Starting phenix.real_space_refine on Fri Jun 13 15:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg0_31103/06_2025/7eg0_31103_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg0_31103/06_2025/7eg0_31103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eg0_31103/06_2025/7eg0_31103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg0_31103/06_2025/7eg0_31103.map" model { file = "/net/cci-nas-00/data/ceres_data/7eg0_31103/06_2025/7eg0_31103_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg0_31103/06_2025/7eg0_31103_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 4 5.21 5 S 98 5.16 5 Cl 4 4.86 5 C 9754 2.51 5 N 2582 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15246 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "B" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' MG': 2, 'J33': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5222 SG CYS B 277 24.263 58.587 74.568 1.00 72.83 S ATOM 5495 SG CYS B 311 24.842 57.312 77.759 1.00 65.90 S ATOM 5501 SG CYS B 312 27.488 59.772 76.145 1.00 64.10 S Restraints were copied for chains: D, C Time building chain proxies: 13.37, per 1000 atoms: 0.88 Number of scatterers: 15246 At special positions: 0 Unit cell: (99.9006, 132.127, 127.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Cl 4 17.00 S 98 16.00 Mg 4 11.99 O 2802 8.00 N 2582 7.00 C 9754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 411 " distance=2.03 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: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 275 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 312 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 277 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 311 " Number of angles added : 6 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 49.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 685 through 690 removed outlier: 4.216A pdb=" N ASN A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 703 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 731 through 746 Processing helix chain 'A' and resid 753 through 769 Processing helix chain 'A' and resid 816 through 820 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 863 through 880 removed outlier: 4.273A pdb=" N ARG A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 907 Processing helix chain 'A' and resid 908 through 911 removed outlier: 6.207A pdb=" N LYS A 911 " --> pdb=" O THR A 908 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 908 through 911' Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 934 through 951 removed outlier: 3.629A pdb=" N ILE A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 956 removed outlier: 3.502A pdb=" N ALA A 955 " --> pdb=" O ASN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 982 removed outlier: 3.521A pdb=" N SER A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'A' and resid 1008 through 1019 removed outlier: 3.555A pdb=" N LEU A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1101 removed outlier: 3.555A pdb=" N GLN A1077 " --> pdb=" O CYS A1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 33 through 54 removed outlier: 3.580A pdb=" N SER B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.772A pdb=" N MET B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 231 removed outlier: 3.738A pdb=" N GLU B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 256 through 271 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.763A pdb=" N GLU B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP B 374 " --> pdb=" O LEU B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 374' Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.122A pdb=" N LYS B 407 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.583A pdb=" N ASP B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 484 Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.961A pdb=" N TYR B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 524 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.517A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 690 removed outlier: 4.216A pdb=" N ASN C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 703 Processing helix chain 'C' and resid 709 through 723 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 731 through 746 Processing helix chain 'C' and resid 753 through 769 Processing helix chain 'C' and resid 816 through 820 Processing helix chain 'C' and resid 822 through 835 Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 853 through 858 Processing helix chain 'C' and resid 863 through 880 removed outlier: 4.272A pdb=" N ARG C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 907 Processing helix chain 'C' and resid 908 through 911 removed outlier: 6.207A pdb=" N LYS C 911 " --> pdb=" O THR C 908 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 908 through 911' Processing helix chain 'C' and resid 912 through 923 Processing helix chain 'C' and resid 934 through 951 removed outlier: 3.500A pdb=" N ARG C 938 " --> pdb=" O ASN C 934 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 956 removed outlier: 3.504A pdb=" N ALA C 955 " --> pdb=" O ASN C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 982 removed outlier: 3.520A pdb=" N SER C 981 " --> pdb=" O ASP C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'C' and resid 1008 through 1019 removed outlier: 3.556A pdb=" N LEU C1012 " --> pdb=" O ILE C1008 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C1019 " --> pdb=" O SER C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1101 removed outlier: 3.555A pdb=" N GLN C1077 " --> pdb=" O CYS C1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 33 through 54 removed outlier: 3.581A pdb=" N SER D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.773A pdb=" N MET D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP D 186 " --> pdb=" O GLY D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 231 removed outlier: 3.738A pdb=" N GLU D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 256 through 271 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 350 through 359 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.762A pdb=" N GLU D 373 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP D 374 " --> pdb=" O LEU D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 374' Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 403 through 414 removed outlier: 4.121A pdb=" N LYS D 407 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 removed outlier: 3.581A pdb=" N ASP D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 484 Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.962A pdb=" N TYR D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 524 " --> pdb=" O SER D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 552 through 559 removed outlier: 3.517A pdb=" N ILE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 772 through 773 Processing sheet with id=AA2, first strand: chain 'A' and resid 1025 through 1026 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.536A pdb=" N SER B 4 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU B 16 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU B 62 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL B 18 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'B' and resid 204 through 207 removed outlier: 6.616A pdb=" N GLU B 205 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AA7, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'B' and resid 442 through 443 removed outlier: 5.893A pdb=" N LEU B 455 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE B 498 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B 457 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 510 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 499 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N CYS B 508 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AB1, first strand: chain 'C' and resid 1025 through 1026 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.535A pdb=" N SER D 4 " --> pdb=" O ASP D 17 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU D 16 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLU D 62 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL D 18 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 204 through 207 removed outlier: 6.617A pdb=" N GLU D 205 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AB6, first strand: chain 'D' and resid 322 through 323 Processing sheet with id=AB7, first strand: chain 'D' and resid 442 through 443 removed outlier: 5.893A pdb=" N LEU D 455 " --> pdb=" O LYS D 496 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE D 498 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR D 457 " --> pdb=" O PHE D 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR D 510 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR D 499 " --> pdb=" O CYS D 508 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N CYS D 508 " --> pdb=" O TYR D 499 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1899 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: 4.72 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4923 1.34 - 1.46: 3482 1.46 - 1.58: 7023 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 15582 Sorted by residual: bond pdb=" C GLU B 393 " pdb=" N ASN B 394 " ideal model delta sigma weight residual 1.329 1.288 0.041 1.79e-02 3.12e+03 5.26e+00 bond pdb=" C GLU D 393 " pdb=" N ASN D 394 " ideal model delta sigma weight residual 1.329 1.288 0.041 1.79e-02 3.12e+03 5.16e+00 bond pdb=" N LYS A1088 " pdb=" CA LYS A1088 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.45e+00 bond pdb=" N LYS C1088 " pdb=" CA LYS C1088 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.29e+00 bond pdb=" N GLU D 345 " pdb=" CA GLU D 345 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.44e-02 4.82e+03 3.85e+00 ... (remaining 15577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 19762 1.50 - 3.00: 1100 3.00 - 4.50: 135 4.50 - 6.00: 39 6.00 - 7.50: 4 Bond angle restraints: 21040 Sorted by residual: angle pdb=" C GLY B 55 " pdb=" N GLY B 56 " pdb=" CA GLY B 56 " ideal model delta sigma weight residual 122.55 119.00 3.55 1.10e+00 8.26e-01 1.04e+01 angle pdb=" C GLY D 55 " pdb=" N GLY D 56 " pdb=" CA GLY D 56 " ideal model delta sigma weight residual 122.55 119.03 3.52 1.10e+00 8.26e-01 1.02e+01 angle pdb=" O ALA D 344 " pdb=" C ALA D 344 " pdb=" N GLU D 345 " ideal model delta sigma weight residual 122.84 119.13 3.71 1.16e+00 7.43e-01 1.02e+01 angle pdb=" N THR D 391 " pdb=" CA THR D 391 " pdb=" C THR D 391 " ideal model delta sigma weight residual 109.81 116.85 -7.04 2.21e+00 2.05e-01 1.01e+01 angle pdb=" N THR B 391 " pdb=" CA THR B 391 " pdb=" C THR B 391 " ideal model delta sigma weight residual 109.81 116.84 -7.03 2.21e+00 2.05e-01 1.01e+01 ... (remaining 21035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8322 17.72 - 35.43: 852 35.43 - 53.14: 172 53.14 - 70.86: 26 70.86 - 88.57: 18 Dihedral angle restraints: 9390 sinusoidal: 3874 harmonic: 5516 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 411 " pdb=" CB CYS B 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.74 -70.74 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CB CYS D 381 " pdb=" SG CYS D 381 " pdb=" SG CYS D 411 " pdb=" CB CYS D 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.71 -70.71 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA TYR B 390 " pdb=" C TYR B 390 " pdb=" N THR B 391 " pdb=" CA THR B 391 " ideal model delta harmonic sigma weight residual 180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 9387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1490 0.040 - 0.080: 592 0.080 - 0.120: 168 0.120 - 0.159: 28 0.159 - 0.199: 8 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA THR B 391 " pdb=" N THR B 391 " pdb=" C THR B 391 " pdb=" CB THR B 391 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA THR D 391 " pdb=" N THR D 391 " pdb=" C THR D 391 " pdb=" CB THR D 391 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA PHE B 550 " pdb=" N PHE B 550 " pdb=" C PHE B 550 " pdb=" CB PHE B 550 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 2283 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 344 " -0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ALA D 344 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA D 344 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU D 345 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 344 " -0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ALA B 344 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA B 344 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU B 345 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1087 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LYS C1087 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS C1087 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS C1088 " -0.019 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 150 2.56 - 3.15: 13299 3.15 - 3.73: 22247 3.73 - 4.32: 32238 4.32 - 4.90: 54786 Nonbonded interactions: 122720 Sorted by model distance: nonbonded pdb=" OD1 ASP A 950 " pdb="MG MG A1202 " model vdw 1.975 2.170 nonbonded pdb=" OD1 ASP C 950 " pdb="MG MG C1202 " model vdw 1.976 2.170 nonbonded pdb=" OD2 ASP A 837 " pdb="MG MG A1202 " model vdw 1.996 2.170 nonbonded pdb=" OD2 ASP C 837 " pdb="MG MG C1202 " model vdw 1.996 2.170 nonbonded pdb=" OD2 ASP A 861 " pdb=" NH1 ARG C 898 " model vdw 2.173 3.120 ... (remaining 122715 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.760 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 43.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 15592 Z= 0.393 Angle : 0.802 16.775 21050 Z= 0.447 Chirality : 0.046 0.199 2286 Planarity : 0.004 0.051 2688 Dihedral : 14.943 88.574 5816 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.91 % Favored : 85.98 % Rotamer: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.18), residues: 1862 helix: -0.66 (0.16), residues: 868 sheet: -2.06 (0.37), residues: 166 loop : -3.50 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 110 HIS 0.005 0.001 HIS C 836 PHE 0.026 0.002 PHE B 145 TYR 0.020 0.002 TYR A 807 ARG 0.009 0.001 ARG C 717 Details of bonding type rmsd hydrogen bonds : bond 0.15422 ( 659) hydrogen bonds : angle 5.51819 ( 1899) metal coordination : bond 0.03799 ( 8) metal coordination : angle 10.17019 ( 6) SS BOND : bond 0.00339 ( 2) SS BOND : angle 2.30949 ( 4) covalent geometry : bond 0.00876 (15582) covalent geometry : angle 0.78319 (21040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 1.979 Fit side-chains REVERT: A 675 GLU cc_start: 0.7199 (mp0) cc_final: 0.6870 (mp0) REVERT: A 717 ARG cc_start: 0.7175 (mmt-90) cc_final: 0.6531 (mmm160) REVERT: A 722 MET cc_start: 0.9197 (mmm) cc_final: 0.8946 (mmm) REVERT: A 736 MET cc_start: 0.8403 (mmm) cc_final: 0.8186 (mmm) REVERT: A 887 ILE cc_start: 0.8683 (tp) cc_final: 0.8463 (tt) REVERT: A 895 LYS cc_start: 0.8170 (tptt) cc_final: 0.7889 (ttpt) REVERT: A 1091 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6452 (mt-10) REVERT: B 144 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 194 GLU cc_start: 0.6404 (pt0) cc_final: 0.6151 (tp30) REVERT: B 219 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7182 (tptp) REVERT: B 270 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7517 (mtmm) REVERT: B 293 TYR cc_start: 0.7024 (m-80) cc_final: 0.6670 (m-80) REVERT: B 299 CYS cc_start: 0.7426 (m) cc_final: 0.7161 (m) REVERT: B 369 TRP cc_start: 0.7215 (m-90) cc_final: 0.6982 (m-10) REVERT: B 483 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8104 (mmtt) REVERT: C 736 MET cc_start: 0.7936 (mmm) cc_final: 0.7316 (mmm) REVERT: C 820 ASN cc_start: 0.8543 (m110) cc_final: 0.8240 (m-40) REVERT: C 835 MET cc_start: 0.8003 (ptt) cc_final: 0.7783 (ptp) REVERT: C 880 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7317 (mmm160) REVERT: C 884 ASN cc_start: 0.7928 (t0) cc_final: 0.7239 (p0) REVERT: C 1084 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7154 (tttt) REVERT: C 1091 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6542 (mt-10) REVERT: D 37 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7647 (ttp80) REVERT: D 194 GLU cc_start: 0.6484 (pt0) cc_final: 0.6136 (tp30) REVERT: D 401 LEU cc_start: 0.8064 (tp) cc_final: 0.7691 (tt) REVERT: D 409 LEU cc_start: 0.8713 (tp) cc_final: 0.8486 (tp) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.3892 time to fit residues: 170.6465 Evaluate side-chains 185 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 867 ASN A 888 ASN A 913 HIS A 943 GLN A1001 GLN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS A1081 GLN B 125 ASN B 172 GLN B 327 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 ASN C 867 ASN C 888 ASN C 943 GLN C1001 GLN ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 HIS C1081 GLN D 26 ASN D 125 ASN D 172 GLN D 327 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111962 restraints weight = 22215.638| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.31 r_work: 0.3173 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15592 Z= 0.125 Angle : 0.573 7.042 21050 Z= 0.297 Chirality : 0.041 0.153 2286 Planarity : 0.004 0.059 2688 Dihedral : 4.641 24.854 2036 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.79 % Allowed : 9.87 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1862 helix: 0.95 (0.17), residues: 864 sheet: -1.16 (0.40), residues: 162 loop : -2.92 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1086 HIS 0.008 0.001 HIS D 367 PHE 0.034 0.002 PHE B 550 TYR 0.021 0.001 TYR B 70 ARG 0.004 0.000 ARG C 733 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 659) hydrogen bonds : angle 3.81006 ( 1899) metal coordination : bond 0.01323 ( 8) metal coordination : angle 3.88383 ( 6) SS BOND : bond 0.00451 ( 2) SS BOND : angle 1.29025 ( 4) covalent geometry : bond 0.00279 (15582) covalent geometry : angle 0.56913 (21040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 1.854 Fit side-chains REVERT: A 675 GLU cc_start: 0.7225 (mp0) cc_final: 0.6852 (mp0) REVERT: A 682 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7092 (pp) REVERT: A 931 ASP cc_start: 0.7439 (t70) cc_final: 0.6944 (t70) REVERT: A 1091 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6529 (mt-10) REVERT: B 37 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7886 (ttp80) REVERT: B 144 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 194 GLU cc_start: 0.6851 (pt0) cc_final: 0.6200 (tp30) REVERT: B 214 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5583 (tp) REVERT: B 219 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7326 (tptp) REVERT: B 270 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7675 (mtmm) REVERT: B 379 HIS cc_start: 0.7474 (t70) cc_final: 0.6958 (t-90) REVERT: B 483 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8180 (mmtt) REVERT: B 552 GLU cc_start: 0.7284 (pm20) cc_final: 0.6943 (pt0) REVERT: B 561 ASP cc_start: 0.6307 (p0) cc_final: 0.5539 (t0) REVERT: C 682 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6617 (pt) REVERT: C 736 MET cc_start: 0.8245 (mmm) cc_final: 0.7789 (mmm) REVERT: C 880 ARG cc_start: 0.7682 (mmt90) cc_final: 0.7470 (mmm-85) REVERT: C 893 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6594 (mm-30) REVERT: C 1084 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7258 (tttt) REVERT: C 1091 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6664 (mt-10) REVERT: D 37 ARG cc_start: 0.8254 (ttm170) cc_final: 0.7904 (ttp80) REVERT: D 170 ASP cc_start: 0.7843 (m-30) cc_final: 0.7386 (p0) REVERT: D 194 GLU cc_start: 0.7029 (pt0) cc_final: 0.6201 (tp30) REVERT: D 479 GLN cc_start: 0.8467 (mt0) cc_final: 0.8228 (mt0) REVERT: D 506 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.6147 (p) REVERT: D 540 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7496 (tpp80) REVERT: D 552 GLU cc_start: 0.7302 (pm20) cc_final: 0.6794 (pt0) REVERT: D 561 ASP cc_start: 0.6210 (p0) cc_final: 0.5977 (t0) outliers start: 30 outliers final: 14 residues processed: 273 average time/residue: 0.2966 time to fit residues: 116.7264 Evaluate side-chains 211 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN C 913 HIS ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107651 restraints weight = 22326.441| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.28 r_work: 0.3107 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15592 Z= 0.174 Angle : 0.580 5.715 21050 Z= 0.303 Chirality : 0.042 0.157 2286 Planarity : 0.004 0.049 2688 Dihedral : 4.595 25.237 2036 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.11 % Allowed : 12.26 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1862 helix: 1.17 (0.18), residues: 868 sheet: -0.59 (0.42), residues: 162 loop : -2.64 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1086 HIS 0.005 0.001 HIS D 323 PHE 0.029 0.002 PHE B 550 TYR 0.019 0.002 TYR B 70 ARG 0.003 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 659) hydrogen bonds : angle 3.80133 ( 1899) metal coordination : bond 0.00811 ( 8) metal coordination : angle 2.77399 ( 6) SS BOND : bond 0.00573 ( 2) SS BOND : angle 0.76351 ( 4) covalent geometry : bond 0.00417 (15582) covalent geometry : angle 0.57836 (21040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 1.944 Fit side-chains REVERT: A 675 GLU cc_start: 0.7153 (mp0) cc_final: 0.6762 (mp0) REVERT: A 893 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 930 ILE cc_start: 0.7572 (mm) cc_final: 0.7177 (tt) REVERT: A 1084 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7598 (tttt) REVERT: A 1091 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6805 (mt-10) REVERT: B 37 ARG cc_start: 0.8446 (ttm170) cc_final: 0.8104 (ttp80) REVERT: B 144 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8555 (tt0) REVERT: B 158 LEU cc_start: 0.3666 (OUTLIER) cc_final: 0.2352 (pt) REVERT: B 194 GLU cc_start: 0.7089 (pt0) cc_final: 0.6281 (tp30) REVERT: B 219 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7544 (tptp) REVERT: B 270 LYS cc_start: 0.7878 (mtpp) cc_final: 0.7675 (mtmm) REVERT: B 299 CYS cc_start: 0.7517 (m) cc_final: 0.7197 (m) REVERT: B 301 TYR cc_start: 0.7007 (m-80) cc_final: 0.6744 (m-10) REVERT: B 379 HIS cc_start: 0.7587 (t70) cc_final: 0.6944 (t-90) REVERT: B 483 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8636 (mtpp) REVERT: C 682 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6961 (pp) REVERT: C 835 MET cc_start: 0.8120 (ptt) cc_final: 0.7701 (ptt) REVERT: C 880 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7701 (mmm160) REVERT: C 893 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7036 (mm-30) REVERT: C 930 ILE cc_start: 0.7435 (mm) cc_final: 0.7090 (tt) REVERT: C 931 ASP cc_start: 0.7547 (t0) cc_final: 0.7042 (t70) REVERT: C 1017 ASP cc_start: 0.7957 (t70) cc_final: 0.7740 (t0) REVERT: C 1084 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7473 (tttt) REVERT: C 1091 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6703 (mt-10) REVERT: D 37 ARG cc_start: 0.8460 (ttm170) cc_final: 0.8185 (ttp80) REVERT: D 158 LEU cc_start: 0.2903 (OUTLIER) cc_final: 0.1469 (pt) REVERT: D 175 ASN cc_start: 0.8628 (m-40) cc_final: 0.8413 (m-40) REVERT: D 193 LYS cc_start: 0.8051 (tppp) cc_final: 0.7838 (mmtt) REVERT: D 194 GLU cc_start: 0.7149 (pt0) cc_final: 0.6304 (tp30) REVERT: D 299 CYS cc_start: 0.7423 (m) cc_final: 0.6946 (m) REVERT: D 506 THR cc_start: 0.6739 (OUTLIER) cc_final: 0.6446 (p) REVERT: D 561 ASP cc_start: 0.6324 (p0) cc_final: 0.5897 (t0) outliers start: 52 outliers final: 32 residues processed: 240 average time/residue: 0.2902 time to fit residues: 102.3839 Evaluate side-chains 210 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 867 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 ASN C 867 ASN ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN D 360 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108990 restraints weight = 22220.267| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.28 r_work: 0.3127 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15592 Z= 0.140 Angle : 0.538 8.399 21050 Z= 0.279 Chirality : 0.041 0.173 2286 Planarity : 0.004 0.046 2688 Dihedral : 4.476 24.825 2036 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.11 % Allowed : 13.70 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1862 helix: 1.39 (0.18), residues: 872 sheet: -0.23 (0.43), residues: 162 loop : -2.56 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1086 HIS 0.003 0.001 HIS D 459 PHE 0.030 0.001 PHE B 550 TYR 0.011 0.001 TYR B 70 ARG 0.003 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 659) hydrogen bonds : angle 3.60821 ( 1899) metal coordination : bond 0.00628 ( 8) metal coordination : angle 2.32479 ( 6) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.73151 ( 4) covalent geometry : bond 0.00331 (15582) covalent geometry : angle 0.53707 (21040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 1.818 Fit side-chains REVERT: A 675 GLU cc_start: 0.7296 (mp0) cc_final: 0.7019 (mp0) REVERT: A 893 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 925 ASN cc_start: 0.6832 (m-40) cc_final: 0.6507 (t0) REVERT: A 930 ILE cc_start: 0.7656 (mm) cc_final: 0.7298 (tt) REVERT: A 1084 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7659 (tttt) REVERT: A 1091 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6787 (mt-10) REVERT: B 144 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8555 (tt0) REVERT: B 158 LEU cc_start: 0.3590 (OUTLIER) cc_final: 0.2329 (pt) REVERT: B 194 GLU cc_start: 0.7119 (pt0) cc_final: 0.6245 (tp30) REVERT: B 213 ARG cc_start: 0.1993 (OUTLIER) cc_final: 0.1766 (tpp-160) REVERT: B 219 LYS cc_start: 0.7746 (ttmt) cc_final: 0.7530 (tptp) REVERT: B 270 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7747 (mtmm) REVERT: B 299 CYS cc_start: 0.7507 (m) cc_final: 0.7137 (m) REVERT: B 301 TYR cc_start: 0.7033 (m-80) cc_final: 0.6751 (m-10) REVERT: B 379 HIS cc_start: 0.7598 (t70) cc_final: 0.6973 (t-90) REVERT: B 483 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8519 (mtpp) REVERT: C 880 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7745 (mmm-85) REVERT: C 893 GLU cc_start: 0.7767 (mt-10) cc_final: 0.6995 (mm-30) REVERT: C 930 ILE cc_start: 0.7577 (mm) cc_final: 0.7298 (tt) REVERT: C 931 ASP cc_start: 0.7527 (t0) cc_final: 0.7046 (t70) REVERT: C 1084 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7578 (tttt) REVERT: C 1091 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6601 (mt-10) REVERT: D 37 ARG cc_start: 0.8445 (ttm170) cc_final: 0.8235 (ttp80) REVERT: D 144 GLU cc_start: 0.8545 (tp30) cc_final: 0.8289 (tm-30) REVERT: D 158 LEU cc_start: 0.3109 (OUTLIER) cc_final: 0.1689 (pt) REVERT: D 175 ASN cc_start: 0.8609 (m-40) cc_final: 0.8378 (m-40) REVERT: D 194 GLU cc_start: 0.7193 (pt0) cc_final: 0.6207 (tp30) REVERT: D 299 CYS cc_start: 0.7404 (m) cc_final: 0.6916 (m) REVERT: D 388 ILE cc_start: 0.9179 (mt) cc_final: 0.8789 (tt) REVERT: D 526 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6962 (mtm180) REVERT: D 561 ASP cc_start: 0.6407 (p0) cc_final: 0.5969 (t0) outliers start: 52 outliers final: 31 residues processed: 233 average time/residue: 0.2934 time to fit residues: 100.0781 Evaluate side-chains 205 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 912 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 526 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 78 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 180 optimal weight: 0.0370 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 HIS ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN C1014 ASN D 360 ASN D 367 HIS D 509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109839 restraints weight = 22461.281| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.29 r_work: 0.3139 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15592 Z= 0.125 Angle : 0.532 8.851 21050 Z= 0.273 Chirality : 0.041 0.151 2286 Planarity : 0.004 0.046 2688 Dihedral : 4.305 23.845 2036 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.81 % Allowed : 14.41 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1862 helix: 1.59 (0.18), residues: 872 sheet: -0.13 (0.43), residues: 164 loop : -2.45 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1086 HIS 0.003 0.001 HIS D 380 PHE 0.029 0.001 PHE B 550 TYR 0.020 0.001 TYR D 301 ARG 0.002 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 659) hydrogen bonds : angle 3.50665 ( 1899) metal coordination : bond 0.00644 ( 8) metal coordination : angle 2.22325 ( 6) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.66020 ( 4) covalent geometry : bond 0.00293 (15582) covalent geometry : angle 0.53083 (21040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.827 Fit side-chains REVERT: A 675 GLU cc_start: 0.7258 (mp0) cc_final: 0.6988 (mp0) REVERT: A 893 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 925 ASN cc_start: 0.6818 (m-40) cc_final: 0.6503 (t0) REVERT: A 1084 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7657 (tttt) REVERT: A 1091 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6773 (mt-10) REVERT: B 144 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8462 (tt0) REVERT: B 158 LEU cc_start: 0.3506 (OUTLIER) cc_final: 0.2327 (pt) REVERT: B 194 GLU cc_start: 0.7143 (pt0) cc_final: 0.6247 (tp30) REVERT: B 219 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7511 (tptp) REVERT: B 221 ILE cc_start: 0.7823 (tt) cc_final: 0.7579 (tt) REVERT: B 299 CYS cc_start: 0.7545 (m) cc_final: 0.7183 (m) REVERT: B 379 HIS cc_start: 0.7554 (t70) cc_final: 0.6844 (t-90) REVERT: B 483 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8486 (mtpp) REVERT: B 526 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7067 (mtt180) REVERT: B 561 ASP cc_start: 0.6516 (p0) cc_final: 0.5818 (t0) REVERT: C 880 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7613 (mmm160) REVERT: C 893 GLU cc_start: 0.7774 (mt-10) cc_final: 0.6992 (mm-30) REVERT: C 930 ILE cc_start: 0.7628 (mm) cc_final: 0.7352 (tt) REVERT: C 1084 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7584 (tttt) REVERT: C 1091 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6620 (mt-10) REVERT: D 144 GLU cc_start: 0.8595 (tp30) cc_final: 0.8343 (tm-30) REVERT: D 158 LEU cc_start: 0.3140 (OUTLIER) cc_final: 0.2378 (mm) REVERT: D 194 GLU cc_start: 0.7084 (pt0) cc_final: 0.6103 (tp30) REVERT: D 220 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6132 (mp0) REVERT: D 299 CYS cc_start: 0.7502 (m) cc_final: 0.7150 (m) REVERT: D 387 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6749 (pmt100) REVERT: D 388 ILE cc_start: 0.9066 (mt) cc_final: 0.8623 (tt) REVERT: D 506 THR cc_start: 0.6308 (OUTLIER) cc_final: 0.6066 (p) REVERT: D 526 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7108 (mtt180) REVERT: D 561 ASP cc_start: 0.6429 (p0) cc_final: 0.6004 (t0) outliers start: 47 outliers final: 30 residues processed: 218 average time/residue: 0.2733 time to fit residues: 88.4811 Evaluate side-chains 210 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 170 optimal weight: 0.9990 chunk 13 optimal weight: 0.0030 chunk 8 optimal weight: 0.8980 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 380 HIS C1014 ASN D 339 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110104 restraints weight = 22279.089| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.30 r_work: 0.3142 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15592 Z= 0.124 Angle : 0.528 9.363 21050 Z= 0.270 Chirality : 0.040 0.149 2286 Planarity : 0.004 0.045 2688 Dihedral : 4.275 23.395 2036 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.17 % Allowed : 14.95 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1862 helix: 1.69 (0.18), residues: 872 sheet: -0.20 (0.44), residues: 168 loop : -2.37 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1086 HIS 0.003 0.001 HIS D 380 PHE 0.029 0.001 PHE B 550 TYR 0.015 0.001 TYR B 301 ARG 0.002 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 659) hydrogen bonds : angle 3.46691 ( 1899) metal coordination : bond 0.00532 ( 8) metal coordination : angle 2.08211 ( 6) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.73044 ( 4) covalent geometry : bond 0.00291 (15582) covalent geometry : angle 0.52731 (21040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 1.869 Fit side-chains REVERT: A 893 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 925 ASN cc_start: 0.6810 (m-40) cc_final: 0.6493 (t0) REVERT: A 1084 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7634 (tttt) REVERT: A 1091 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6748 (mt-10) REVERT: B 144 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 158 LEU cc_start: 0.3652 (OUTLIER) cc_final: 0.2528 (pt) REVERT: B 194 GLU cc_start: 0.7156 (pt0) cc_final: 0.6173 (tp30) REVERT: B 196 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7854 (mt) REVERT: B 219 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7485 (tptp) REVERT: B 221 ILE cc_start: 0.7859 (tt) cc_final: 0.7599 (tt) REVERT: B 299 CYS cc_start: 0.7571 (m) cc_final: 0.7231 (m) REVERT: B 379 HIS cc_start: 0.7590 (t70) cc_final: 0.6872 (t-90) REVERT: B 483 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8500 (mtpp) REVERT: B 506 THR cc_start: 0.6012 (OUTLIER) cc_final: 0.5700 (p) REVERT: B 526 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7289 (mtt180) REVERT: B 561 ASP cc_start: 0.6636 (p0) cc_final: 0.5875 (t0) REVERT: C 736 MET cc_start: 0.8676 (mmm) cc_final: 0.8475 (mmp) REVERT: C 887 ILE cc_start: 0.8575 (tp) cc_final: 0.8348 (tt) REVERT: C 930 ILE cc_start: 0.7654 (mm) cc_final: 0.7402 (tt) REVERT: C 1084 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7555 (tttt) REVERT: C 1091 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6597 (mt-10) REVERT: D 144 GLU cc_start: 0.8586 (tp30) cc_final: 0.8346 (tm-30) REVERT: D 158 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.2553 (mm) REVERT: D 196 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7714 (mt) REVERT: D 299 CYS cc_start: 0.7577 (m) cc_final: 0.7067 (m) REVERT: D 388 ILE cc_start: 0.9079 (mt) cc_final: 0.8664 (tt) REVERT: D 506 THR cc_start: 0.5869 (OUTLIER) cc_final: 0.5634 (p) REVERT: D 526 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7057 (mtt180) outliers start: 53 outliers final: 32 residues processed: 225 average time/residue: 0.2865 time to fit residues: 96.6252 Evaluate side-chains 208 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 ASN B 339 GLN C1014 ASN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110846 restraints weight = 22417.563| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.30 r_work: 0.3156 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15592 Z= 0.110 Angle : 0.519 9.671 21050 Z= 0.264 Chirality : 0.040 0.150 2286 Planarity : 0.003 0.045 2688 Dihedral : 4.139 22.608 2036 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.63 % Allowed : 15.91 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1862 helix: 1.81 (0.18), residues: 872 sheet: -0.08 (0.44), residues: 168 loop : -2.26 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 932 HIS 0.006 0.001 HIS B 380 PHE 0.028 0.001 PHE B 550 TYR 0.013 0.001 TYR D 301 ARG 0.004 0.000 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.02889 ( 659) hydrogen bonds : angle 3.38885 ( 1899) metal coordination : bond 0.00556 ( 8) metal coordination : angle 2.00702 ( 6) SS BOND : bond 0.00574 ( 2) SS BOND : angle 0.59737 ( 4) covalent geometry : bond 0.00255 (15582) covalent geometry : angle 0.51747 (21040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 1.745 Fit side-chains REVERT: A 893 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 925 ASN cc_start: 0.6768 (m-40) cc_final: 0.6463 (t0) REVERT: A 1084 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7628 (tttt) REVERT: A 1091 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6761 (mt-10) REVERT: B 144 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 158 LEU cc_start: 0.3427 (OUTLIER) cc_final: 0.2451 (pt) REVERT: B 194 GLU cc_start: 0.7208 (pt0) cc_final: 0.6279 (tp30) REVERT: B 196 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7826 (mt) REVERT: B 219 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7466 (tptp) REVERT: B 221 ILE cc_start: 0.7858 (tt) cc_final: 0.7593 (tt) REVERT: B 276 PHE cc_start: 0.8146 (m-80) cc_final: 0.7666 (m-80) REVERT: B 299 CYS cc_start: 0.7612 (m) cc_final: 0.7289 (m) REVERT: B 353 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 378 ARG cc_start: 0.7602 (mtp85) cc_final: 0.7257 (mtt-85) REVERT: B 380 HIS cc_start: 0.6789 (m-70) cc_final: 0.5379 (m-70) REVERT: B 483 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8465 (mtpp) REVERT: B 506 THR cc_start: 0.6003 (OUTLIER) cc_final: 0.5776 (p) REVERT: B 526 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7209 (mtt180) REVERT: B 561 ASP cc_start: 0.6341 (p0) cc_final: 0.5836 (t0) REVERT: C 835 MET cc_start: 0.8122 (ptt) cc_final: 0.7815 (ptt) REVERT: C 887 ILE cc_start: 0.8583 (tp) cc_final: 0.8351 (tt) REVERT: C 930 ILE cc_start: 0.7630 (mm) cc_final: 0.7386 (tt) REVERT: C 1084 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7579 (tttt) REVERT: C 1091 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6570 (mt-10) REVERT: D 144 GLU cc_start: 0.8575 (tp30) cc_final: 0.8321 (tm-30) REVERT: D 158 LEU cc_start: 0.3328 (OUTLIER) cc_final: 0.2577 (mm) REVERT: D 196 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7577 (mt) REVERT: D 299 CYS cc_start: 0.7560 (m) cc_final: 0.7203 (m) REVERT: D 388 ILE cc_start: 0.9074 (mt) cc_final: 0.8640 (tt) REVERT: D 506 THR cc_start: 0.5933 (OUTLIER) cc_final: 0.5723 (p) outliers start: 44 outliers final: 27 residues processed: 226 average time/residue: 0.2649 time to fit residues: 89.7454 Evaluate side-chains 208 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 912 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 87 optimal weight: 0.0470 chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 ASN C1014 ASN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111236 restraints weight = 22290.092| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.33 r_work: 0.3159 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15592 Z= 0.109 Angle : 0.518 9.996 21050 Z= 0.265 Chirality : 0.040 0.150 2286 Planarity : 0.003 0.045 2688 Dihedral : 4.107 22.084 2036 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.45 % Allowed : 16.45 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1862 helix: 1.87 (0.18), residues: 872 sheet: -0.02 (0.44), residues: 168 loop : -2.21 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 932 HIS 0.006 0.001 HIS B 380 PHE 0.028 0.001 PHE B 550 TYR 0.012 0.001 TYR B 70 ARG 0.005 0.000 ARG C 880 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 659) hydrogen bonds : angle 3.36847 ( 1899) metal coordination : bond 0.00505 ( 8) metal coordination : angle 1.97017 ( 6) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.72948 ( 4) covalent geometry : bond 0.00252 (15582) covalent geometry : angle 0.51683 (21040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.833 Fit side-chains REVERT: A 893 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 1084 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7601 (tttt) REVERT: A 1091 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6689 (mt-10) REVERT: B 144 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 158 LEU cc_start: 0.3215 (OUTLIER) cc_final: 0.2476 (pt) REVERT: B 194 GLU cc_start: 0.7064 (pt0) cc_final: 0.6263 (tp30) REVERT: B 196 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7779 (mt) REVERT: B 219 LYS cc_start: 0.7637 (ttmt) cc_final: 0.7437 (tptp) REVERT: B 221 ILE cc_start: 0.7793 (tt) cc_final: 0.7551 (tt) REVERT: B 276 PHE cc_start: 0.8084 (m-80) cc_final: 0.7619 (m-80) REVERT: B 299 CYS cc_start: 0.7615 (m) cc_final: 0.7319 (m) REVERT: B 353 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 378 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7175 (mtt-85) REVERT: B 483 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8346 (mtpp) REVERT: B 526 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7151 (mtt180) REVERT: B 561 ASP cc_start: 0.6223 (p0) cc_final: 0.5797 (t0) REVERT: C 887 ILE cc_start: 0.8534 (tp) cc_final: 0.8312 (tt) REVERT: C 930 ILE cc_start: 0.7561 (mm) cc_final: 0.7323 (tt) REVERT: C 1084 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7516 (tttt) REVERT: C 1091 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6559 (mt-10) REVERT: D 144 GLU cc_start: 0.8359 (tp30) cc_final: 0.8100 (tm-30) REVERT: D 158 LEU cc_start: 0.3267 (OUTLIER) cc_final: 0.2031 (pt) REVERT: D 196 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7507 (mt) REVERT: D 254 MET cc_start: 0.6687 (tpt) cc_final: 0.6002 (tpt) REVERT: D 299 CYS cc_start: 0.7582 (m) cc_final: 0.7095 (m) REVERT: D 388 ILE cc_start: 0.8943 (mt) cc_final: 0.8564 (tt) REVERT: D 526 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7030 (mtt180) outliers start: 41 outliers final: 29 residues processed: 215 average time/residue: 0.2592 time to fit residues: 84.7139 Evaluate side-chains 204 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 912 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1014 ASN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109110 restraints weight = 22322.807| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.28 r_work: 0.3131 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15592 Z= 0.141 Angle : 0.545 10.152 21050 Z= 0.281 Chirality : 0.041 0.151 2286 Planarity : 0.004 0.044 2688 Dihedral : 4.240 23.120 2036 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.27 % Allowed : 16.87 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1862 helix: 1.77 (0.18), residues: 870 sheet: -0.06 (0.44), residues: 168 loop : -2.22 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 932 HIS 0.008 0.001 HIS B 380 PHE 0.028 0.001 PHE D 550 TYR 0.014 0.001 TYR B 70 ARG 0.004 0.000 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 659) hydrogen bonds : angle 3.49862 ( 1899) metal coordination : bond 0.00518 ( 8) metal coordination : angle 1.96758 ( 6) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.76270 ( 4) covalent geometry : bond 0.00335 (15582) covalent geometry : angle 0.54444 (21040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.692 Fit side-chains REVERT: A 893 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 925 ASN cc_start: 0.6763 (m-40) cc_final: 0.6478 (t0) REVERT: A 1084 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7648 (tttt) REVERT: A 1091 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6842 (mt-10) REVERT: B 48 MET cc_start: 0.8664 (ttt) cc_final: 0.8406 (ttt) REVERT: B 144 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 194 GLU cc_start: 0.7228 (pt0) cc_final: 0.6252 (tp30) REVERT: B 196 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7901 (mt) REVERT: B 219 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7400 (tptp) REVERT: B 221 ILE cc_start: 0.7895 (tt) cc_final: 0.7632 (tt) REVERT: B 276 PHE cc_start: 0.8212 (m-80) cc_final: 0.7710 (m-80) REVERT: B 299 CYS cc_start: 0.7814 (m) cc_final: 0.7482 (m) REVERT: B 483 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8346 (mtpp) REVERT: B 526 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7171 (mtt180) REVERT: C 736 MET cc_start: 0.8841 (mmm) cc_final: 0.8589 (mmp) REVERT: C 835 MET cc_start: 0.8138 (ptt) cc_final: 0.7834 (ptt) REVERT: C 887 ILE cc_start: 0.8601 (tp) cc_final: 0.8394 (tt) REVERT: C 930 ILE cc_start: 0.7665 (mm) cc_final: 0.7410 (tt) REVERT: C 1084 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7579 (tttt) REVERT: C 1091 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6581 (mt-10) REVERT: D 144 GLU cc_start: 0.8587 (tp30) cc_final: 0.8361 (tm-30) REVERT: D 158 LEU cc_start: 0.3465 (OUTLIER) cc_final: 0.2202 (pt) REVERT: D 196 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7731 (mt) REVERT: D 299 CYS cc_start: 0.7692 (m) cc_final: 0.7195 (m) REVERT: D 388 ILE cc_start: 0.9158 (mt) cc_final: 0.8741 (tt) REVERT: D 526 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7182 (mtt180) outliers start: 38 outliers final: 28 residues processed: 209 average time/residue: 0.2629 time to fit residues: 83.6755 Evaluate side-chains 203 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 1013 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 912 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 526 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 176 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108296 restraints weight = 22414.158| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.29 r_work: 0.3116 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15592 Z= 0.161 Angle : 0.586 13.719 21050 Z= 0.294 Chirality : 0.042 0.219 2286 Planarity : 0.004 0.045 2688 Dihedral : 4.378 24.321 2036 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 2.27 % Allowed : 17.05 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.20), residues: 1862 helix: 1.68 (0.18), residues: 870 sheet: -0.13 (0.44), residues: 168 loop : -2.28 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 322 HIS 0.007 0.001 HIS B 380 PHE 0.030 0.001 PHE B 550 TYR 0.021 0.001 TYR B 70 ARG 0.004 0.000 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 659) hydrogen bonds : angle 3.56611 ( 1899) metal coordination : bond 0.00557 ( 8) metal coordination : angle 2.08217 ( 6) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.81137 ( 4) covalent geometry : bond 0.00384 (15582) covalent geometry : angle 0.58481 (21040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.904 Fit side-chains REVERT: A 881 PRO cc_start: 0.8280 (Cg_endo) cc_final: 0.8018 (Cg_exo) REVERT: A 893 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 925 ASN cc_start: 0.6747 (m-40) cc_final: 0.6453 (t0) REVERT: A 1084 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7665 (tttt) REVERT: A 1091 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6807 (mt-10) REVERT: B 144 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 194 GLU cc_start: 0.7200 (pt0) cc_final: 0.6206 (tp30) REVERT: B 196 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7911 (mt) REVERT: B 219 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7400 (tptp) REVERT: B 221 ILE cc_start: 0.7898 (tt) cc_final: 0.7623 (tt) REVERT: B 276 PHE cc_start: 0.8197 (m-80) cc_final: 0.7754 (m-80) REVERT: B 299 CYS cc_start: 0.7750 (m) cc_final: 0.7246 (m) REVERT: B 301 TYR cc_start: 0.7116 (m-80) cc_final: 0.6692 (m-10) REVERT: B 483 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8398 (mtpp) REVERT: B 526 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7143 (mtt180) REVERT: C 835 MET cc_start: 0.8149 (ptt) cc_final: 0.7859 (ptt) REVERT: C 887 ILE cc_start: 0.8602 (tp) cc_final: 0.8395 (tt) REVERT: C 930 ILE cc_start: 0.7691 (mm) cc_final: 0.7454 (tt) REVERT: C 1084 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7632 (tttt) REVERT: C 1091 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6561 (mt-10) REVERT: D 144 GLU cc_start: 0.8594 (tp30) cc_final: 0.8370 (tm-30) REVERT: D 196 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7742 (mt) REVERT: D 299 CYS cc_start: 0.7747 (m) cc_final: 0.7238 (m) REVERT: D 526 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7000 (mtm180) outliers start: 38 outliers final: 31 residues processed: 205 average time/residue: 0.2683 time to fit residues: 83.7957 Evaluate side-chains 204 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1013 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 912 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 526 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 116 optimal weight: 0.0970 chunk 157 optimal weight: 0.1980 chunk 107 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 92 optimal weight: 0.0030 chunk 100 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115195 restraints weight = 22325.907| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.30 r_work: 0.3212 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15592 Z= 0.097 Angle : 0.548 15.841 21050 Z= 0.268 Chirality : 0.039 0.158 2286 Planarity : 0.003 0.045 2688 Dihedral : 4.021 21.070 2036 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 1.32 % Allowed : 18.06 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1862 helix: 2.01 (0.18), residues: 870 sheet: -0.01 (0.44), residues: 168 loop : -2.18 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 932 HIS 0.003 0.000 HIS B 380 PHE 0.026 0.001 PHE B 550 TYR 0.011 0.001 TYR B 70 ARG 0.004 0.000 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.02486 ( 659) hydrogen bonds : angle 3.30888 ( 1899) metal coordination : bond 0.00631 ( 8) metal coordination : angle 2.60101 ( 6) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.41709 ( 4) covalent geometry : bond 0.00212 (15582) covalent geometry : angle 0.54653 (21040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7033.27 seconds wall clock time: 121 minutes 57.73 seconds (7317.73 seconds total)