671 VAL Chi-restraints excluded: chain D residue 717 ILE 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 931 LYS Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 999 HIS Chi-restraints excluded: chain D residue 1028 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 414 optimal weight: 50.0000 chunk 71 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 333 optimal weight: 8.9990 chunk 317 optimal weight: 0.1980 chunk 213 optimal weight: 0.6980 chunk 375 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN D 438 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.101069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068614 restraints weight = 79869.809| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.32 r_work: 0.2945 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 38702 Z= 0.120 Angle : 0.569 11.826 53243 Z= 0.302 Chirality : 0.043 0.349 5739 Planarity : 0.004 0.048 6185 Dihedral : 23.234 178.930 6813 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.44 % Allowed : 26.81 % Favored : 70.75 % 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: -0.15 (0.13), residues: 4029 helix: 0.98 (0.12), residues: 1919 sheet: -0.18 (0.25), residues: 402 loop : -1.33 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 291 TYR 0.020 0.001 TYR D 994 PHE 0.011 0.001 PHE D 882 TRP 0.040 0.001 TRP C 960 HIS 0.010 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (38702) covalent geometry : angle 0.56908 / 0.30 (53243) hydrogen bonds : bond 0.04023 / 2.65 ( 1804) hydrogen bonds : angle 4.48077 / 3.22 ( 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 272 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 188 time to evaluate : 1.371 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: 0.7742 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 110 ARG cc_start: 0.8599 (tpp80) cc_final: 0.8337 (mmt-90) REVERT: A 119 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: A 126 MET cc_start: 0.9263 (mmm) cc_final: 0.8179 (mtm) REVERT: A 224 ASP cc_start: 0.8671 (t0) cc_final: 0.8259 (t0) REVERT: A 259 LYS cc_start: 0.9257 (tppt) cc_final: 0.8858 (tppp) REVERT: A 329 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 365 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8682 (mtt-85) REVERT: A 642 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 648 LYS cc_start: 0.9205 (mptt) cc_final: 0.8955 (pptt) REVERT: A 908 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8396 (tmmt) REVERT: A 1029 MET cc_start: 0.7852 (mtp) cc_final: 0.7467 (mtp) REVERT: B 161 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8745 (ttp) REVERT: B 238 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9023 (mt) REVERT: B 277 GLU cc_start: 0.9193 (tp30) cc_final: 0.8410 (tp30) REVERT: B 367 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: B 638 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7865 (t0) REVERT: C 1 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7376 (mpp) REVERT: C 203 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7884 (ttp80) REVERT: C 316 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 602 ARG cc_start: 0.8334 (ptp90) cc_final: 0.7910 (ptp90) REVERT: C 652 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7895 (tm-30) REVERT: C 705 LEU cc_start: 0.8403 (tp) cc_final: 0.7980 (tm) REVERT: C 709 MET cc_start: 0.8652 (tpp) cc_final: 0.8088 (mpp) REVERT: C 753 MET cc_start: 0.8347 (ttp) cc_final: 0.7860 (tmm) REVERT: C 818 MET cc_start: 0.8831 (mpp) cc_final: 0.8562 (pmm) REVERT: C 933 GLN cc_start: 0.7972 (mt0) cc_final: 0.7549 (mp10) REVERT: C 952 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6631 (tt) REVERT: C 1002 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8652 (pmm-80) REVERT: D 14 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8116 (mp0) REVERT: D 451 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: D 642 PHE cc_start: 0.7738 (m-80) cc_final: 0.7530 (m-10) REVERT: D 728 GLN cc_start: 0.7505 (mt0) cc_final: 0.7220 (mm-40) REVERT: D 762 MET cc_start: 0.6435 (mmt) cc_final: 0.6137 (mmt) REVERT: D 765 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6634 (mp10) REVERT: D 782 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7962 (tm) REVERT: D 905 TYR cc_start: 0.7478 (t80) cc_final: 0.6980 (m-80) REVERT: D 1016 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8164 (tm-30) outliers start: 84 outliers final: 44 residues processed: 259 average time/residue: 0.7599 time to fit residues: 237.2194 Evaluate side-chains 226 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 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 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 B residue 161 MET 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 561 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 642 PHE 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 951 THR Chi-restraints excluded: chain C residue 1 MET 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 561 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 719 MET 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 43 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 214 LEU 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 717 ILE Chi-restraints excluded: chain D residue 765 GLN Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 267 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 410 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 160 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 407 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** 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 = 0.3657 r_free = 0.3657 target = 0.100976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.068436 restraints weight = 80335.222| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.34 r_work: 0.2928 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38702 Z= 0.130 Angle : 0.575 13.908 53243 Z= 0.304 Chirality : 0.043 0.355 5739 Planarity : 0.004 0.047 6185 Dihedral : 23.089 179.685 6806 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.32 % Allowed : 27.07 % Favored : 70.60 % 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: -0.05 (0.13), residues: 4029 helix: 1.05 (0.12), residues: 1932 sheet: -0.11 (0.25), residues: 404 loop : -1.28 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 110 TYR 0.025 0.001 TYR D 666 PHE 0.013 0.001 PHE C 882 TRP 0.021 0.001 TRP C 960 HIS 0.008 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (38702) covalent geometry : angle 0.57482 / 0.30 (53243) hydrogen bonds : bond 0.04028 / 2.66 ( 1804) hydrogen bonds : angle 4.42694 / 3.18 ( 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 256 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 176 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 110 ARG cc_start: 0.8581 (tpp80) cc_final: 0.8315 (mmt-90) REVERT: A 119 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: A 126 MET cc_start: 0.9236 (mmm) cc_final: 0.8103 (mtm) REVERT: A 224 ASP cc_start: 0.8667 (t0) cc_final: 0.8328 (t0) REVERT: A 259 LYS cc_start: 0.9249 (tppt) cc_final: 0.8854 (tppp) REVERT: A 329 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 642 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 648 LYS cc_start: 0.9192 (mptt) cc_final: 0.8938 (pptt) REVERT: A 908 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8380 (tmmt) REVERT: A 1029 MET cc_start: 0.7826 (mtp) cc_final: 0.7425 (mtp) REVERT: B 125 ASP cc_start: 0.8853 (t0) cc_final: 0.8613 (t0) REVERT: B 128 ASP cc_start: 0.8763 (t70) cc_final: 0.8092 (t0) REVERT: B 277 GLU cc_start: 0.9204 (tp30) cc_final: 0.8401 (tp30) REVERT: B 367 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: B 638 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7890 (t0) REVERT: B 893 MET cc_start: 0.7400 (ttp) cc_final: 0.7164 (ttp) REVERT: C 1 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7502 (mpp) REVERT: C 203 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7884 (ttp80) REVERT: C 316 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 602 ARG cc_start: 0.8324 (ptp90) cc_final: 0.7906 (ptp90) REVERT: C 652 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8014 (tm-30) REVERT: C 705 LEU cc_start: 0.8400 (tp) cc_final: 0.7966 (tm) REVERT: C 709 MET cc_start: 0.8612 (tpp) cc_final: 0.8049 (mpp) REVERT: C 753 MET cc_start: 0.8301 (ttp) cc_final: 0.7770 (tmm) REVERT: C 818 MET cc_start: 0.8860 (mpp) cc_final: 0.8589 (pmm) REVERT: C 1002 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8704 (pmm-80) REVERT: D 14 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8066 (mp0) REVERT: D 451 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: D 475 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7900 (mtpp) REVERT: D 642 PHE cc_start: 0.7795 (m-80) cc_final: 0.7584 (m-10) REVERT: D 728 GLN cc_start: 0.7454 (mt0) cc_final: 0.7151 (mm-40) REVERT: D 762 MET cc_start: 0.6388 (mmt) cc_final: 0.6074 (mmt) REVERT: D 765 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6683 (mp10) REVERT: D 782 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7803 (tm) REVERT: D 905 TYR cc_start: 0.7499 (t80) cc_final: 0.6988 (m-80) REVERT: D 1016 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8167 (tm-30) REVERT: D 1029 MET cc_start: 0.7375 (mpm) cc_final: 0.6775 (mpt) outliers start: 80 outliers final: 45 residues processed: 244 average time/residue: 0.7628 time to fit residues: 225.2046 Evaluate side-chains 221 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 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 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 684 ASP 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 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 393 MET 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 638 ASP Chi-restraints excluded: chain B residue 642 PHE 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 878 PHE 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 147 VAL Chi-restraints excluded: chain C residue 203 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 719 MET Chi-restraints excluded: chain C residue 793 VAL 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 113 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 765 GLN 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 931 LYS Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 1.9990 chunk 414 optimal weight: 50.0000 chunk 301 optimal weight: 0.9990 chunk 297 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 85 optimal weight: 0.0050 chunk 110 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 73 GLN C 462 ASN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069165 restraints weight = 80043.135| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.34 r_work: 0.2944 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 38702 Z= 0.118 Angle : 0.562 13.651 53243 Z= 0.298 Chirality : 0.042 0.354 5739 Planarity : 0.004 0.047 6185 Dihedral : 22.970 179.946 6806 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 27.34 % Favored : 70.66 % 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: 0.03 (0.13), residues: 4029 helix: 1.11 (0.12), residues: 1940 sheet: 0.02 (0.25), residues: 398 loop : -1.27 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 110 TYR 0.020 0.001 TYR D 181 PHE 0.011 0.001 PHE D 882 TRP 0.014 0.001 TRP C 960 HIS 0.007 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (38702) covalent geometry : angle 0.56165 / 0.30 (53243) hydrogen bonds : bond 0.03810 / 2.51 ( 1804) hydrogen bonds : angle 4.35749 / 3.13 ( 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 246 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 177 time to evaluate : 1.362 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: 0.7731 (tm-30) cc_final: 0.7442 (tm-30) REVERT: A 110 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8332 (mmt-90) REVERT: A 119 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: A 126 MET cc_start: 0.9222 (mmm) cc_final: 0.8025 (mtm) REVERT: A 149 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8328 (mm-30) REVERT: A 224 ASP cc_start: 0.8678 (t0) cc_final: 0.8309 (t0) REVERT: A 259 LYS cc_start: 0.9219 (tppt) cc_final: 0.8808 (tppp) REVERT: A 329 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: A 642 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: A 648 LYS cc_start: 0.9142 (mptt) cc_final: 0.8906 (pptt) REVERT: A 908 LYS cc_start: 0.8854 (ttmm) cc_final: 0.8387 (tmmt) REVERT: A 1029 MET cc_start: 0.7735 (mtp) cc_final: 0.7418 (mtp) REVERT: B 128 ASP cc_start: 0.8755 (t70) cc_final: 0.8132 (t0) REVERT: B 238 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8983 (mt) REVERT: B 277 GLU cc_start: 0.9169 (tp30) cc_final: 0.8380 (tp30) REVERT: B 367 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: B 638 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7855 (t0) REVERT: B 652 GLN cc_start: 0.7963 (pp30) cc_final: 0.7629 (pp30) REVERT: C 1 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7438 (mpp) REVERT: C 203 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7907 (ttp80) REVERT: C 316 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 362 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8293 (tp40) REVERT: C 602 ARG cc_start: 0.8314 (ptp90) cc_final: 0.7885 (ptp90) REVERT: C 652 GLN cc_start: 0.8572 (mm-40) cc_final: 0.7994 (tm-30) REVERT: C 705 LEU cc_start: 0.8393 (tp) cc_final: 0.8055 (tm) REVERT: C 709 MET cc_start: 0.8602 (tpp) cc_final: 0.8165 (mpp) REVERT: C 753 MET cc_start: 0.8263 (ttp) cc_final: 0.7741 (tmm) REVERT: C 818 MET cc_start: 0.8888 (mpp) cc_final: 0.8622 (pmm) REVERT: C 933 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: C 1002 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8615 (pmm-80) REVERT: D 14 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8056 (mp0) REVERT: D 451 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: D 728 GLN cc_start: 0.7399 (mt0) cc_final: 0.7068 (mm-40) REVERT: D 762 MET cc_start: 0.6324 (mmt) cc_final: 0.6017 (mmt) REVERT: D 765 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: D 782 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7836 (tm) REVERT: D 905 TYR cc_start: 0.7502 (t80) cc_final: 0.6980 (m-80) REVERT: D 1016 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8131 (tm-30) REVERT: D 1029 MET cc_start: 0.7305 (mpm) cc_final: 0.6792 (mpt) outliers start: 69 outliers final: 41 residues processed: 237 average time/residue: 0.7752 time to fit residues: 221.7468 Evaluate side-chains 222 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 684 ASP 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 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 595 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 642 PHE 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 951 THR Chi-restraints excluded: chain C residue 1 MET 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 362 GLN 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 719 MET 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 113 VAL Chi-restraints excluded: chain D residue 214 LEU 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 717 ILE Chi-restraints excluded: chain D residue 765 GLN 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 931 LYS 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: 0.6980 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 273 optimal weight: 0.2980 chunk 209 optimal weight: 0.7980 chunk 322 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069263 restraints weight = 80252.878| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.34 r_work: 0.2950 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38702 Z= 0.121 Angle : 0.570 13.615 53243 Z= 0.300 Chirality : 0.042 0.356 5739 Planarity : 0.004 0.047 6185 Dihedral : 22.891 179.702 6804 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.97 % Allowed : 27.54 % Favored : 70.49 % 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: 1937 sheet: 0.08 (0.25), residues: 408 loop : -1.25 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 600 TYR 0.023 0.001 TYR D 181 PHE 0.029 0.001 PHE D 878 TRP 0.012 0.001 TRP C 960 HIS 0.006 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (38702) covalent geometry : angle 0.56991 / 0.30 (53243) hydrogen bonds : bond 0.03799 / 2.51 ( 1804) hydrogen bonds : angle 4.33029 / 3.11 ( 4954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14878.43 seconds wall clock time: 253 minutes 40.01 seconds (15220.01 seconds total)