Starting phenix.real_space_refine on Wed Feb 4 10:10:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l4k_62814/02_2026/9l4k_62814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l4k_62814/02_2026/9l4k_62814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l4k_62814/02_2026/9l4k_62814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l4k_62814/02_2026/9l4k_62814.map" model { file = "/net/cci-nas-00/data/ceres_data/9l4k_62814/02_2026/9l4k_62814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l4k_62814/02_2026/9l4k_62814.cif" } resolution = 3.41 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= 0.020 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: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 6253 2.51 5 N 1692 2.21 5 O 1810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9832 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6754 Classifications: {'peptide': 860} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 826} Chain breaks: 4 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2309 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 289} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 769 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 85} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.24 Number of scatterers: 9832 At special positions: 0 Unit cell: (81.4, 92.4, 205.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 1810 8.00 N 1692 7.00 C 6253 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: 0.69 Conformation dependent library (CDL) restraints added in 439.5 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 44.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 157 through 172 removed outlier: 4.294A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 247 through 253 removed outlier: 4.059A pdb=" N ARG A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.922A pdb=" N GLY A 294 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.272A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 374 through 387 removed outlier: 3.515A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 397 through 415 Processing helix chain 'A' and resid 417 through 424 removed outlier: 4.467A pdb=" N THR A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.534A pdb=" N LEU A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 460 removed outlier: 4.319A pdb=" N ALA A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 476 through 486 removed outlier: 3.584A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 562 through 574 Processing helix chain 'A' and resid 579 through 589 removed outlier: 3.622A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 586 " --> pdb=" O LYS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 Processing helix chain 'A' and resid 614 through 623 removed outlier: 3.676A pdb=" N VAL A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.638A pdb=" N LYS A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 Proline residue: A 686 - end of helix removed outlier: 3.618A pdb=" N SER A 693 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 740 through 750 Processing helix chain 'A' and resid 769 through 780 removed outlier: 4.006A pdb=" N ALA A 773 " --> pdb=" O ASP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 810 Processing helix chain 'A' and resid 824 through 836 Processing helix chain 'A' and resid 853 through 867 Processing helix chain 'A' and resid 881 through 894 removed outlier: 4.423A pdb=" N TYR A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 923 removed outlier: 3.992A pdb=" N GLU A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 950 Processing helix chain 'A' and resid 967 through 981 removed outlier: 4.026A pdb=" N ASP A 973 " --> pdb=" O PHE A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1009 removed outlier: 4.068A pdb=" N LYS A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1038 Processing helix chain 'A' and resid 1058 through 1062 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 99 through 127 Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 246 removed outlier: 3.643A pdb=" N ASP A 288 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 331 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 209 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR A 336 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 211 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 208 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 354 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 210 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 652 through 655 removed outlier: 6.490A pdb=" N MET A 653 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN A 707 " --> pdb=" O MET A 653 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 655 " --> pdb=" O ASN A 707 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 733 " --> pdb=" O TYR A 759 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 760 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 791 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 762 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 788 " --> pdb=" O ASN A 817 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N SER A 819 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 790 " --> pdb=" O SER A 819 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 816 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N GLU A 848 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 818 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 876 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP A 905 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU A 902 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N GLY A 933 " --> pdb=" O LEU A 902 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 904 " --> pdb=" O GLY A 933 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 930 " --> pdb=" O TRP A 960 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TRP A 962 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU A 932 " --> pdb=" O TRP A 962 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 959 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 988 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU A1016 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.781A pdb=" N ILE B 282 " --> pdb=" O ASP B 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA7, first strand: chain 'B' and resid 291 through 294 removed outlier: 3.710A pdb=" N ALA B 291 " --> pdb=" O CYS B 304 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 326 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 342 removed outlier: 7.167A pdb=" N GLY B 352 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS B 340 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 350 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU B 342 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER B 348 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 360 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY B 353 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER B 358 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 361 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU B 373 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP B 363 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 371 " --> pdb=" O ASP B 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 386 through 388 removed outlier: 3.669A pdb=" N VAL B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 426 through 430 removed outlier: 3.588A pdb=" N GLY B 437 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 463 through 468 removed outlier: 4.035A pdb=" N SER B 465 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 485 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN B 484 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 504 through 509 removed outlier: 3.515A pdb=" N GLY B 526 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 520 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B 524 " --> pdb=" O GLY B 520 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 525 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU B 538 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 527 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 534 " --> pdb=" O SER B 529 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 50 through 55 removed outlier: 6.675A pdb=" N LEU C 91 " --> pdb=" O VAL C 86 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1356 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: 1.70 Time building geometry restraints manager: 0.97 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: 3242 1.34 - 1.46: 2164 1.46 - 1.58: 4524 1.58 - 1.70: 0 1.70 - 1.81: 103 Bond restraints: 10033 Sorted by residual: bond pdb=" C GLU A 350 " pdb=" N PRO A 351 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.23e-02 6.61e+03 2.84e+00 bond pdb=" C VAL A 638 " pdb=" N PRO A 639 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.67e+00 bond pdb=" C GLU A 350 " pdb=" O GLU A 350 " ideal model delta sigma weight residual 1.235 1.230 0.005 4.70e-03 4.53e+04 1.08e+00 bond pdb=" CA ILE A 273 " pdb=" CB ILE A 273 " ideal model delta sigma weight residual 1.537 1.542 -0.005 5.00e-03 4.00e+04 9.74e-01 bond pdb=" CA ILE A 193 " pdb=" CB ILE A 193 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.55e-02 4.16e+03 8.71e-01 ... (remaining 10028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13259 1.42 - 2.84: 284 2.84 - 4.25: 39 4.25 - 5.67: 17 5.67 - 7.09: 3 Bond angle restraints: 13602 Sorted by residual: angle pdb=" N ASP A 233 " pdb=" CA ASP A 233 " pdb=" C ASP A 233 " ideal model delta sigma weight residual 113.56 108.44 5.12 1.39e+00 5.18e-01 1.36e+01 angle pdb=" C ILE A 273 " pdb=" CA ILE A 273 " pdb=" CB ILE A 273 " ideal model delta sigma weight residual 113.70 110.36 3.34 9.50e-01 1.11e+00 1.23e+01 angle pdb=" N GLY A 995 " pdb=" CA GLY A 995 " pdb=" C GLY A 995 " ideal model delta sigma weight residual 113.18 119.84 -6.66 2.37e+00 1.78e-01 7.91e+00 angle pdb=" N GLY A 440 " pdb=" CA GLY A 440 " pdb=" C GLY A 440 " ideal model delta sigma weight residual 110.58 113.95 -3.37 1.35e+00 5.49e-01 6.23e+00 angle pdb=" C ASP A 272 " pdb=" N ILE A 273 " pdb=" CA ILE A 273 " ideal model delta sigma weight residual 120.43 122.57 -2.14 9.60e-01 1.09e+00 4.97e+00 ... (remaining 13597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5645 17.33 - 34.67: 302 34.67 - 52.00: 78 52.00 - 69.34: 16 69.34 - 86.67: 5 Dihedral angle restraints: 6046 sinusoidal: 2409 harmonic: 3637 Sorted by residual: dihedral pdb=" CA LYS B 279 " pdb=" C LYS B 279 " pdb=" N MET B 280 " pdb=" CA MET B 280 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB ARG A 893 " pdb=" CG ARG A 893 " pdb=" CD ARG A 893 " pdb=" NE ARG A 893 " ideal model delta sinusoidal sigma weight residual 180.00 -121.09 -58.91 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN A 982 " pdb=" CB GLN A 982 " pdb=" CG GLN A 982 " pdb=" CD GLN A 982 " ideal model delta sinusoidal sigma weight residual 180.00 121.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 932 0.027 - 0.055: 398 0.055 - 0.082: 113 0.082 - 0.109: 77 0.109 - 0.137: 29 Chirality restraints: 1549 Sorted by residual: chirality pdb=" CA ILE B 309 " pdb=" N ILE B 309 " pdb=" C ILE B 309 " pdb=" CB ILE B 309 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PHE A 771 " pdb=" N PHE A 771 " pdb=" C PHE A 771 " pdb=" CB PHE A 771 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1546 not shown) Planarity restraints: 1743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 966 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 967 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 967 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 967 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 530 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 531 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 531 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 531 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 417 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 418 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " 0.020 5.00e-02 4.00e+02 ... (remaining 1740 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 154 2.69 - 3.24: 9470 3.24 - 3.80: 14600 3.80 - 4.35: 18964 4.35 - 4.90: 31724 Nonbonded interactions: 74912 Sorted by model distance: nonbonded pdb=" O LEU A 609 " pdb=" OG SER A 612 " model vdw 2.140 3.040 nonbonded pdb=" O THR A1012 " pdb=" NH1 ARG A1014 " model vdw 2.168 3.120 nonbonded pdb=" O PRO C 100 " pdb=" ND2 ASN C 104 " model vdw 2.248 3.120 nonbonded pdb=" O GLU A1004 " pdb=" OG1 THR A1007 " model vdw 2.254 3.040 nonbonded pdb=" O LYS A 537 " pdb=" OG SER A 540 " model vdw 2.258 3.040 ... (remaining 74907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 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 : 0.002 0.021 10033 Z= 0.130 Angle : 0.556 7.090 13602 Z= 0.306 Chirality : 0.039 0.137 1549 Planarity : 0.004 0.051 1743 Dihedral : 12.116 86.671 3682 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.09 % Allowed : 7.24 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1242 helix: 1.68 (0.23), residues: 512 sheet: 0.46 (0.31), residues: 281 loop : -0.45 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 370 TYR 0.008 0.001 TYR B 528 PHE 0.013 0.001 PHE C 63 TRP 0.009 0.002 TRP B 516 HIS 0.003 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00243 (10033) covalent geometry : angle 0.55572 (13602) hydrogen bonds : bond 0.18647 ( 466) hydrogen bonds : angle 6.56081 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8259 (mp) cc_final: 0.7781 (tt) REVERT: A 622 MET cc_start: 0.7148 (mmt) cc_final: 0.6880 (mmt) REVERT: A 708 ASP cc_start: 0.7128 (m-30) cc_final: 0.6721 (t0) REVERT: B 313 SER cc_start: 0.5999 (t) cc_final: 0.5536 (p) REVERT: B 509 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.3308 (t80) REVERT: C 127 MET cc_start: 0.3463 (tpt) cc_final: 0.2259 (ptm) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.1216 time to fit residues: 43.4294 Evaluate side-chains 146 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN A 562 ASN A 583 GLN A 603 GLN A 698 ASN A 722 GLN A 780 HIS A 882 ASN A 900 GLN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS B 468 HIS B 471 GLN B 554 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.175303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.140897 restraints weight = 16610.020| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.54 r_work: 0.3781 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10033 Z= 0.209 Angle : 0.751 11.002 13602 Z= 0.376 Chirality : 0.046 0.186 1549 Planarity : 0.006 0.067 1743 Dihedral : 5.388 70.370 1347 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.90 % Allowed : 13.18 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1242 helix: 1.45 (0.22), residues: 529 sheet: 0.44 (0.30), residues: 291 loop : -0.81 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 732 TYR 0.024 0.002 TYR A 555 PHE 0.021 0.002 PHE A 243 TRP 0.023 0.002 TRP B 446 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00473 (10033) covalent geometry : angle 0.75059 (13602) hydrogen bonds : bond 0.04844 ( 466) hydrogen bonds : angle 5.05662 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8347 (mp) cc_final: 0.7718 (tt) REVERT: A 615 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6234 (pp20) REVERT: A 708 ASP cc_start: 0.7890 (m-30) cc_final: 0.6749 (t0) REVERT: A 825 ASP cc_start: 0.7502 (m-30) cc_final: 0.6631 (p0) REVERT: A 918 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7602 (m) REVERT: A 971 CYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8122 (m) REVERT: A 1017 ARG cc_start: 0.6447 (ptm-80) cc_final: 0.5472 (mpp80) REVERT: B 313 SER cc_start: 0.6782 (t) cc_final: 0.6372 (p) REVERT: B 509 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.4037 (t80) REVERT: C 105 ARG cc_start: 0.6636 (ttt-90) cc_final: 0.6275 (ttp-110) REVERT: C 127 MET cc_start: 0.3004 (tpt) cc_final: 0.2088 (ptm) outliers start: 42 outliers final: 15 residues processed: 190 average time/residue: 0.0950 time to fit residues: 24.8969 Evaluate side-chains 145 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 54 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 381 ASN B 468 HIS B 553 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.175271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.138471 restraints weight = 16606.392| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.61 r_work: 0.3785 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10033 Z= 0.130 Angle : 0.623 9.311 13602 Z= 0.310 Chirality : 0.042 0.164 1549 Planarity : 0.004 0.045 1743 Dihedral : 5.004 60.554 1347 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.88 % Allowed : 14.76 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1242 helix: 1.73 (0.23), residues: 530 sheet: 0.67 (0.30), residues: 289 loop : -0.64 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 370 TYR 0.016 0.001 TYR B 568 PHE 0.023 0.001 PHE A 514 TRP 0.019 0.001 TRP B 446 HIS 0.009 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00289 (10033) covalent geometry : angle 0.62299 (13602) hydrogen bonds : bond 0.04214 ( 466) hydrogen bonds : angle 4.74744 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8232 (mp) cc_final: 0.7622 (tt) REVERT: A 489 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6132 (pp) REVERT: A 514 PHE cc_start: 0.4521 (t80) cc_final: 0.4241 (t80) REVERT: A 615 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5797 (pp20) REVERT: A 708 ASP cc_start: 0.7908 (m-30) cc_final: 0.6798 (t0) REVERT: A 813 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7261 (pp) REVERT: A 825 ASP cc_start: 0.7447 (m-30) cc_final: 0.6619 (p0) REVERT: A 1017 ARG cc_start: 0.6220 (ptm-80) cc_final: 0.5276 (mpp80) REVERT: B 313 SER cc_start: 0.6792 (t) cc_final: 0.6460 (p) REVERT: B 325 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5487 (mm-30) REVERT: B 509 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.3846 (t80) REVERT: B 553 ASN cc_start: 0.8058 (t0) cc_final: 0.7839 (t0) REVERT: C 109 MET cc_start: 0.7177 (tpp) cc_final: 0.6521 (ptt) REVERT: C 127 MET cc_start: 0.3125 (tpt) cc_final: 0.2187 (ptm) outliers start: 31 outliers final: 20 residues processed: 155 average time/residue: 0.0764 time to fit residues: 17.5516 Evaluate side-chains 141 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.173461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.138327 restraints weight = 16874.167| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 3.52 r_work: 0.3756 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10033 Z= 0.140 Angle : 0.619 8.560 13602 Z= 0.308 Chirality : 0.042 0.169 1549 Planarity : 0.004 0.047 1743 Dihedral : 4.864 57.069 1347 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.71 % Allowed : 14.39 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1242 helix: 1.81 (0.23), residues: 525 sheet: 0.74 (0.31), residues: 283 loop : -0.64 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 37 TYR 0.016 0.002 TYR B 568 PHE 0.021 0.002 PHE A 243 TRP 0.017 0.001 TRP B 446 HIS 0.010 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00323 (10033) covalent geometry : angle 0.61855 (13602) hydrogen bonds : bond 0.04058 ( 466) hydrogen bonds : angle 4.63275 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8209 (mp) cc_final: 0.7592 (tt) REVERT: A 489 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6161 (pp) REVERT: A 493 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6264 (mpp-170) REVERT: A 514 PHE cc_start: 0.4814 (t80) cc_final: 0.4550 (t80) REVERT: A 708 ASP cc_start: 0.7871 (m-30) cc_final: 0.6761 (t0) REVERT: A 825 ASP cc_start: 0.7447 (m-30) cc_final: 0.6735 (p0) REVERT: A 1000 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6541 (tptt) REVERT: A 1017 ARG cc_start: 0.6069 (ptm-80) cc_final: 0.5140 (mpp80) REVERT: A 1061 MET cc_start: 0.7942 (tpp) cc_final: 0.7389 (mpp) REVERT: B 313 SER cc_start: 0.6502 (t) cc_final: 0.6094 (p) REVERT: B 374 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6720 (mp-120) REVERT: B 509 PHE cc_start: 0.6378 (OUTLIER) cc_final: 0.3979 (t80) REVERT: B 554 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7985 (m-40) REVERT: C 109 MET cc_start: 0.7520 (tpp) cc_final: 0.6722 (ptt) REVERT: C 127 MET cc_start: 0.3079 (tpt) cc_final: 0.2207 (mtt) outliers start: 40 outliers final: 26 residues processed: 149 average time/residue: 0.0736 time to fit residues: 15.9857 Evaluate side-chains 143 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS B 553 ASN C 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.173061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136453 restraints weight = 16662.108| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.53 r_work: 0.3762 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10033 Z= 0.121 Angle : 0.586 7.832 13602 Z= 0.293 Chirality : 0.041 0.154 1549 Planarity : 0.004 0.041 1743 Dihedral : 4.787 53.442 1347 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.53 % Allowed : 15.60 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1242 helix: 1.96 (0.23), residues: 519 sheet: 0.75 (0.31), residues: 287 loop : -0.60 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.016 0.001 TYR B 568 PHE 0.018 0.001 PHE A 243 TRP 0.015 0.001 TRP B 446 HIS 0.010 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00271 (10033) covalent geometry : angle 0.58634 (13602) hydrogen bonds : bond 0.03700 ( 466) hydrogen bonds : angle 4.57692 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8259 (mp) cc_final: 0.7635 (tt) REVERT: A 489 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6105 (pp) REVERT: A 493 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6192 (mpp-170) REVERT: A 708 ASP cc_start: 0.7797 (m-30) cc_final: 0.6729 (t0) REVERT: A 825 ASP cc_start: 0.7481 (m-30) cc_final: 0.6794 (p0) REVERT: A 1017 ARG cc_start: 0.5948 (ptm-80) cc_final: 0.5013 (mpp80) REVERT: A 1061 MET cc_start: 0.7918 (tpp) cc_final: 0.7380 (mpp) REVERT: B 313 SER cc_start: 0.6530 (t) cc_final: 0.6061 (p) REVERT: B 374 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6861 (mp-120) REVERT: B 509 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.4336 (t80) REVERT: B 553 ASN cc_start: 0.8061 (t0) cc_final: 0.7779 (t0) REVERT: B 554 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7952 (m-40) REVERT: C 109 MET cc_start: 0.7572 (tpp) cc_final: 0.6753 (ptt) REVERT: C 127 MET cc_start: 0.3254 (tpt) cc_final: 0.2337 (mtt) outliers start: 38 outliers final: 26 residues processed: 148 average time/residue: 0.0790 time to fit residues: 17.0605 Evaluate side-chains 148 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 98 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 93 optimal weight: 0.0020 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.170622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.136148 restraints weight = 16753.843| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.42 r_work: 0.3720 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10033 Z= 0.146 Angle : 0.620 8.351 13602 Z= 0.311 Chirality : 0.042 0.159 1549 Planarity : 0.004 0.045 1743 Dihedral : 4.852 53.150 1347 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.99 % Allowed : 16.34 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1242 helix: 1.87 (0.23), residues: 519 sheet: 0.59 (0.31), residues: 283 loop : -0.71 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.023 0.001 TYR B 568 PHE 0.017 0.001 PHE C 41 TRP 0.015 0.002 TRP B 446 HIS 0.019 0.002 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00334 (10033) covalent geometry : angle 0.61977 (13602) hydrogen bonds : bond 0.04031 ( 466) hydrogen bonds : angle 4.66445 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8065 (mmm) cc_final: 0.7806 (mmm) REVERT: A 253 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7012 (mp) REVERT: A 489 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6110 (pp) REVERT: A 584 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: A 708 ASP cc_start: 0.7898 (m-30) cc_final: 0.6775 (t0) REVERT: A 825 ASP cc_start: 0.7448 (m-30) cc_final: 0.6797 (p0) REVERT: A 1017 ARG cc_start: 0.6000 (ptm-80) cc_final: 0.5072 (mpp80) REVERT: A 1061 MET cc_start: 0.7984 (tpp) cc_final: 0.7650 (mpp) REVERT: B 313 SER cc_start: 0.6473 (t) cc_final: 0.6075 (p) REVERT: B 374 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6946 (mp-120) REVERT: B 453 LYS cc_start: 0.8018 (mppt) cc_final: 0.7792 (mmmt) REVERT: B 461 SER cc_start: 0.5401 (OUTLIER) cc_final: 0.4829 (m) REVERT: B 509 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.4209 (t80) REVERT: B 521 MET cc_start: 0.8292 (tpp) cc_final: 0.7887 (mtp) REVERT: B 553 ASN cc_start: 0.7994 (t0) cc_final: 0.7676 (t0) REVERT: B 554 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8022 (m-40) REVERT: C 109 MET cc_start: 0.7641 (tpp) cc_final: 0.6863 (ptt) REVERT: C 127 MET cc_start: 0.3297 (tpt) cc_final: 0.2345 (mtt) outliers start: 43 outliers final: 30 residues processed: 155 average time/residue: 0.0785 time to fit residues: 17.6120 Evaluate side-chains 153 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 16 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 49 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.171452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134384 restraints weight = 16649.027| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.60 r_work: 0.3731 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10033 Z= 0.126 Angle : 0.594 7.878 13602 Z= 0.297 Chirality : 0.042 0.161 1549 Planarity : 0.004 0.043 1743 Dihedral : 4.743 49.392 1347 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.99 % Allowed : 16.16 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.25), residues: 1242 helix: 1.91 (0.23), residues: 520 sheet: 0.56 (0.31), residues: 283 loop : -0.67 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 37 TYR 0.023 0.001 TYR B 568 PHE 0.016 0.001 PHE A 514 TRP 0.014 0.001 TRP B 446 HIS 0.021 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00291 (10033) covalent geometry : angle 0.59446 (13602) hydrogen bonds : bond 0.03674 ( 466) hydrogen bonds : angle 4.57616 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8066 (mmm) cc_final: 0.7751 (mmm) REVERT: A 285 PHE cc_start: 0.8434 (m-80) cc_final: 0.8181 (m-80) REVERT: A 410 LEU cc_start: 0.7595 (tp) cc_final: 0.7389 (tp) REVERT: A 437 PHE cc_start: 0.8346 (t80) cc_final: 0.8067 (t80) REVERT: A 489 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6056 (pp) REVERT: A 493 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6143 (mpp-170) REVERT: A 615 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5861 (pp20) REVERT: A 708 ASP cc_start: 0.7754 (m-30) cc_final: 0.6647 (t0) REVERT: A 825 ASP cc_start: 0.7378 (m-30) cc_final: 0.6760 (p0) REVERT: A 921 LEU cc_start: 0.8157 (mt) cc_final: 0.7944 (mp) REVERT: A 1017 ARG cc_start: 0.5948 (ptm-80) cc_final: 0.4981 (mpp80) REVERT: A 1061 MET cc_start: 0.8018 (tpp) cc_final: 0.7727 (mpp) REVERT: B 313 SER cc_start: 0.6501 (t) cc_final: 0.6174 (p) REVERT: B 453 LYS cc_start: 0.8125 (mppt) cc_final: 0.7717 (mmmt) REVERT: B 472 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 509 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.4260 (t80) REVERT: B 521 MET cc_start: 0.8211 (tpp) cc_final: 0.7784 (mtp) REVERT: B 538 GLU cc_start: 0.4327 (pm20) cc_final: 0.4046 (pm20) REVERT: B 553 ASN cc_start: 0.7893 (t0) cc_final: 0.7549 (t0) REVERT: B 554 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: C 109 MET cc_start: 0.7659 (tpp) cc_final: 0.6973 (ptt) REVERT: C 127 MET cc_start: 0.3299 (tpt) cc_final: 0.2321 (mtt) outliers start: 43 outliers final: 28 residues processed: 161 average time/residue: 0.0888 time to fit residues: 20.2978 Evaluate side-chains 155 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.0060 chunk 72 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 HIS ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.171414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135190 restraints weight = 16533.488| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.46 r_work: 0.3748 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10033 Z= 0.116 Angle : 0.600 10.054 13602 Z= 0.295 Chirality : 0.041 0.195 1549 Planarity : 0.004 0.040 1743 Dihedral : 4.646 46.985 1347 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.71 % Allowed : 17.18 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1242 helix: 1.94 (0.23), residues: 519 sheet: 0.51 (0.31), residues: 288 loop : -0.63 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 555 TYR 0.021 0.001 TYR B 568 PHE 0.015 0.001 PHE C 41 TRP 0.013 0.001 TRP B 446 HIS 0.015 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00264 (10033) covalent geometry : angle 0.60047 (13602) hydrogen bonds : bond 0.03531 ( 466) hydrogen bonds : angle 4.51681 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8024 (mmm) cc_final: 0.7746 (mmm) REVERT: A 285 PHE cc_start: 0.8365 (m-80) cc_final: 0.8132 (m-80) REVERT: A 410 LEU cc_start: 0.7715 (tp) cc_final: 0.7500 (tp) REVERT: A 437 PHE cc_start: 0.8388 (t80) cc_final: 0.8080 (t80) REVERT: A 489 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6109 (pp) REVERT: A 708 ASP cc_start: 0.7719 (m-30) cc_final: 0.6675 (t0) REVERT: A 825 ASP cc_start: 0.7453 (m-30) cc_final: 0.6834 (p0) REVERT: A 921 LEU cc_start: 0.8114 (mt) cc_final: 0.7914 (mp) REVERT: A 942 MET cc_start: 0.8064 (tpp) cc_final: 0.7835 (tpp) REVERT: A 1017 ARG cc_start: 0.5965 (ptm-80) cc_final: 0.4993 (mpp80) REVERT: A 1061 MET cc_start: 0.7922 (tpp) cc_final: 0.7640 (mpp) REVERT: B 313 SER cc_start: 0.6438 (t) cc_final: 0.6099 (p) REVERT: B 374 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6523 (mp-120) REVERT: B 417 LEU cc_start: 0.7018 (mt) cc_final: 0.5944 (mt) REVERT: B 446 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.5642 (m-10) REVERT: B 453 LYS cc_start: 0.8091 (mppt) cc_final: 0.7755 (mmmt) REVERT: B 509 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.4203 (t80) REVERT: B 521 MET cc_start: 0.8199 (tpp) cc_final: 0.7756 (mtp) REVERT: B 538 GLU cc_start: 0.4196 (pm20) cc_final: 0.3866 (pm20) REVERT: B 553 ASN cc_start: 0.7749 (t0) cc_final: 0.7364 (t0) REVERT: B 554 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8018 (m-40) REVERT: C 109 MET cc_start: 0.7620 (tpp) cc_final: 0.6966 (ptt) REVERT: C 127 MET cc_start: 0.3319 (tpt) cc_final: 0.2340 (mtt) outliers start: 40 outliers final: 27 residues processed: 151 average time/residue: 0.0783 time to fit residues: 17.9323 Evaluate side-chains 149 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 44 GLN C 117 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.170017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133654 restraints weight = 16635.346| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.45 r_work: 0.3723 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10033 Z= 0.147 Angle : 0.635 9.174 13602 Z= 0.313 Chirality : 0.043 0.263 1549 Planarity : 0.004 0.043 1743 Dihedral : 4.738 48.126 1347 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.25 % Allowed : 17.46 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1242 helix: 1.84 (0.23), residues: 520 sheet: 0.43 (0.31), residues: 288 loop : -0.76 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 555 TYR 0.020 0.001 TYR B 568 PHE 0.014 0.001 PHE C 41 TRP 0.012 0.001 TRP B 446 HIS 0.020 0.002 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00345 (10033) covalent geometry : angle 0.63461 (13602) hydrogen bonds : bond 0.03832 ( 466) hydrogen bonds : angle 4.61751 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8006 (mmm) cc_final: 0.7683 (mmm) REVERT: A 285 PHE cc_start: 0.8361 (m-80) cc_final: 0.8126 (m-80) REVERT: A 410 LEU cc_start: 0.7703 (tp) cc_final: 0.7488 (tp) REVERT: A 437 PHE cc_start: 0.8402 (t80) cc_final: 0.8131 (t80) REVERT: A 489 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6037 (pp) REVERT: A 584 GLU cc_start: 0.7340 (mp0) cc_final: 0.7008 (mp0) REVERT: A 708 ASP cc_start: 0.7767 (m-30) cc_final: 0.6704 (t0) REVERT: A 825 ASP cc_start: 0.7421 (m-30) cc_final: 0.6806 (p0) REVERT: A 1017 ARG cc_start: 0.5968 (ptm-80) cc_final: 0.4997 (mpp80) REVERT: A 1061 MET cc_start: 0.7873 (tpp) cc_final: 0.7349 (mpp) REVERT: B 313 SER cc_start: 0.6482 (t) cc_final: 0.6160 (p) REVERT: B 446 TRP cc_start: 0.8007 (OUTLIER) cc_final: 0.5619 (m-10) REVERT: B 453 LYS cc_start: 0.8169 (mppt) cc_final: 0.7828 (mmmt) REVERT: B 472 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: B 509 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.4318 (t80) REVERT: B 521 MET cc_start: 0.8206 (tpp) cc_final: 0.7751 (mtp) REVERT: B 538 GLU cc_start: 0.4226 (pm20) cc_final: 0.3860 (pm20) REVERT: B 553 ASN cc_start: 0.7761 (t0) cc_final: 0.7373 (t0) REVERT: B 554 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7997 (m-40) REVERT: C 109 MET cc_start: 0.7658 (tpp) cc_final: 0.7107 (ptt) REVERT: C 127 MET cc_start: 0.3513 (tpt) cc_final: 0.2422 (mtt) outliers start: 35 outliers final: 29 residues processed: 147 average time/residue: 0.0610 time to fit residues: 13.9260 Evaluate side-chains 151 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 116 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 767 GLN ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.170233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.133740 restraints weight = 16478.993| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.52 r_work: 0.3727 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10033 Z= 0.126 Angle : 0.630 9.529 13602 Z= 0.308 Chirality : 0.042 0.236 1549 Planarity : 0.005 0.085 1743 Dihedral : 4.732 47.277 1347 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.34 % Allowed : 17.55 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1242 helix: 1.86 (0.23), residues: 520 sheet: 0.42 (0.31), residues: 288 loop : -0.75 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 555 TYR 0.021 0.001 TYR B 568 PHE 0.013 0.001 PHE C 41 TRP 0.011 0.001 TRP B 446 HIS 0.018 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00292 (10033) covalent geometry : angle 0.62998 (13602) hydrogen bonds : bond 0.03666 ( 466) hydrogen bonds : angle 4.56822 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7984 (mmm) cc_final: 0.7712 (mmm) REVERT: A 253 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6857 (mp) REVERT: A 285 PHE cc_start: 0.8397 (m-80) cc_final: 0.8158 (m-80) REVERT: A 437 PHE cc_start: 0.8356 (t80) cc_final: 0.8071 (t80) REVERT: A 489 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6098 (pp) REVERT: A 492 ASP cc_start: 0.7983 (m-30) cc_final: 0.7515 (p0) REVERT: A 708 ASP cc_start: 0.7758 (m-30) cc_final: 0.6681 (t0) REVERT: A 825 ASP cc_start: 0.7398 (m-30) cc_final: 0.6806 (p0) REVERT: A 1017 ARG cc_start: 0.5828 (ptm-80) cc_final: 0.4925 (mpp80) REVERT: A 1061 MET cc_start: 0.7845 (tpp) cc_final: 0.7322 (mpp) REVERT: B 313 SER cc_start: 0.6475 (t) cc_final: 0.6150 (p) REVERT: B 446 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.5644 (m-10) REVERT: B 453 LYS cc_start: 0.8175 (mppt) cc_final: 0.7846 (mmmt) REVERT: B 472 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: B 509 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.4361 (t80) REVERT: B 521 MET cc_start: 0.8180 (tpp) cc_final: 0.7724 (mtp) REVERT: B 538 GLU cc_start: 0.4236 (pm20) cc_final: 0.3871 (pm20) REVERT: B 553 ASN cc_start: 0.7707 (t0) cc_final: 0.7292 (t0) REVERT: B 554 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8026 (m-40) REVERT: C 109 MET cc_start: 0.7668 (tpp) cc_final: 0.7108 (ptt) REVERT: C 127 MET cc_start: 0.3477 (tpt) cc_final: 0.2436 (mtt) outliers start: 36 outliers final: 29 residues processed: 145 average time/residue: 0.0641 time to fit residues: 14.3570 Evaluate side-chains 153 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.168892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.132151 restraints weight = 16626.793| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.53 r_work: 0.3702 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10033 Z= 0.145 Angle : 0.656 9.393 13602 Z= 0.321 Chirality : 0.043 0.206 1549 Planarity : 0.005 0.072 1743 Dihedral : 4.850 47.959 1347 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.34 % Allowed : 17.64 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1242 helix: 1.78 (0.23), residues: 516 sheet: 0.27 (0.32), residues: 279 loop : -0.82 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 555 TYR 0.020 0.001 TYR B 568 PHE 0.015 0.001 PHE C 41 TRP 0.011 0.001 TRP A 688 HIS 0.018 0.002 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00338 (10033) covalent geometry : angle 0.65603 (13602) hydrogen bonds : bond 0.03918 ( 466) hydrogen bonds : angle 4.67261 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.99 seconds wall clock time: 35 minutes 51.99 seconds (2151.99 seconds total)