Starting phenix.real_space_refine on Wed Aug 27 01:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atu_15663/08_2025/8atu_15663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atu_15663/08_2025/8atu_15663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8atu_15663/08_2025/8atu_15663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atu_15663/08_2025/8atu_15663.map" model { file = "/net/cci-nas-00/data/ceres_data/8atu_15663/08_2025/8atu_15663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atu_15663/08_2025/8atu_15663.cif" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 302 5.16 5 C 28038 2.51 5 N 7422 2.21 5 O 8118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43882 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2837, 21940 Classifications: {'peptide': 2837} Link IDs: {'PCIS': 4, 'PTRANS': 141, 'TRANS': 2691} Chain breaks: 45 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2095 SG CYS A 328 86.076 66.782 78.733 1.00236.65 S ATOM 2119 SG CYS A 331 85.794 68.456 82.166 1.00239.46 S ATOM 2316 SG CYS A 355 85.364 64.660 81.945 1.00235.55 S Restraints were copied for chains: B Time building chain proxies: 39.15, per 1000 atoms: 0.89 Number of scatterers: 43882 At special positions: 0 Unit cell: (193.05, 204.75, 194.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 302 16.00 O 8118 8.00 N 7422 7.00 C 28038 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: 3.41 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4901 " pdb="ZN ZN A4901 " - pdb=" NE2 HIS A 348 " pdb="ZN ZN A4901 " - pdb=" SG CYS A 331 " pdb="ZN ZN A4901 " - pdb=" SG CYS A 328 " pdb="ZN ZN A4901 " - pdb=" SG CYS A 355 " pdb=" ZN B4901 " pdb="ZN ZN B4901 " - pdb=" NE2 HIS B 348 " pdb="ZN ZN B4901 " - pdb=" SG CYS B 331 " pdb="ZN ZN B4901 " - pdb=" SG CYS B 355 " pdb="ZN ZN B4901 " - pdb=" SG CYS B 328 " Number of angles added : 6 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10776 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 32 sheets defined 53.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 166 through 180 Processing helix chain 'A' and resid 188 through 208 removed outlier: 4.288A pdb=" N HIS A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 225 through 242 removed outlier: 3.658A pdb=" N ILE A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.738A pdb=" N VAL A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 281 through 284 removed outlier: 3.601A pdb=" N TYR A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.569A pdb=" N ARG A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 removed outlier: 3.515A pdb=" N TRP A 296 " --> pdb=" O PHE A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.626A pdb=" N GLN A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.520A pdb=" N THR A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.825A pdb=" N GLU A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.644A pdb=" N THR A 855 " --> pdb=" O PRO A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 869 removed outlier: 3.569A pdb=" N ILE A 866 " --> pdb=" O PRO A 863 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 869 " --> pdb=" O ILE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1029 Processing helix chain 'A' and resid 1171 through 1177 removed outlier: 3.544A pdb=" N HIS A1177 " --> pdb=" O PHE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1191 No H-bonds generated for 'chain 'A' and resid 1189 through 1191' Processing helix chain 'A' and resid 1205 through 1213 removed outlier: 3.666A pdb=" N VAL A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1294 Processing helix chain 'A' and resid 1313 through 1324 removed outlier: 3.799A pdb=" N GLN A1317 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A1322 " --> pdb=" O ARG A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1337 removed outlier: 3.800A pdb=" N GLU A1329 " --> pdb=" O SER A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1363 Processing helix chain 'A' and resid 1371 through 1384 removed outlier: 3.549A pdb=" N PHE A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1394 Processing helix chain 'A' and resid 1397 through 1414 Processing helix chain 'A' and resid 1423 through 1434 removed outlier: 4.218A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1442 Processing helix chain 'A' and resid 1444 through 1459 Processing helix chain 'A' and resid 1463 through 1482 removed outlier: 3.619A pdb=" N GLN A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1497 Processing helix chain 'A' and resid 1551 through 1557 removed outlier: 4.245A pdb=" N THR A1555 " --> pdb=" O GLY A1552 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A1557 " --> pdb=" O PHE A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1770 Processing helix chain 'A' and resid 1885 through 1890 Processing helix chain 'A' and resid 1909 through 1940 removed outlier: 3.660A pdb=" N HIS A1913 " --> pdb=" O GLU A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1954 Processing helix chain 'A' and resid 1965 through 1999 Processing helix chain 'A' and resid 2010 through 2017 Processing helix chain 'A' and resid 2019 through 2040 Processing helix chain 'A' and resid 2047 through 2054 removed outlier: 3.655A pdb=" N GLN A2051 " --> pdb=" O PRO A2047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A2054 " --> pdb=" O LEU A2050 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2071 through 2087 Processing helix chain 'A' and resid 2091 through 2104 Processing helix chain 'A' and resid 2113 through 2128 Processing helix chain 'A' and resid 2129 through 2131 No H-bonds generated for 'chain 'A' and resid 2129 through 2131' Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.920A pdb=" N GLU A2136 " --> pdb=" O SER A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2150 Processing helix chain 'A' and resid 2164 through 2189 Processing helix chain 'A' and resid 2201 through 2206 removed outlier: 4.539A pdb=" N ASN A2205 " --> pdb=" O TRP A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2341 Processing helix chain 'A' and resid 2347 through 2365 removed outlier: 3.522A pdb=" N LEU A2351 " --> pdb=" O HIS A2347 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2389 Processing helix chain 'A' and resid 2394 through 2398 removed outlier: 4.125A pdb=" N ILE A2397 " --> pdb=" O ARG A2394 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A2398 " --> pdb=" O GLY A2395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2394 through 2398' Processing helix chain 'A' and resid 2400 through 2420 removed outlier: 3.904A pdb=" N ALA A2404 " --> pdb=" O GLY A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2569 through 2574 removed outlier: 3.853A pdb=" N VAL A2573 " --> pdb=" O ARG A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2576 through 2600 Processing helix chain 'A' and resid 2635 through 2650 Processing helix chain 'A' and resid 2651 through 2653 No H-bonds generated for 'chain 'A' and resid 2651 through 2653' Processing helix chain 'A' and resid 2656 through 2668 Processing helix chain 'A' and resid 2697 through 2711 Processing helix chain 'A' and resid 2715 through 2732 Processing helix chain 'A' and resid 2747 through 2755 removed outlier: 3.850A pdb=" N ASP A2755 " --> pdb=" O LEU A2751 " (cutoff:3.500A) Processing helix chain 'A' and resid 2755 through 2768 removed outlier: 4.347A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A2768 " --> pdb=" O LYS A2764 " (cutoff:3.500A) Processing helix chain 'A' and resid 2782 through 2802 removed outlier: 4.347A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2820 removed outlier: 4.068A pdb=" N PHE A2808 " --> pdb=" O CYS A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2829 Processing helix chain 'A' and resid 2832 through 2845 removed outlier: 3.972A pdb=" N GLU A2845 " --> pdb=" O GLU A2841 " (cutoff:3.500A) Processing helix chain 'A' and resid 2852 through 2873 Processing helix chain 'A' and resid 2914 through 2931 removed outlier: 3.546A pdb=" N LEU A2918 " --> pdb=" O THR A2914 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A2931 " --> pdb=" O ASN A2927 " (cutoff:3.500A) Processing helix chain 'A' and resid 2979 through 2987 removed outlier: 3.959A pdb=" N LEU A2983 " --> pdb=" O TYR A2979 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3000 removed outlier: 3.501A pdb=" N MET A2991 " --> pdb=" O ASN A2987 " (cutoff:3.500A) Processing helix chain 'A' and resid 3031 through 3046 Processing helix chain 'A' and resid 3050 through 3064 Proline residue: A3056 - end of helix Processing helix chain 'A' and resid 3078 through 3089 Processing helix chain 'A' and resid 3091 through 3101 Processing helix chain 'A' and resid 3103 through 3118 Processing helix chain 'A' and resid 3124 through 3132 removed outlier: 3.586A pdb=" N THR A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A3132 " --> pdb=" O THR A3128 " (cutoff:3.500A) Processing helix chain 'A' and resid 3178 through 3184 removed outlier: 4.448A pdb=" N VAL A3181 " --> pdb=" O PRO A3178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A3184 " --> pdb=" O VAL A3181 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3235 removed outlier: 3.745A pdb=" N THR A3234 " --> pdb=" O SER A3231 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3325 removed outlier: 4.141A pdb=" N LYS A3325 " --> pdb=" O ASP A3321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3321 through 3325' Processing helix chain 'A' and resid 3327 through 3340 Processing helix chain 'A' and resid 3344 through 3353 removed outlier: 3.617A pdb=" N MET A3348 " --> pdb=" O LEU A3344 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3367 Processing helix chain 'A' and resid 3368 through 3373 removed outlier: 4.072A pdb=" N MET A3373 " --> pdb=" O TYR A3370 " (cutoff:3.500A) Processing helix chain 'A' and resid 3374 through 3387 Processing helix chain 'A' and resid 3389 through 3402 Processing helix chain 'A' and resid 3429 through 3441 removed outlier: 3.671A pdb=" N THR A3441 " --> pdb=" O GLN A3437 " (cutoff:3.500A) Processing helix chain 'A' and resid 3445 through 3467 Processing helix chain 'A' and resid 3483 through 3488 Processing helix chain 'A' and resid 3490 through 3507 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.915A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A3517 " --> pdb=" O LEU A3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3512 through 3517' Processing helix chain 'A' and resid 3518 through 3531 Processing helix chain 'A' and resid 3536 through 3553 removed outlier: 4.332A pdb=" N LYS A3540 " --> pdb=" O MET A3536 " (cutoff:3.500A) Processing helix chain 'A' and resid 3553 through 3562 removed outlier: 3.666A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A3562 " --> pdb=" O SER A3558 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3616 Processing helix chain 'A' and resid 3619 through 3629 Processing helix chain 'A' and resid 3630 through 3652 Processing helix chain 'A' and resid 3682 through 3694 Processing helix chain 'A' and resid 3696 through 3704 Processing helix chain 'A' and resid 3709 through 3721 Processing helix chain 'A' and resid 3752 through 3771 removed outlier: 3.534A pdb=" N ILE A3771 " --> pdb=" O PHE A3767 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3791 Processing helix chain 'A' and resid 3805 through 3815 Processing helix chain 'A' and resid 3846 through 3850 removed outlier: 3.693A pdb=" N GLY A3850 " --> pdb=" O PRO A3847 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3872 removed outlier: 3.580A pdb=" N VAL A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3992 Processing helix chain 'A' and resid 4069 through 4077 removed outlier: 4.202A pdb=" N MET A4077 " --> pdb=" O VAL A4073 " (cutoff:3.500A) Processing helix chain 'A' and resid 4078 through 4086 removed outlier: 3.691A pdb=" N LEU A4082 " --> pdb=" O GLY A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4154 through 4165 removed outlier: 4.014A pdb=" N LEU A4158 " --> pdb=" O PRO A4154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A4162 " --> pdb=" O LEU A4158 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A4163 " --> pdb=" O ALA A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 removed outlier: 3.670A pdb=" N VAL A4173 " --> pdb=" O GLY A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4177 through 4190 Processing helix chain 'A' and resid 4211 through 4224 removed outlier: 3.847A pdb=" N LEU A4217 " --> pdb=" O PRO A4213 " (cutoff:3.500A) Processing helix chain 'A' and resid 4228 through 4242 removed outlier: 3.811A pdb=" N VAL A4232 " --> pdb=" O THR A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4242 through 4256 removed outlier: 3.555A pdb=" N LEU A4246 " --> pdb=" O GLY A4242 " (cutoff:3.500A) Processing helix chain 'A' and resid 4315 through 4332 Processing helix chain 'A' and resid 4357 through 4365 removed outlier: 4.051A pdb=" N LEU A4361 " --> pdb=" O PRO A4357 " (cutoff:3.500A) Processing helix chain 'A' and resid 4368 through 4378 Processing helix chain 'A' and resid 4391 through 4405 Processing helix chain 'A' and resid 4406 through 4413 Proline residue: A4410 - end of helix removed outlier: 3.711A pdb=" N LEU A4413 " --> pdb=" O PRO A4410 " (cutoff:3.500A) Processing helix chain 'A' and resid 4432 through 4445 Processing helix chain 'A' and resid 4478 through 4496 Processing helix chain 'B' and resid 166 through 180 Processing helix chain 'B' and resid 188 through 208 removed outlier: 4.288A pdb=" N HIS B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.658A pdb=" N ILE B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 263 removed outlier: 3.739A pdb=" N VAL B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 281 through 284 removed outlier: 3.601A pdb=" N TYR B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.569A pdb=" N ARG B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 296 removed outlier: 3.516A pdb=" N TRP B 296 " --> pdb=" O PHE B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.626A pdb=" N GLN B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.520A pdb=" N THR B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 723 through 729 removed outlier: 3.826A pdb=" N GLU B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.644A pdb=" N THR B 855 " --> pdb=" O PRO B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 869 removed outlier: 3.569A pdb=" N ILE B 866 " --> pdb=" O PRO B 863 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 869 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1029 Processing helix chain 'B' and resid 1171 through 1177 removed outlier: 3.544A pdb=" N HIS B1177 " --> pdb=" O PHE B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1191 No H-bonds generated for 'chain 'B' and resid 1189 through 1191' Processing helix chain 'B' and resid 1205 through 1213 removed outlier: 3.667A pdb=" N VAL B1209 " --> pdb=" O SER B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1294 Processing helix chain 'B' and resid 1313 through 1324 removed outlier: 3.799A pdb=" N GLN B1317 " --> pdb=" O LYS B1313 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B1321 " --> pdb=" O GLN B1317 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B1322 " --> pdb=" O ARG B1318 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1337 removed outlier: 3.801A pdb=" N GLU B1329 " --> pdb=" O SER B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1363 Processing helix chain 'B' and resid 1371 through 1384 removed outlier: 3.549A pdb=" N PHE B1384 " --> pdb=" O LYS B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1394 Processing helix chain 'B' and resid 1397 through 1414 Processing helix chain 'B' and resid 1423 through 1434 removed outlier: 4.218A pdb=" N VAL B1427 " --> pdb=" O ALA B1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1442 Processing helix chain 'B' and resid 1444 through 1459 Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 3.619A pdb=" N GLN B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1487 through 1497 Processing helix chain 'B' and resid 1551 through 1557 removed outlier: 4.246A pdb=" N THR B1555 " --> pdb=" O GLY B1552 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B1557 " --> pdb=" O PHE B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1770 Processing helix chain 'B' and resid 1885 through 1890 Processing helix chain 'B' and resid 1909 through 1940 removed outlier: 3.660A pdb=" N HIS B1913 " --> pdb=" O GLU B1909 " (cutoff:3.500A) Processing helix chain 'B' and resid 1949 through 1954 Processing helix chain 'B' and resid 1965 through 1999 Processing helix chain 'B' and resid 2010 through 2017 Processing helix chain 'B' and resid 2019 through 2040 Processing helix chain 'B' and resid 2047 through 2054 removed outlier: 3.655A pdb=" N GLN B2051 " --> pdb=" O PRO B2047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B2054 " --> pdb=" O LEU B2050 " (cutoff:3.500A) Processing helix chain 'B' and resid 2055 through 2067 Processing helix chain 'B' and resid 2071 through 2087 Processing helix chain 'B' and resid 2091 through 2104 Processing helix chain 'B' and resid 2113 through 2128 Processing helix chain 'B' and resid 2129 through 2131 No H-bonds generated for 'chain 'B' and resid 2129 through 2131' Processing helix chain 'B' and resid 2132 through 2146 removed outlier: 3.919A pdb=" N GLU B2136 " --> pdb=" O SER B2132 " (cutoff:3.500A) Processing helix chain 'B' and resid 2147 through 2150 Processing helix chain 'B' and resid 2164 through 2189 Processing helix chain 'B' and resid 2201 through 2206 removed outlier: 4.539A pdb=" N ASN B2205 " --> pdb=" O TRP B2201 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 Processing helix chain 'B' and resid 2347 through 2365 removed outlier: 3.522A pdb=" N LEU B2351 " --> pdb=" O HIS B2347 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2389 Processing helix chain 'B' and resid 2394 through 2398 removed outlier: 4.126A pdb=" N ILE B2397 " --> pdb=" O ARG B2394 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B2398 " --> pdb=" O GLY B2395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2394 through 2398' Processing helix chain 'B' and resid 2400 through 2420 removed outlier: 3.905A pdb=" N ALA B2404 " --> pdb=" O GLY B2400 " (cutoff:3.500A) Processing helix chain 'B' and resid 2569 through 2574 removed outlier: 3.854A pdb=" N VAL B2573 " --> pdb=" O ARG B2570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2576 through 2600 Processing helix chain 'B' and resid 2635 through 2650 Processing helix chain 'B' and resid 2651 through 2653 No H-bonds generated for 'chain 'B' and resid 2651 through 2653' Processing helix chain 'B' and resid 2656 through 2668 Processing helix chain 'B' and resid 2697 through 2711 Processing helix chain 'B' and resid 2715 through 2732 Processing helix chain 'B' and resid 2747 through 2755 removed outlier: 3.849A pdb=" N ASP B2755 " --> pdb=" O LEU B2751 " (cutoff:3.500A) Processing helix chain 'B' and resid 2755 through 2768 removed outlier: 4.347A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B2768 " --> pdb=" O LYS B2764 " (cutoff:3.500A) Processing helix chain 'B' and resid 2782 through 2802 removed outlier: 4.347A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2820 removed outlier: 4.068A pdb=" N PHE B2808 " --> pdb=" O CYS B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2824 through 2829 Processing helix chain 'B' and resid 2832 through 2845 removed outlier: 3.972A pdb=" N GLU B2845 " --> pdb=" O GLU B2841 " (cutoff:3.500A) Processing helix chain 'B' and resid 2852 through 2873 Processing helix chain 'B' and resid 2914 through 2931 removed outlier: 3.546A pdb=" N LEU B2918 " --> pdb=" O THR B2914 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B2931 " --> pdb=" O ASN B2927 " (cutoff:3.500A) Processing helix chain 'B' and resid 2979 through 2987 removed outlier: 3.959A pdb=" N LEU B2983 " --> pdb=" O TYR B2979 " (cutoff:3.500A) Processing helix chain 'B' and resid 2987 through 3000 removed outlier: 3.502A pdb=" N MET B2991 " --> pdb=" O ASN B2987 " (cutoff:3.500A) Processing helix chain 'B' and resid 3031 through 3046 Processing helix chain 'B' and resid 3050 through 3064 Proline residue: B3056 - end of helix Processing helix chain 'B' and resid 3078 through 3089 Processing helix chain 'B' and resid 3091 through 3101 Processing helix chain 'B' and resid 3103 through 3118 Processing helix chain 'B' and resid 3124 through 3132 removed outlier: 3.587A pdb=" N THR B3128 " --> pdb=" O SER B3124 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B3132 " --> pdb=" O THR B3128 " (cutoff:3.500A) Processing helix chain 'B' and resid 3178 through 3184 removed outlier: 4.447A pdb=" N VAL B3181 " --> pdb=" O PRO B3178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B3184 " --> pdb=" O VAL B3181 " (cutoff:3.500A) Processing helix chain 'B' and resid 3231 through 3235 removed outlier: 3.745A pdb=" N THR B3234 " --> pdb=" O SER B3231 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3325 removed outlier: 4.141A pdb=" N LYS B3325 " --> pdb=" O ASP B3321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3321 through 3325' Processing helix chain 'B' and resid 3327 through 3340 Processing helix chain 'B' and resid 3344 through 3353 removed outlier: 3.616A pdb=" N MET B3348 " --> pdb=" O LEU B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3357 through 3367 Processing helix chain 'B' and resid 3368 through 3373 removed outlier: 4.072A pdb=" N MET B3373 " --> pdb=" O TYR B3370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3374 through 3387 Processing helix chain 'B' and resid 3389 through 3402 Processing helix chain 'B' and resid 3429 through 3441 removed outlier: 3.671A pdb=" N THR B3441 " --> pdb=" O GLN B3437 " (cutoff:3.500A) Processing helix chain 'B' and resid 3445 through 3467 Processing helix chain 'B' and resid 3483 through 3488 Processing helix chain 'B' and resid 3490 through 3507 Processing helix chain 'B' and resid 3512 through 3517 removed outlier: 3.915A pdb=" N LEU B3516 " --> pdb=" O ASP B3512 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B3517 " --> pdb=" O LEU B3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3512 through 3517' Processing helix chain 'B' and resid 3518 through 3531 Processing helix chain 'B' and resid 3536 through 3553 removed outlier: 4.332A pdb=" N LYS B3540 " --> pdb=" O MET B3536 " (cutoff:3.500A) Processing helix chain 'B' and resid 3553 through 3562 removed outlier: 3.666A pdb=" N PHE B3557 " --> pdb=" O HIS B3553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B3562 " --> pdb=" O SER B3558 " (cutoff:3.500A) Processing helix chain 'B' and resid 3606 through 3616 Processing helix chain 'B' and resid 3619 through 3629 Processing helix chain 'B' and resid 3630 through 3652 Processing helix chain 'B' and resid 3682 through 3694 Processing helix chain 'B' and resid 3696 through 3704 Processing helix chain 'B' and resid 3709 through 3721 Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 3.534A pdb=" N ILE B3771 " --> pdb=" O PHE B3767 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3791 Processing helix chain 'B' and resid 3805 through 3815 Processing helix chain 'B' and resid 3846 through 3850 removed outlier: 3.692A pdb=" N GLY B3850 " --> pdb=" O PRO B3847 " (cutoff:3.500A) Processing helix chain 'B' and resid 3865 through 3872 removed outlier: 3.581A pdb=" N VAL B3869 " --> pdb=" O THR B3865 " (cutoff:3.500A) Processing helix chain 'B' and resid 3982 through 3992 Processing helix chain 'B' and resid 4069 through 4077 removed outlier: 4.202A pdb=" N MET B4077 " --> pdb=" O VAL B4073 " (cutoff:3.500A) Processing helix chain 'B' and resid 4078 through 4086 removed outlier: 3.691A pdb=" N LEU B4082 " --> pdb=" O GLY B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4154 through 4165 removed outlier: 4.014A pdb=" N LEU B4158 " --> pdb=" O PRO B4154 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B4162 " --> pdb=" O LEU B4158 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B4163 " --> pdb=" O ALA B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 removed outlier: 3.669A pdb=" N VAL B4173 " --> pdb=" O GLY B4169 " (cutoff:3.500A) Processing helix chain 'B' and resid 4177 through 4190 Processing helix chain 'B' and resid 4211 through 4224 removed outlier: 3.847A pdb=" N LEU B4217 " --> pdb=" O PRO B4213 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4242 removed outlier: 3.811A pdb=" N VAL B4232 " --> pdb=" O THR B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4242 through 4256 removed outlier: 3.555A pdb=" N LEU B4246 " --> pdb=" O GLY B4242 " (cutoff:3.500A) Processing helix chain 'B' and resid 4315 through 4332 Processing helix chain 'B' and resid 4357 through 4365 removed outlier: 4.050A pdb=" N LEU B4361 " --> pdb=" O PRO B4357 " (cutoff:3.500A) Processing helix chain 'B' and resid 4368 through 4378 Processing helix chain 'B' and resid 4391 through 4405 Processing helix chain 'B' and resid 4406 through 4413 Proline residue: B4410 - end of helix removed outlier: 3.711A pdb=" N LEU B4413 " --> pdb=" O PRO B4410 " (cutoff:3.500A) Processing helix chain 'B' and resid 4432 through 4445 Processing helix chain 'B' and resid 4478 through 4496 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 64 removed outlier: 5.611A pdb=" N ARG A 59 " --> pdb=" O GLN A 965 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN A 965 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY A 61 " --> pdb=" O PHE A 963 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 963 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 942 " --> pdb=" O CYS A 955 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 72 current: chain 'A' and resid 81 through 86 removed outlier: 5.553A pdb=" N ASP A 95 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N THR A 101 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 165 removed outlier: 3.546A pdb=" N LEU A 223 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 392 removed outlier: 7.416A pdb=" N ALA A 403 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE A 391 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA A 401 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 503 through 513 removed outlier: 7.385A pdb=" N VAL A 503 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS A 576 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 505 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR A 574 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 507 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 572 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 509 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG A 721 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 630 " --> pdb=" O CYS A 719 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N CYS A 719 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 632 " --> pdb=" O VAL A 717 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 731 through 738 removed outlier: 5.444A pdb=" N ILE A 733 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 750 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 824 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 862 removed outlier: 3.854A pdb=" N SER A 858 " --> pdb=" O THR A 906 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS A 902 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 916 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 922 " --> pdb=" O ASP A 916 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1031 through 1033 current: chain 'A' and resid 1075 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1075 through 1079 current: chain 'A' and resid 1198 through 1203 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 4.017A pdb=" N VAL A1186 " --> pdb=" O VAL A1122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1564 through 1565 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1564 through 1565 current: chain 'A' and resid 1788 through 1806 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1788 through 1806 current: chain 'A' and resid 1829 through 1834 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1577 through 1581 Processing sheet with id=AB6, first strand: chain 'A' and resid 2877 through 2880 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2877 through 2880 current: chain 'A' and resid 3251 through 3252 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 3855 through 3861 Processing sheet with id=AB8, first strand: chain 'B' and resid 57 through 64 removed outlier: 5.610A pdb=" N ARG B 59 " --> pdb=" O GLN B 965 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN B 965 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY B 61 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 963 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 942 " --> pdb=" O CYS B 955 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 70 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 72 current: chain 'B' and resid 81 through 86 removed outlier: 5.553A pdb=" N ASP B 95 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N THR B 101 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AC2, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 165 removed outlier: 3.547A pdb=" N LEU B 223 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 314 through 316 Processing sheet with id=AC5, first strand: chain 'B' and resid 388 through 392 removed outlier: 7.415A pdb=" N ALA B 403 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 391 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA B 401 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 503 through 513 removed outlier: 7.385A pdb=" N VAL B 503 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS B 576 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU B 505 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 574 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 507 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 572 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 509 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG B 721 " --> pdb=" O PRO B 628 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 630 " --> pdb=" O CYS B 719 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS B 719 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 632 " --> pdb=" O VAL B 717 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 731 through 738 removed outlier: 5.443A pdb=" N ILE B 733 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 750 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 824 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 858 through 862 removed outlier: 3.854A pdb=" N SER B 858 " --> pdb=" O THR B 906 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS B 902 " --> pdb=" O LEU B 862 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 916 " --> pdb=" O ILE B 922 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 922 " --> pdb=" O ASP B 916 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1031 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1031 through 1033 current: chain 'B' and resid 1075 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1075 through 1079 current: chain 'B' and resid 1198 through 1203 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 1039 through 1041 removed outlier: 4.016A pdb=" N VAL B1186 " --> pdb=" O VAL B1122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1564 through 1565 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1564 through 1565 current: chain 'B' and resid 1788 through 1806 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1788 through 1806 current: chain 'B' and resid 1829 through 1834 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1577 through 1581 Processing sheet with id=AD4, first strand: chain 'B' and resid 2877 through 2880 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2877 through 2880 current: chain 'B' and resid 3251 through 3252 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 3855 through 3861 2216 hydrogen bonds defined for protein. 6468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.05 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14148 1.34 - 1.46: 9493 1.46 - 1.58: 20617 1.58 - 1.70: 4 1.70 - 1.82: 438 Bond restraints: 44700 Sorted by residual: bond pdb=" CB PRO B1807 " pdb=" CG PRO B1807 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" CB PRO B1426 " pdb=" CG PRO B1426 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" CB PRO A1807 " pdb=" CG PRO A1807 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" CB PRO A1426 " pdb=" CG PRO A1426 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.95e+00 bond pdb=" C VAL A4409 " pdb=" N PRO A4410 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.02e+00 ... (remaining 44695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 60290 3.57 - 7.14: 341 7.14 - 10.71: 73 10.71 - 14.28: 16 14.28 - 17.85: 4 Bond angle restraints: 60724 Sorted by residual: angle pdb=" CA PRO A1807 " pdb=" N PRO A1807 " pdb=" CD PRO A1807 " ideal model delta sigma weight residual 112.00 94.15 17.85 1.40e+00 5.10e-01 1.63e+02 angle pdb=" CA PRO B1807 " pdb=" N PRO B1807 " pdb=" CD PRO B1807 " ideal model delta sigma weight residual 112.00 94.16 17.84 1.40e+00 5.10e-01 1.62e+02 angle pdb=" CA PRO B1426 " pdb=" N PRO B1426 " pdb=" CD PRO B1426 " ideal model delta sigma weight residual 112.00 98.52 13.48 1.40e+00 5.10e-01 9.27e+01 angle pdb=" CA PRO A1426 " pdb=" N PRO A1426 " pdb=" CD PRO A1426 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.22e+01 angle pdb=" N VAL B2850 " pdb=" CA VAL B2850 " pdb=" C VAL B2850 " ideal model delta sigma weight residual 113.20 108.11 5.09 9.60e-01 1.09e+00 2.81e+01 ... (remaining 60719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 23421 17.98 - 35.96: 2811 35.96 - 53.94: 656 53.94 - 71.93: 128 71.93 - 89.91: 38 Dihedral angle restraints: 27054 sinusoidal: 10586 harmonic: 16468 Sorted by residual: dihedral pdb=" CA SER B2941 " pdb=" C SER B2941 " pdb=" N ALA B2942 " pdb=" CA ALA B2942 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER A2941 " pdb=" C SER A2941 " pdb=" N ALA A2942 " pdb=" CA ALA A2942 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER A2398 " pdb=" C SER A2398 " pdb=" N TRP A2399 " pdb=" CA TRP A2399 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 27051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6001 0.053 - 0.106: 1097 0.106 - 0.158: 246 0.158 - 0.211: 14 0.211 - 0.264: 6 Chirality restraints: 7364 Sorted by residual: chirality pdb=" CG LEU A1939 " pdb=" CB LEU A1939 " pdb=" CD1 LEU A1939 " pdb=" CD2 LEU A1939 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU B1939 " pdb=" CB LEU B1939 " pdb=" CD1 LEU B1939 " pdb=" CD2 LEU B1939 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL B3693 " pdb=" CA VAL B3693 " pdb=" CG1 VAL B3693 " pdb=" CG2 VAL B3693 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 7361 not shown) Planarity restraints: 7594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1806 " -0.124 5.00e-02 4.00e+02 1.70e-01 4.65e+01 pdb=" N PRO A1807 " 0.294 5.00e-02 4.00e+02 pdb=" CA PRO A1807 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO A1807 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B1806 " 0.124 5.00e-02 4.00e+02 1.70e-01 4.64e+01 pdb=" N PRO B1807 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO B1807 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B1807 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B1425 " 0.100 5.00e-02 4.00e+02 1.42e-01 3.20e+01 pdb=" N PRO B1426 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO B1426 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B1426 " 0.072 5.00e-02 4.00e+02 ... (remaining 7591 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 10007 2.79 - 3.32: 40139 3.32 - 3.85: 74741 3.85 - 4.37: 82286 4.37 - 4.90: 143484 Nonbonded interactions: 350657 Sorted by model distance: nonbonded pdb=" O SER B3616 " pdb=" OG SER B3616 " model vdw 2.263 3.040 nonbonded pdb=" O SER A3616 " pdb=" OG SER A3616 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP B3443 " pdb=" OG1 THR B3446 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP A3443 " pdb=" OG1 THR A3446 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 945 " pdb=" OD1 ASP A 950 " model vdw 2.283 3.040 ... (remaining 350652 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.080 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 73.610 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 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 : 0.003 0.158 44708 Z= 0.152 Angle : 0.764 17.851 60730 Z= 0.375 Chirality : 0.044 0.264 7364 Planarity : 0.007 0.170 7594 Dihedral : 16.626 89.907 16278 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.36 % Allowed : 22.19 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -1.00 (0.10), residues: 5490 helix: -0.44 (0.09), residues: 2756 sheet: 0.19 (0.19), residues: 776 loop : -1.15 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2717 TYR 0.040 0.001 TYR B2711 PHE 0.051 0.001 PHE A3689 TRP 0.014 0.001 TRP B2710 HIS 0.007 0.001 HIS A1845 Details of bonding type rmsd covalent geometry : bond 0.00346 (44700) covalent geometry : angle 0.76398 (60724) hydrogen bonds : bond 0.12567 ( 2216) hydrogen bonds : angle 5.62977 ( 6468) metal coordination : bond 0.00571 ( 8) metal coordination : angle 1.74168 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 348 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2030 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7735 (pp) REVERT: A 3101 MET cc_start: 0.7087 (ptp) cc_final: 0.6840 (ptt) REVERT: B 309 MET cc_start: 0.3239 (tmm) cc_final: 0.2822 (ttp) REVERT: B 3101 MET cc_start: 0.7051 (ptp) cc_final: 0.6803 (ptt) outliers start: 18 outliers final: 7 residues processed: 360 average time/residue: 0.2478 time to fit residues: 155.2907 Evaluate side-chains 331 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain A residue 3333 LEU Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 2582 MET Chi-restraints excluded: chain B residue 3333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 394 optimal weight: 0.1980 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN ** A2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS A4245 HIS A4332 ASN B1376 ASN ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS B4245 HIS B4332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.224636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162826 restraints weight = 78476.648| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 4.44 r_work: 0.3736 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44708 Z= 0.127 Angle : 0.561 9.296 60730 Z= 0.270 Chirality : 0.039 0.270 7364 Planarity : 0.005 0.088 7594 Dihedral : 3.933 55.380 5932 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.70 % Allowed : 20.12 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.30 (0.11), residues: 5490 helix: 0.88 (0.10), residues: 2790 sheet: 0.36 (0.19), residues: 776 loop : -0.77 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1934 TYR 0.008 0.001 TYR A3484 PHE 0.013 0.001 PHE B1091 TRP 0.009 0.001 TRP B3712 HIS 0.005 0.001 HIS B2777 Details of bonding type rmsd covalent geometry : bond 0.00303 (44700) covalent geometry : angle 0.55929 (60724) hydrogen bonds : bond 0.03330 ( 2216) hydrogen bonds : angle 4.24786 ( 6468) metal coordination : bond 0.01051 ( 8) metal coordination : angle 3.89337 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 355 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.2206 (tmm) cc_final: 0.1948 (ttp) REVERT: A 1942 ILE cc_start: 0.3846 (OUTLIER) cc_final: 0.3454 (mt) REVERT: A 1998 LEU cc_start: 0.8027 (tp) cc_final: 0.7745 (tt) REVERT: A 2030 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7701 (pt) REVERT: A 2582 MET cc_start: 0.6526 (ttp) cc_final: 0.6246 (ttp) REVERT: A 2777 HIS cc_start: 0.1696 (OUTLIER) cc_final: 0.0823 (p-80) REVERT: A 2935 SER cc_start: 0.5509 (OUTLIER) cc_final: 0.5261 (t) REVERT: A 3043 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 3488 MET cc_start: 0.7669 (ptt) cc_final: 0.7355 (ptp) REVERT: A 3557 PHE cc_start: 0.6697 (t80) cc_final: 0.6399 (t80) REVERT: A 3676 MET cc_start: 0.5949 (tmm) cc_final: 0.5648 (ppp) REVERT: A 3699 MET cc_start: 0.6600 (mmp) cc_final: 0.6275 (mmm) REVERT: A 3760 GLU cc_start: 0.7315 (tt0) cc_final: 0.6705 (tt0) REVERT: A 3810 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.4458 (mtm180) REVERT: A 3848 MET cc_start: 0.7639 (mtp) cc_final: 0.7257 (mtp) REVERT: B 309 MET cc_start: 0.2206 (tmm) cc_final: 0.1956 (ttp) REVERT: B 1942 ILE cc_start: 0.3859 (OUTLIER) cc_final: 0.3465 (mt) REVERT: B 1998 LEU cc_start: 0.8028 (tp) cc_final: 0.7757 (tt) REVERT: B 2777 HIS cc_start: 0.1794 (OUTLIER) cc_final: 0.0884 (p-80) REVERT: B 2935 SER cc_start: 0.5510 (OUTLIER) cc_final: 0.5261 (t) REVERT: B 3043 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 3488 MET cc_start: 0.7666 (ptt) cc_final: 0.7296 (ptp) REVERT: B 3557 PHE cc_start: 0.6585 (t80) cc_final: 0.6297 (t80) REVERT: B 3676 MET cc_start: 0.5939 (tmm) cc_final: 0.5645 (ppp) REVERT: B 3699 MET cc_start: 0.6563 (mmp) cc_final: 0.6240 (mmm) REVERT: B 3760 GLU cc_start: 0.7307 (tt0) cc_final: 0.6679 (tt0) REVERT: B 3810 ARG cc_start: 0.6019 (OUTLIER) cc_final: 0.4506 (mtm180) REVERT: B 3990 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6866 (mm) outliers start: 135 outliers final: 72 residues processed: 467 average time/residue: 0.2361 time to fit residues: 193.6776 Evaluate side-chains 412 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 328 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2935 SER Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3043 LEU Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4173 VAL Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2573 VAL Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2935 SER Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3043 LEU Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 3990 LEU Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4173 VAL Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 277 optimal weight: 9.9990 chunk 448 optimal weight: 0.9980 chunk 345 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 558 optimal weight: 8.9990 chunk 442 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 451 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 378 GLN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2797 GLN A2931 GLN ** A3076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3226 GLN ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS A4156 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 378 GLN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2797 GLN B2931 GLN ** B3076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3226 GLN ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS B4156 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.218738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153991 restraints weight = 76500.875| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.32 r_work: 0.3624 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 44708 Z= 0.272 Angle : 0.710 13.629 60730 Z= 0.344 Chirality : 0.045 0.320 7364 Planarity : 0.005 0.067 7594 Dihedral : 4.418 54.859 5922 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.81 % Allowed : 19.36 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.11), residues: 5490 helix: 0.88 (0.10), residues: 2796 sheet: 0.26 (0.19), residues: 740 loop : -0.80 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1934 TYR 0.016 0.002 TYR B2979 PHE 0.021 0.002 PHE B2353 TRP 0.015 0.002 TRP A2719 HIS 0.013 0.002 HIS A2777 Details of bonding type rmsd covalent geometry : bond 0.00672 (44700) covalent geometry : angle 0.70893 (60724) hydrogen bonds : bond 0.04005 ( 2216) hydrogen bonds : angle 4.55718 ( 6468) metal coordination : bond 0.00807 ( 8) metal coordination : angle 3.26619 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 366 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0203 (OUTLIER) cc_final: -0.0363 (m-70) REVERT: A 309 MET cc_start: 0.2111 (tmm) cc_final: 0.1895 (ttp) REVERT: A 1429 LEU cc_start: 0.7118 (tt) cc_final: 0.6897 (tp) REVERT: A 1538 LEU cc_start: 0.5358 (OUTLIER) cc_final: 0.4907 (tt) REVERT: A 1942 ILE cc_start: 0.4728 (OUTLIER) cc_final: 0.4384 (mt) REVERT: A 2327 ARG cc_start: 0.5836 (ppt170) cc_final: 0.4898 (mmm160) REVERT: A 2352 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8995 (mp) REVERT: A 2576 GLU cc_start: 0.7182 (pm20) cc_final: 0.6750 (mm-30) REVERT: A 2711 TYR cc_start: 0.6813 (t80) cc_final: 0.6560 (t80) REVERT: A 2777 HIS cc_start: 0.2301 (OUTLIER) cc_final: 0.1924 (p-80) REVERT: A 2876 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8285 (mtpt) REVERT: A 2880 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.4617 (mmt-90) REVERT: A 3052 MET cc_start: 0.8479 (ptp) cc_final: 0.8175 (ptp) REVERT: A 3396 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7645 (pp) REVERT: A 3510 GLU cc_start: 0.7804 (pp20) cc_final: 0.7459 (pp20) REVERT: A 3535 ASN cc_start: 0.5725 (OUTLIER) cc_final: 0.5437 (m110) REVERT: A 3699 MET cc_start: 0.6427 (mmp) cc_final: 0.6121 (mmm) REVERT: A 3760 GLU cc_start: 0.7429 (tt0) cc_final: 0.6860 (tt0) REVERT: A 3810 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4260 (mtm180) REVERT: A 3848 MET cc_start: 0.7758 (mtp) cc_final: 0.7359 (mtp) REVERT: A 3865 THR cc_start: 0.7137 (p) cc_final: 0.6925 (t) REVERT: B 222 HIS cc_start: 0.0202 (OUTLIER) cc_final: -0.0359 (m-70) REVERT: B 309 MET cc_start: 0.2135 (tmm) cc_final: 0.1933 (ttp) REVERT: B 378 GLN cc_start: 0.2009 (OUTLIER) cc_final: 0.1808 (tp-100) REVERT: B 1429 LEU cc_start: 0.7136 (tt) cc_final: 0.6906 (tp) REVERT: B 1538 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.4909 (tt) REVERT: B 1814 SER cc_start: 0.7058 (OUTLIER) cc_final: 0.6795 (m) REVERT: B 1942 ILE cc_start: 0.4506 (OUTLIER) cc_final: 0.4125 (mt) REVERT: B 2327 ARG cc_start: 0.5923 (ppt170) cc_final: 0.4982 (mmm160) REVERT: B 2352 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9003 (mp) REVERT: B 2576 GLU cc_start: 0.7237 (pm20) cc_final: 0.6817 (mm-30) REVERT: B 2777 HIS cc_start: 0.2292 (OUTLIER) cc_final: 0.1917 (p-80) REVERT: B 2876 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8286 (mtpt) REVERT: B 2880 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.4621 (mmt-90) REVERT: B 3052 MET cc_start: 0.8493 (ptp) cc_final: 0.8153 (ptp) REVERT: B 3396 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7680 (pp) REVERT: B 3510 GLU cc_start: 0.7863 (pp20) cc_final: 0.7543 (pp20) REVERT: B 3535 ASN cc_start: 0.5722 (OUTLIER) cc_final: 0.5437 (m110) REVERT: B 3699 MET cc_start: 0.6443 (mmp) cc_final: 0.6136 (mmm) REVERT: B 3760 GLU cc_start: 0.7426 (tt0) cc_final: 0.6794 (tt0) REVERT: B 3810 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.4240 (mtm180) REVERT: B 3845 GLN cc_start: 0.8191 (mt0) cc_final: 0.7934 (mt0) REVERT: B 3865 THR cc_start: 0.7131 (p) cc_final: 0.6926 (t) outliers start: 240 outliers final: 129 residues processed: 576 average time/residue: 0.2380 time to fit residues: 238.7378 Evaluate side-chains 486 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 335 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1873 ILE Chi-restraints excluded: chain A residue 1881 HIS Chi-restraints excluded: chain A residue 1888 GLU Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 1986 LEU Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2322 THR Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2352 LEU Chi-restraints excluded: chain A residue 2375 VAL Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2926 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3229 LEU Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3545 LEU Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3616 SER Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3786 CYS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4173 VAL Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1444 THR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1814 SER Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1873 ILE Chi-restraints excluded: chain B residue 1881 HIS Chi-restraints excluded: chain B residue 1888 GLU Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2322 THR Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2352 LEU Chi-restraints excluded: chain B residue 2375 VAL Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2728 LEU Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2852 SER Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2926 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3545 LEU Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3610 LEU Chi-restraints excluded: chain B residue 3616 SER Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4173 VAL Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 415 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 chunk 525 optimal weight: 6.9990 chunk 426 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 289 optimal weight: 8.9990 chunk 29 optimal weight: 0.0970 chunk 356 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 472 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 HIS A1881 HIS A2077 HIS ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 HIS B1881 HIS ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2077 HIS ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.222012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.159330 restraints weight = 76618.383| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 4.07 r_work: 0.3681 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44708 Z= 0.110 Angle : 0.552 10.568 60730 Z= 0.263 Chirality : 0.039 0.188 7364 Planarity : 0.004 0.058 7594 Dihedral : 3.910 24.570 5920 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.42 % Allowed : 20.91 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.73 (0.11), residues: 5490 helix: 1.37 (0.10), residues: 2792 sheet: 0.29 (0.19), residues: 762 loop : -0.67 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1934 TYR 0.020 0.001 TYR B2711 PHE 0.017 0.001 PHE B2353 TRP 0.011 0.001 TRP B1358 HIS 0.004 0.001 HIS A3335 Details of bonding type rmsd covalent geometry : bond 0.00256 (44700) covalent geometry : angle 0.55145 (60724) hydrogen bonds : bond 0.03134 ( 2216) hydrogen bonds : angle 4.21556 ( 6468) metal coordination : bond 0.00550 ( 8) metal coordination : angle 2.69541 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 369 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1538 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.4987 (tt) REVERT: A 1814 SER cc_start: 0.7111 (OUTLIER) cc_final: 0.6854 (m) REVERT: A 2777 HIS cc_start: 0.2134 (OUTLIER) cc_final: 0.1361 (p-80) REVERT: A 2876 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8325 (mtpt) REVERT: A 2880 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.4284 (mmt-90) REVERT: A 3052 MET cc_start: 0.8538 (ptp) cc_final: 0.8209 (ptp) REVERT: A 3101 MET cc_start: 0.8447 (ptp) cc_final: 0.8237 (ptp) REVERT: A 3396 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7693 (pp) REVERT: A 3535 ASN cc_start: 0.5755 (OUTLIER) cc_final: 0.5469 (m110) REVERT: A 3760 GLU cc_start: 0.7443 (tt0) cc_final: 0.6830 (tt0) REVERT: A 3810 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.4314 (mtt180) REVERT: A 3848 MET cc_start: 0.7678 (mtp) cc_final: 0.7412 (mtp) REVERT: B 309 MET cc_start: 0.2123 (tmm) cc_final: 0.1915 (ttp) REVERT: B 1538 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.4984 (tt) REVERT: B 2777 HIS cc_start: 0.2121 (OUTLIER) cc_final: 0.1351 (p-80) REVERT: B 2876 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8321 (mtpt) REVERT: B 2880 ARG cc_start: 0.5982 (OUTLIER) cc_final: 0.4301 (mmt-90) REVERT: B 3052 MET cc_start: 0.8546 (ptp) cc_final: 0.8216 (ptp) REVERT: B 3101 MET cc_start: 0.8445 (ptp) cc_final: 0.8235 (ptp) REVERT: B 3396 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7699 (pp) REVERT: B 3535 ASN cc_start: 0.5751 (OUTLIER) cc_final: 0.5467 (m110) REVERT: B 3550 CYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7155 (p) REVERT: B 3699 MET cc_start: 0.6301 (mmp) cc_final: 0.6098 (mmm) REVERT: B 3760 GLU cc_start: 0.7392 (tt0) cc_final: 0.6677 (tt0) REVERT: B 3764 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.6328 (p) REVERT: B 3810 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.4240 (mtm180) outliers start: 171 outliers final: 92 residues processed: 505 average time/residue: 0.2134 time to fit residues: 188.2031 Evaluate side-chains 440 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 331 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1814 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2935 SER Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3119 VAL Chi-restraints excluded: chain A residue 3229 LEU Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3678 ILE Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2204 ILE Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2935 SER Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3119 VAL Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3443 ASP Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3678 ILE Chi-restraints excluded: chain B residue 3764 VAL Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 368 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 316 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 376 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 313 optimal weight: 0.0670 chunk 475 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3076 GLN ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3076 GLN ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 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 = 0.4681 r_free = 0.4681 target = 0.221849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.160598 restraints weight = 76734.324| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 4.70 r_work: 0.3667 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44708 Z= 0.120 Angle : 0.555 12.645 60730 Z= 0.263 Chirality : 0.040 0.289 7364 Planarity : 0.004 0.053 7594 Dihedral : 3.778 23.629 5918 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.36 % Allowed : 21.43 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.96 (0.11), residues: 5490 helix: 1.58 (0.10), residues: 2792 sheet: 0.36 (0.19), residues: 744 loop : -0.57 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1934 TYR 0.010 0.001 TYR B2870 PHE 0.017 0.001 PHE A2353 TRP 0.011 0.001 TRP A3712 HIS 0.005 0.001 HIS B2777 Details of bonding type rmsd covalent geometry : bond 0.00291 (44700) covalent geometry : angle 0.55451 (60724) hydrogen bonds : bond 0.03075 ( 2216) hydrogen bonds : angle 4.13657 ( 6468) metal coordination : bond 0.00505 ( 8) metal coordination : angle 2.52538 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 358 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0140 (OUTLIER) cc_final: -0.0343 (m-70) REVERT: A 1538 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.4876 (tt) REVERT: A 1863 ARG cc_start: 0.3298 (mtm180) cc_final: 0.3057 (mtm180) REVERT: A 1883 TYR cc_start: 0.6205 (t80) cc_final: 0.5766 (t80) REVERT: A 1942 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4943 (mt) REVERT: A 2327 ARG cc_start: 0.5768 (ppt170) cc_final: 0.5005 (mmm160) REVERT: A 2777 HIS cc_start: 0.1866 (OUTLIER) cc_final: 0.1045 (p-80) REVERT: A 2876 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8402 (mtpt) REVERT: A 2880 ARG cc_start: 0.6040 (OUTLIER) cc_final: 0.4363 (mmt-90) REVERT: A 3052 MET cc_start: 0.8556 (ptp) cc_final: 0.8228 (ptp) REVERT: A 3396 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7686 (pp) REVERT: A 3436 TYR cc_start: 0.7939 (t80) cc_final: 0.7659 (t80) REVERT: A 3487 LEU cc_start: 0.6811 (mt) cc_final: 0.6568 (tp) REVERT: A 3535 ASN cc_start: 0.5763 (OUTLIER) cc_final: 0.5474 (m110) REVERT: A 3760 GLU cc_start: 0.7259 (tt0) cc_final: 0.6761 (tt0) REVERT: A 3810 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.4354 (mtm180) REVERT: A 3817 LEU cc_start: 0.4594 (mp) cc_final: 0.3826 (tt) REVERT: A 3848 MET cc_start: 0.7688 (mtp) cc_final: 0.7487 (mtp) REVERT: B 222 HIS cc_start: 0.0142 (OUTLIER) cc_final: -0.0338 (m-70) REVERT: B 309 MET cc_start: 0.2181 (tmm) cc_final: 0.1976 (ttp) REVERT: B 1538 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.4878 (tt) REVERT: B 1863 ARG cc_start: 0.3261 (OUTLIER) cc_final: 0.3004 (mtm180) REVERT: B 1883 TYR cc_start: 0.6212 (t80) cc_final: 0.5775 (t80) REVERT: B 1942 ILE cc_start: 0.5296 (OUTLIER) cc_final: 0.5027 (mt) REVERT: B 2327 ARG cc_start: 0.5766 (ppt170) cc_final: 0.5014 (mmm160) REVERT: B 2777 HIS cc_start: 0.1845 (OUTLIER) cc_final: 0.0907 (p-80) REVERT: B 2876 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8398 (mtpt) REVERT: B 2880 ARG cc_start: 0.6042 (OUTLIER) cc_final: 0.4360 (mmt-90) REVERT: B 3052 MET cc_start: 0.8554 (ptp) cc_final: 0.8225 (ptp) REVERT: B 3381 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8734 (p) REVERT: B 3396 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7669 (pp) REVERT: B 3436 TYR cc_start: 0.7936 (t80) cc_final: 0.7660 (t80) REVERT: B 3487 LEU cc_start: 0.6815 (mt) cc_final: 0.6571 (tp) REVERT: B 3535 ASN cc_start: 0.5758 (OUTLIER) cc_final: 0.5479 (m110) REVERT: B 3760 GLU cc_start: 0.7039 (tt0) cc_final: 0.6455 (tt0) REVERT: B 3810 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.4300 (mtm180) REVERT: B 3817 LEU cc_start: 0.4636 (mp) cc_final: 0.3858 (tt) outliers start: 168 outliers final: 115 residues processed: 502 average time/residue: 0.2229 time to fit residues: 194.7541 Evaluate side-chains 462 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 327 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1888 GLU Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2935 SER Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3119 VAL Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3678 ILE Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1863 ARG Chi-restraints excluded: chain B residue 1888 GLU Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 1986 LEU Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2031 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2204 ILE Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2935 SER Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3119 VAL Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3268 GLN Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3381 VAL Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3443 ASP Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3678 ILE Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 53 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 446 optimal weight: 9.9990 chunk 398 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 417 optimal weight: 0.6980 chunk 500 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 378 GLN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1365 ASN A3226 GLN ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 378 GLN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3226 GLN ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.217190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155252 restraints weight = 76094.378| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.12 r_work: 0.3626 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 44708 Z= 0.267 Angle : 0.717 13.976 60730 Z= 0.344 Chirality : 0.045 0.231 7364 Planarity : 0.005 0.059 7594 Dihedral : 4.341 27.964 5918 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.61 % Allowed : 20.95 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.49 (0.11), residues: 5490 helix: 1.15 (0.10), residues: 2810 sheet: 0.21 (0.20), residues: 714 loop : -0.77 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1934 TYR 0.022 0.002 TYR B1883 PHE 0.027 0.002 PHE A2353 TRP 0.015 0.002 TRP A2719 HIS 0.015 0.002 HIS A1881 Details of bonding type rmsd covalent geometry : bond 0.00660 (44700) covalent geometry : angle 0.71654 (60724) hydrogen bonds : bond 0.03891 ( 2216) hydrogen bonds : angle 4.55845 ( 6468) metal coordination : bond 0.01093 ( 8) metal coordination : angle 3.48756 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 365 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0235 (OUTLIER) cc_final: -0.0307 (m-70) REVERT: A 1436 MET cc_start: 0.8329 (tpp) cc_final: 0.8022 (mtp) REVERT: A 1538 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4625 (tt) REVERT: A 1564 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: A 1942 ILE cc_start: 0.5543 (OUTLIER) cc_final: 0.5266 (mt) REVERT: A 1966 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6432 (tm-30) REVERT: A 1975 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7504 (tp-100) REVERT: A 2327 ARG cc_start: 0.6024 (ppt170) cc_final: 0.5075 (mmm160) REVERT: A 2352 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9083 (mp) REVERT: A 2394 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6694 (ptt90) REVERT: A 2414 ASP cc_start: 0.8093 (m-30) cc_final: 0.7783 (m-30) REVERT: A 2576 GLU cc_start: 0.7279 (pm20) cc_final: 0.6801 (mm-30) REVERT: A 2777 HIS cc_start: 0.2683 (OUTLIER) cc_final: 0.2218 (p-80) REVERT: A 2876 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8425 (mtpt) REVERT: A 2880 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.4827 (mmt-90) REVERT: A 3052 MET cc_start: 0.8744 (ptp) cc_final: 0.8519 (ptp) REVERT: A 3116 ARG cc_start: 0.7237 (ttm170) cc_final: 0.6005 (tpt90) REVERT: A 3184 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: A 3226 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8581 (tp40) REVERT: A 3389 SER cc_start: 0.7748 (t) cc_final: 0.7372 (p) REVERT: A 3436 TYR cc_start: 0.8129 (t80) cc_final: 0.7869 (t80) REVERT: A 3487 LEU cc_start: 0.7348 (mt) cc_final: 0.6993 (tp) REVERT: A 3510 GLU cc_start: 0.7807 (pp20) cc_final: 0.7445 (pp20) REVERT: A 3535 ASN cc_start: 0.5794 (OUTLIER) cc_final: 0.5469 (m110) REVERT: A 3760 GLU cc_start: 0.7510 (tt0) cc_final: 0.6852 (tt0) REVERT: A 3810 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.4499 (mtm180) REVERT: A 3817 LEU cc_start: 0.4914 (mp) cc_final: 0.4072 (tt) REVERT: A 3845 GLN cc_start: 0.8305 (mt0) cc_final: 0.8064 (mt0) REVERT: A 3848 MET cc_start: 0.7868 (mtp) cc_final: 0.7649 (mtp) REVERT: A 4247 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1348 (mt) REVERT: B 222 HIS cc_start: 0.0245 (OUTLIER) cc_final: -0.0272 (m-70) REVERT: B 378 GLN cc_start: 0.2163 (OUTLIER) cc_final: 0.1947 (tp-100) REVERT: B 1436 MET cc_start: 0.8429 (tpp) cc_final: 0.8194 (mtp) REVERT: B 1538 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.4641 (tt) REVERT: B 1564 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: B 1942 ILE cc_start: 0.5558 (OUTLIER) cc_final: 0.5274 (mt) REVERT: B 1966 GLU cc_start: 0.6542 (tm-30) cc_final: 0.6320 (tm-30) REVERT: B 2327 ARG cc_start: 0.6218 (ppt170) cc_final: 0.5110 (mmm160) REVERT: B 2352 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9081 (mp) REVERT: B 2394 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6185 (ptt90) REVERT: B 2414 ASP cc_start: 0.8085 (m-30) cc_final: 0.7772 (m-30) REVERT: B 2576 GLU cc_start: 0.7242 (pm20) cc_final: 0.6691 (mm-30) REVERT: B 2777 HIS cc_start: 0.2645 (OUTLIER) cc_final: 0.2184 (p-80) REVERT: B 2876 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8424 (mtpt) REVERT: B 2880 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.4819 (mmt-90) REVERT: B 3052 MET cc_start: 0.8746 (ptp) cc_final: 0.8522 (ptp) REVERT: B 3116 ARG cc_start: 0.7225 (ttm170) cc_final: 0.5999 (tpt90) REVERT: B 3184 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: B 3226 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8585 (tp40) REVERT: B 3389 SER cc_start: 0.7747 (t) cc_final: 0.7365 (p) REVERT: B 3436 TYR cc_start: 0.8146 (t80) cc_final: 0.7888 (t80) REVERT: B 3487 LEU cc_start: 0.7355 (mt) cc_final: 0.7004 (tp) REVERT: B 3510 GLU cc_start: 0.7803 (pp20) cc_final: 0.7441 (pp20) REVERT: B 3535 ASN cc_start: 0.5885 (OUTLIER) cc_final: 0.5565 (m110) REVERT: B 3760 GLU cc_start: 0.7434 (tt0) cc_final: 0.6694 (tt0) REVERT: B 3810 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.4357 (mtm180) REVERT: B 3817 LEU cc_start: 0.4866 (mp) cc_final: 0.4034 (tt) REVERT: B 3845 GLN cc_start: 0.8309 (mt0) cc_final: 0.8067 (mt0) REVERT: B 4247 ILE cc_start: 0.1606 (OUTLIER) cc_final: 0.1118 (mt) outliers start: 230 outliers final: 158 residues processed: 570 average time/residue: 0.2014 time to fit residues: 199.5362 Evaluate side-chains 528 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 340 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1570 CYS Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 1975 GLN Chi-restraints excluded: chain A residue 1986 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2083 VAL Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2322 THR Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2352 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2394 ARG Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3119 VAL Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3184 GLN Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3226 GLN Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3240 SER Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3255 THR Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3545 LEU Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3678 ILE Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3786 CYS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4173 VAL Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1564 GLU Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 1986 LEU Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2083 VAL Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2322 THR Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2352 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2394 ARG Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2714 THR Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3119 VAL Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3184 GLN Chi-restraints excluded: chain B residue 3210 LEU Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3226 GLN Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3240 SER Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3255 THR Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3545 LEU Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3610 LEU Chi-restraints excluded: chain B residue 3678 ILE Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 4064 THR Chi-restraints excluded: chain B residue 4173 VAL Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4319 HIS Chi-restraints excluded: chain B residue 4478 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 434 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 chunk 565 optimal weight: 8.9990 chunk 513 optimal weight: 4.9990 chunk 479 optimal weight: 4.9990 chunk 378 optimal weight: 0.7980 chunk 413 optimal weight: 0.6980 chunk 461 optimal weight: 0.6980 chunk 161 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3226 GLN ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1365 ASN B3226 GLN ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.221219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160223 restraints weight = 76472.201| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 4.40 r_work: 0.3690 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 44708 Z= 0.107 Angle : 0.569 11.417 60730 Z= 0.269 Chirality : 0.040 0.215 7364 Planarity : 0.004 0.050 7594 Dihedral : 3.907 21.786 5918 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.04 % Allowed : 22.71 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.92 (0.12), residues: 5490 helix: 1.56 (0.10), residues: 2790 sheet: 0.25 (0.20), residues: 734 loop : -0.58 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1934 TYR 0.013 0.001 TYR A2870 PHE 0.018 0.001 PHE B1091 TRP 0.014 0.001 TRP A1358 HIS 0.005 0.001 HIS B3228 Details of bonding type rmsd covalent geometry : bond 0.00249 (44700) covalent geometry : angle 0.56851 (60724) hydrogen bonds : bond 0.03098 ( 2216) hydrogen bonds : angle 4.20760 ( 6468) metal coordination : bond 0.00447 ( 8) metal coordination : angle 2.67501 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 367 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0111 (OUTLIER) cc_final: -0.0414 (m-70) REVERT: A 1538 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4743 (tt) REVERT: A 1863 ARG cc_start: 0.3678 (mtm180) cc_final: 0.3437 (mtm180) REVERT: A 1966 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6310 (tm-30) REVERT: A 2394 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6463 (ptt90) REVERT: A 2584 LYS cc_start: 0.6970 (tttt) cc_final: 0.6627 (ttmm) REVERT: A 2777 HIS cc_start: 0.1877 (OUTLIER) cc_final: 0.0364 (p-80) REVERT: A 2876 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8361 (mtpt) REVERT: A 3052 MET cc_start: 0.8578 (ptp) cc_final: 0.8281 (ptp) REVERT: A 3487 LEU cc_start: 0.6978 (mt) cc_final: 0.6660 (tp) REVERT: A 3760 GLU cc_start: 0.6967 (tt0) cc_final: 0.6676 (tt0) REVERT: A 3810 ARG cc_start: 0.6022 (OUTLIER) cc_final: 0.4374 (mtm180) REVERT: A 3817 LEU cc_start: 0.4683 (mp) cc_final: 0.3888 (tt) REVERT: A 3845 GLN cc_start: 0.7994 (mt0) cc_final: 0.7721 (mt0) REVERT: A 3848 MET cc_start: 0.7728 (mtp) cc_final: 0.7476 (mtp) REVERT: B 222 HIS cc_start: 0.0112 (OUTLIER) cc_final: -0.0415 (m-70) REVERT: B 1192 LEU cc_start: 0.5703 (tp) cc_final: 0.5348 (tp) REVERT: B 1436 MET cc_start: 0.8221 (tpp) cc_final: 0.7961 (mtp) REVERT: B 1538 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.4712 (tt) REVERT: B 1863 ARG cc_start: 0.3635 (mtm180) cc_final: 0.3330 (mtm180) REVERT: B 1966 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6261 (tm-30) REVERT: B 2394 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6460 (ptt90) REVERT: B 2582 MET cc_start: 0.6588 (ttp) cc_final: 0.6307 (ttp) REVERT: B 2584 LYS cc_start: 0.6935 (tttt) cc_final: 0.6654 (ttmm) REVERT: B 2711 TYR cc_start: 0.6908 (t80) cc_final: 0.6524 (t80) REVERT: B 2777 HIS cc_start: 0.1886 (OUTLIER) cc_final: 0.0366 (p-80) REVERT: B 2876 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: B 3052 MET cc_start: 0.8575 (ptp) cc_final: 0.8274 (ptp) REVERT: B 3487 LEU cc_start: 0.6896 (mt) cc_final: 0.6682 (tp) REVERT: B 3760 GLU cc_start: 0.6915 (tt0) cc_final: 0.6683 (tt0) REVERT: B 3810 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.4392 (mtm180) REVERT: B 3817 LEU cc_start: 0.4699 (mp) cc_final: 0.3901 (tt) REVERT: B 3845 GLN cc_start: 0.7994 (mt0) cc_final: 0.7723 (mt0) outliers start: 152 outliers final: 104 residues processed: 494 average time/residue: 0.2098 time to fit residues: 180.1120 Evaluate side-chains 459 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 343 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2394 ARG Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2935 SER Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3359 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3678 ILE Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2394 ARG Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2935 SER Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3381 VAL Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3443 ASP Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3678 ILE Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 170 optimal weight: 2.9990 chunk 303 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 141 optimal weight: 0.3980 chunk 509 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 451 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 chunk 473 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.221122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157388 restraints weight = 76801.192| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.40 r_work: 0.3696 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 44708 Z= 0.108 Angle : 0.558 11.496 60730 Z= 0.262 Chirality : 0.040 0.311 7364 Planarity : 0.004 0.049 7594 Dihedral : 3.739 20.566 5918 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.76 % Allowed : 22.73 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 1.08 (0.12), residues: 5490 helix: 1.74 (0.10), residues: 2786 sheet: 0.22 (0.20), residues: 718 loop : -0.51 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1934 TYR 0.020 0.001 TYR A3436 PHE 0.016 0.001 PHE B1091 TRP 0.012 0.001 TRP A3712 HIS 0.004 0.001 HIS A3609 Details of bonding type rmsd covalent geometry : bond 0.00260 (44700) covalent geometry : angle 0.55756 (60724) hydrogen bonds : bond 0.02995 ( 2216) hydrogen bonds : angle 4.07052 ( 6468) metal coordination : bond 0.00472 ( 8) metal coordination : angle 2.36038 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 363 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0138 (OUTLIER) cc_final: -0.0361 (m-70) REVERT: A 1863 ARG cc_start: 0.3546 (mtm180) cc_final: 0.3224 (mtm180) REVERT: A 1942 ILE cc_start: 0.5179 (OUTLIER) cc_final: 0.4906 (mt) REVERT: A 1966 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6259 (tm-30) REVERT: A 2777 HIS cc_start: 0.1929 (OUTLIER) cc_final: 0.0486 (p-80) REVERT: A 2876 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8367 (mtpt) REVERT: A 3052 MET cc_start: 0.8464 (ptp) cc_final: 0.8184 (ptp) REVERT: A 3467 LYS cc_start: 0.6701 (tptp) cc_final: 0.6388 (mtmt) REVERT: A 3535 ASN cc_start: 0.5753 (OUTLIER) cc_final: 0.5439 (m110) REVERT: A 3760 GLU cc_start: 0.7040 (tt0) cc_final: 0.6760 (tt0) REVERT: A 3810 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.4399 (mtm180) REVERT: A 3817 LEU cc_start: 0.4683 (mp) cc_final: 0.3834 (tt) REVERT: A 3848 MET cc_start: 0.7640 (mtp) cc_final: 0.7423 (mtp) REVERT: A 3985 GLN cc_start: 0.7020 (mt0) cc_final: 0.6603 (mt0) REVERT: B 222 HIS cc_start: 0.0328 (OUTLIER) cc_final: -0.0160 (m-70) REVERT: B 1863 ARG cc_start: 0.3529 (mtm180) cc_final: 0.3223 (mtm180) REVERT: B 1942 ILE cc_start: 0.5194 (OUTLIER) cc_final: 0.4916 (mt) REVERT: B 1966 GLU cc_start: 0.6446 (tm-30) cc_final: 0.6209 (tm-30) REVERT: B 2143 ASP cc_start: 0.8200 (t0) cc_final: 0.7897 (t0) REVERT: B 2327 ARG cc_start: 0.5748 (ppt170) cc_final: 0.5043 (mmm160) REVERT: B 2584 LYS cc_start: 0.6996 (tttt) cc_final: 0.6676 (ttmm) REVERT: B 2711 TYR cc_start: 0.6893 (t80) cc_final: 0.6564 (t80) REVERT: B 2777 HIS cc_start: 0.1931 (OUTLIER) cc_final: 0.0490 (p-80) REVERT: B 3052 MET cc_start: 0.8467 (ptp) cc_final: 0.8186 (ptp) REVERT: B 3396 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7645 (pp) REVERT: B 3487 LEU cc_start: 0.6861 (mt) cc_final: 0.6641 (tp) REVERT: B 3535 ASN cc_start: 0.5770 (OUTLIER) cc_final: 0.5453 (m110) REVERT: B 3760 GLU cc_start: 0.6955 (tt0) cc_final: 0.6739 (tt0) REVERT: B 3810 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.4385 (mtm180) REVERT: B 3817 LEU cc_start: 0.4676 (mp) cc_final: 0.3826 (tt) REVERT: B 3845 GLN cc_start: 0.7934 (mt0) cc_final: 0.7730 (mt0) outliers start: 138 outliers final: 102 residues processed: 485 average time/residue: 0.2160 time to fit residues: 182.6015 Evaluate side-chains 460 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 346 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3359 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3678 ILE Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4173 VAL Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2030 LEU Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3443 ASP Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3678 ILE Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4064 THR Chi-restraints excluded: chain B residue 4173 VAL Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 196 optimal weight: 10.0000 chunk 454 optimal weight: 5.9990 chunk 534 optimal weight: 0.0670 chunk 113 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 186 optimal weight: 0.5980 chunk 78 optimal weight: 0.0770 chunk 353 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3845 GLN ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.222066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162005 restraints weight = 76537.701| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 4.40 r_work: 0.3717 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 44708 Z= 0.097 Angle : 0.548 11.398 60730 Z= 0.257 Chirality : 0.039 0.339 7364 Planarity : 0.004 0.048 7594 Dihedral : 3.619 19.439 5918 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.46 % Allowed : 23.15 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 1.21 (0.12), residues: 5490 helix: 1.84 (0.10), residues: 2796 sheet: 0.43 (0.20), residues: 730 loop : -0.53 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2570 TYR 0.014 0.001 TYR A3436 PHE 0.016 0.001 PHE B1091 TRP 0.013 0.001 TRP A3712 HIS 0.006 0.001 HIS A3609 Details of bonding type rmsd covalent geometry : bond 0.00227 (44700) covalent geometry : angle 0.54808 (60724) hydrogen bonds : bond 0.02912 ( 2216) hydrogen bonds : angle 3.98038 ( 6468) metal coordination : bond 0.00400 ( 8) metal coordination : angle 2.05215 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 369 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0316 (OUTLIER) cc_final: -0.0130 (m-70) REVERT: A 1863 ARG cc_start: 0.3728 (mtm180) cc_final: 0.3447 (mtm180) REVERT: A 1966 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6220 (tm-30) REVERT: A 2777 HIS cc_start: 0.1148 (OUTLIER) cc_final: -0.0245 (p-80) REVERT: A 3130 MET cc_start: 0.7511 (tpp) cc_final: 0.7188 (tpp) REVERT: A 3487 LEU cc_start: 0.6926 (mt) cc_final: 0.6708 (tp) REVERT: A 3488 MET cc_start: 0.7679 (ptt) cc_final: 0.7404 (ptp) REVERT: A 3535 ASN cc_start: 0.5715 (OUTLIER) cc_final: 0.5423 (m110) REVERT: A 3760 GLU cc_start: 0.7015 (tt0) cc_final: 0.6749 (tt0) REVERT: A 3810 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.4388 (mtm180) REVERT: A 3817 LEU cc_start: 0.4631 (mp) cc_final: 0.3792 (tt) REVERT: A 3848 MET cc_start: 0.7607 (mtp) cc_final: 0.7399 (mtp) REVERT: A 3985 GLN cc_start: 0.7027 (mt0) cc_final: 0.6583 (mt0) REVERT: B 222 HIS cc_start: 0.0321 (OUTLIER) cc_final: -0.0123 (m-70) REVERT: B 1863 ARG cc_start: 0.3708 (mtm180) cc_final: 0.3424 (mtm180) REVERT: B 1966 GLU cc_start: 0.6457 (tm-30) cc_final: 0.6209 (tm-30) REVERT: B 2584 LYS cc_start: 0.6931 (tttt) cc_final: 0.6658 (ttmm) REVERT: B 2711 TYR cc_start: 0.6855 (t80) cc_final: 0.6575 (t80) REVERT: B 2777 HIS cc_start: 0.1254 (OUTLIER) cc_final: -0.0089 (p-80) REVERT: B 3396 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7688 (pp) REVERT: B 3487 LEU cc_start: 0.6876 (mt) cc_final: 0.6655 (tp) REVERT: B 3488 MET cc_start: 0.7669 (ptt) cc_final: 0.7396 (ptp) REVERT: B 3535 ASN cc_start: 0.5718 (OUTLIER) cc_final: 0.5425 (m110) REVERT: B 3760 GLU cc_start: 0.6952 (tt0) cc_final: 0.6672 (tt0) REVERT: B 3810 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.4364 (mtm180) REVERT: B 3817 LEU cc_start: 0.4665 (mp) cc_final: 0.3819 (tt) outliers start: 123 outliers final: 96 residues processed: 481 average time/residue: 0.1542 time to fit residues: 130.2664 Evaluate side-chains 448 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 343 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3127 SER Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3359 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3678 ILE Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2030 LEU Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3443 ASP Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3678 ILE Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4064 THR Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 535 optimal weight: 0.0980 chunk 286 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 514 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 450 optimal weight: 2.9990 chunk 537 optimal weight: 7.9990 chunk 425 optimal weight: 0.9990 chunk 338 optimal weight: 20.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS A4319 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.218559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.156507 restraints weight = 75946.966| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 3.82 r_work: 0.3664 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 44708 Z= 0.190 Angle : 0.640 11.907 60730 Z= 0.304 Chirality : 0.042 0.324 7364 Planarity : 0.004 0.061 7594 Dihedral : 3.942 24.928 5918 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 22.89 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.94 (0.11), residues: 5490 helix: 1.60 (0.10), residues: 2794 sheet: 0.26 (0.20), residues: 724 loop : -0.60 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1934 TYR 0.015 0.002 TYR A3436 PHE 0.025 0.002 PHE A2353 TRP 0.010 0.002 TRP A2719 HIS 0.011 0.001 HIS A2777 Details of bonding type rmsd covalent geometry : bond 0.00466 (44700) covalent geometry : angle 0.63917 (60724) hydrogen bonds : bond 0.03465 ( 2216) hydrogen bonds : angle 4.23724 ( 6468) metal coordination : bond 0.00895 ( 8) metal coordination : angle 2.75419 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 352 time to evaluate : 1.066 Fit side-chains REVERT: A 222 HIS cc_start: 0.0115 (OUTLIER) cc_final: -0.0421 (m-70) REVERT: A 1863 ARG cc_start: 0.3869 (mtm180) cc_final: 0.3440 (mtm180) REVERT: A 1942 ILE cc_start: 0.5165 (OUTLIER) cc_final: 0.4873 (mt) REVERT: A 1966 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6337 (tm-30) REVERT: A 2327 ARG cc_start: 0.5907 (ppt170) cc_final: 0.5135 (mmm160) REVERT: A 2584 LYS cc_start: 0.7119 (tttt) cc_final: 0.6809 (ttmm) REVERT: A 2777 HIS cc_start: 0.1653 (OUTLIER) cc_final: 0.0636 (p-80) REVERT: A 3083 TRP cc_start: 0.8260 (m-10) cc_final: 0.7574 (m-10) REVERT: A 3389 SER cc_start: 0.7624 (t) cc_final: 0.7187 (p) REVERT: A 3487 LEU cc_start: 0.7376 (mt) cc_final: 0.7004 (tp) REVERT: A 3488 MET cc_start: 0.7861 (ptt) cc_final: 0.7615 (ptp) REVERT: A 3535 ASN cc_start: 0.5844 (OUTLIER) cc_final: 0.5518 (m110) REVERT: A 3760 GLU cc_start: 0.7203 (tt0) cc_final: 0.6796 (tt0) REVERT: A 3810 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.4499 (mtm180) REVERT: A 3848 MET cc_start: 0.7784 (mtp) cc_final: 0.7570 (mtp) REVERT: B 222 HIS cc_start: 0.0115 (OUTLIER) cc_final: -0.0424 (m-70) REVERT: B 1192 LEU cc_start: 0.6017 (tp) cc_final: 0.5709 (tp) REVERT: B 1863 ARG cc_start: 0.3694 (mtm180) cc_final: 0.3350 (mtm180) REVERT: B 1942 ILE cc_start: 0.5268 (OUTLIER) cc_final: 0.4985 (mt) REVERT: B 1966 GLU cc_start: 0.6545 (tm-30) cc_final: 0.6301 (tm-30) REVERT: B 2327 ARG cc_start: 0.5900 (ppt170) cc_final: 0.5137 (mmm160) REVERT: B 2584 LYS cc_start: 0.6990 (tttt) cc_final: 0.6759 (ttmm) REVERT: B 2777 HIS cc_start: 0.1640 (OUTLIER) cc_final: 0.0628 (p-80) REVERT: B 3083 TRP cc_start: 0.8233 (m-10) cc_final: 0.7554 (m-10) REVERT: B 3389 SER cc_start: 0.7600 (t) cc_final: 0.7238 (p) REVERT: B 3396 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7767 (pp) REVERT: B 3487 LEU cc_start: 0.7303 (mt) cc_final: 0.6941 (tp) REVERT: B 3488 MET cc_start: 0.7899 (ptt) cc_final: 0.7654 (ptp) REVERT: B 3535 ASN cc_start: 0.5850 (OUTLIER) cc_final: 0.5524 (m110) REVERT: B 3760 GLU cc_start: 0.7143 (tt0) cc_final: 0.6794 (tt0) REVERT: B 3810 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.4520 (mtm180) REVERT: B 3845 GLN cc_start: 0.8241 (mt0) cc_final: 0.7984 (mt0) REVERT: B 3848 MET cc_start: 0.7515 (mtp) cc_final: 0.7267 (mtp) outliers start: 134 outliers final: 116 residues processed: 475 average time/residue: 0.1651 time to fit residues: 137.0436 Evaluate side-chains 474 residues out of total 4994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 347 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3359 LEU Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3678 ILE Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3828 SER Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1842 LEU Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3678 ILE Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3828 SER Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4064 THR Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain B residue 4319 HIS Chi-restraints excluded: chain B residue 4478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 29 optimal weight: 0.0040 chunk 91 optimal weight: 7.9990 chunk 385 optimal weight: 4.9990 chunk 504 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 397 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 501 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 102 optimal weight: 0.0020 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.219936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158861 restraints weight = 76298.089| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.87 r_work: 0.3664 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 44708 Z= 0.123 Angle : 0.578 11.454 60730 Z= 0.272 Chirality : 0.040 0.321 7364 Planarity : 0.004 0.050 7594 Dihedral : 3.819 22.237 5918 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.44 % Allowed : 23.15 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 1.05 (0.12), residues: 5490 helix: 1.72 (0.10), residues: 2794 sheet: 0.33 (0.20), residues: 720 loop : -0.61 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1934 TYR 0.016 0.001 TYR B3436 PHE 0.025 0.001 PHE A3807 TRP 0.011 0.001 TRP A1358 HIS 0.005 0.001 HIS A2777 Details of bonding type rmsd covalent geometry : bond 0.00299 (44700) covalent geometry : angle 0.57758 (60724) hydrogen bonds : bond 0.03132 ( 2216) hydrogen bonds : angle 4.12130 ( 6468) metal coordination : bond 0.00484 ( 8) metal coordination : angle 2.58732 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14176.98 seconds wall clock time: 242 minutes 19.85 seconds (14539.85 seconds total)