Starting phenix.real_space_refine on Wed Mar 4 17:26:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg0_31103/03_2026/7eg0_31103_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg0_31103/03_2026/7eg0_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_31103/03_2026/7eg0_31103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg0_31103/03_2026/7eg0_31103.map" model { file = "/net/cci-nas-00/data/ceres_data/7eg0_31103/03_2026/7eg0_31103_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg0_31103/03_2026/7eg0_31103_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: C, D Time building chain proxies: 4.24, per 1000 atoms: 0.28 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: 1.43 Conformation dependent library (CDL) restraints added in 603.2 milliseconds 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: 0.42 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: 2.41 Time building geometry restraints manager: 1.89 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.730 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: 0.030 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.080 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- 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 : 20.62 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG C 717 TYR 0.020 0.002 TYR A 807 PHE 0.026 0.002 PHE B 145 TRP 0.013 0.002 TRP D 110 HIS 0.005 0.001 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00876 (15582) covalent geometry : angle 0.78319 (21040) SS BOND : bond 0.00339 ( 2) SS BOND : angle 2.30949 ( 4) hydrogen bonds : bond 0.15422 ( 659) hydrogen bonds : angle 5.51819 ( 1899) metal coordination : bond 0.03799 ( 8) metal coordination : angle 10.17019 ( 6) *********************** 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 : 0.532 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: 0.8599 (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: 0.7318 (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: 0.1656 time to fit residues: 72.8370 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 : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS A1081 GLN B 125 ASN 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 ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111417 restraints weight = 22280.575| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.31 r_work: 0.3163 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15592 Z= 0.129 Angle : 0.579 7.434 21050 Z= 0.300 Chirality : 0.042 0.156 2286 Planarity : 0.004 0.059 2688 Dihedral : 4.658 24.936 2036 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 1.97 % Allowed : 9.81 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.20), residues: 1862 helix: 0.95 (0.17), residues: 864 sheet: -1.15 (0.40), residues: 162 loop : -2.91 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 733 TYR 0.020 0.001 TYR B 70 PHE 0.035 0.002 PHE B 550 TRP 0.013 0.002 TRP A1086 HIS 0.007 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00293 (15582) covalent geometry : angle 0.57495 (21040) SS BOND : bond 0.00541 ( 2) SS BOND : angle 1.13517 ( 4) hydrogen bonds : bond 0.03547 ( 659) hydrogen bonds : angle 3.81383 ( 1899) metal coordination : bond 0.01262 ( 8) metal coordination : angle 3.84576 ( 6) *********************** 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: 33 poor density : 251 time to evaluate : 0.458 Fit side-chains REVERT: A 675 GLU cc_start: 0.7187 (mp0) cc_final: 0.6817 (mp0) REVERT: A 682 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7091 (pp) REVERT: A 931 ASP cc_start: 0.7467 (t70) cc_final: 0.6966 (t70) REVERT: A 1091 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6523 (mt-10) REVERT: B 37 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7878 (ttp80) REVERT: B 144 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8433 (tm-30) REVERT: B 194 GLU cc_start: 0.6858 (pt0) cc_final: 0.6197 (tp30) REVERT: B 214 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5558 (tp) REVERT: B 219 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7323 (tptp) REVERT: B 270 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7686 (mtmm) REVERT: B 379 HIS cc_start: 0.7486 (t70) cc_final: 0.6961 (t-90) REVERT: B 483 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8248 (mmtt) REVERT: B 552 GLU cc_start: 0.7289 (pm20) cc_final: 0.6944 (pt0) REVERT: B 561 ASP cc_start: 0.6338 (p0) cc_final: 0.5538 (t0) REVERT: C 682 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6621 (pt) REVERT: C 736 MET cc_start: 0.8268 (mmm) cc_final: 0.7807 (mmm) REVERT: C 880 ARG cc_start: 0.7699 (mmt90) cc_final: 0.7482 (mmm-85) REVERT: C 893 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6620 (mm-30) REVERT: C 979 GLU cc_start: 0.7197 (tt0) cc_final: 0.6980 (tt0) REVERT: C 1084 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7283 (tttt) REVERT: C 1091 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6654 (mt-10) REVERT: D 37 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7912 (ttp80) REVERT: D 170 ASP cc_start: 0.7775 (m-30) cc_final: 0.7385 (p0) REVERT: D 194 GLU cc_start: 0.6986 (pt0) cc_final: 0.6191 (tp30) REVERT: D 378 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6322 (mtt-85) REVERT: D 506 THR cc_start: 0.6430 (OUTLIER) cc_final: 0.6156 (p) REVERT: D 540 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7468 (tpp80) REVERT: D 552 GLU cc_start: 0.7322 (pm20) cc_final: 0.6825 (pt0) REVERT: D 561 ASP cc_start: 0.6195 (p0) cc_final: 0.5950 (t0) outliers start: 33 outliers final: 15 residues processed: 272 average time/residue: 0.1306 time to fit residues: 51.4718 Evaluate side-chains 210 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 202 THR 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 13 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 11 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 479 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112100 restraints weight = 22383.859| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.29 r_work: 0.3161 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 15592 Z= 0.121 Angle : 0.525 6.288 21050 Z= 0.274 Chirality : 0.040 0.153 2286 Planarity : 0.004 0.047 2688 Dihedral : 4.306 22.829 2036 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.51 % Allowed : 12.32 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1862 helix: 1.46 (0.18), residues: 864 sheet: -0.53 (0.42), residues: 164 loop : -2.67 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 129 TYR 0.012 0.001 TYR D 70 PHE 0.031 0.001 PHE D 550 TRP 0.009 0.001 TRP A1086 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00282 (15582) covalent geometry : angle 0.52390 (21040) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.76519 ( 4) hydrogen bonds : bond 0.03306 ( 659) hydrogen bonds : angle 3.59430 ( 1899) metal coordination : bond 0.00799 ( 8) metal coordination : angle 2.43126 ( 6) *********************** 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 250 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.499 Fit side-chains REVERT: A 675 GLU cc_start: 0.7215 (mp0) cc_final: 0.6830 (mp0) REVERT: A 736 MET cc_start: 0.8725 (mmm) cc_final: 0.8231 (mmm) REVERT: A 893 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7164 (mt-10) REVERT: A 930 ILE cc_start: 0.7432 (mm) cc_final: 0.7057 (tt) REVERT: A 1084 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7503 (tttt) REVERT: A 1091 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6690 (mt-10) REVERT: B 37 ARG cc_start: 0.8400 (ttm170) cc_final: 0.7959 (ttp80) REVERT: B 144 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 158 LEU cc_start: 0.3208 (OUTLIER) cc_final: 0.2109 (pt) REVERT: B 194 GLU cc_start: 0.6988 (pt0) cc_final: 0.6328 (tp30) REVERT: B 219 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7386 (tptp) REVERT: B 270 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7614 (mtmm) REVERT: B 379 HIS cc_start: 0.7525 (t70) cc_final: 0.6924 (t-90) REVERT: B 483 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8264 (mmtt) REVERT: B 561 ASP cc_start: 0.6395 (p0) cc_final: 0.5889 (t0) REVERT: C 736 MET cc_start: 0.8444 (mmm) cc_final: 0.7897 (mmm) REVERT: C 835 MET cc_start: 0.7815 (ptt) cc_final: 0.7322 (ptt) REVERT: C 893 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6623 (mm-30) REVERT: C 930 ILE cc_start: 0.7303 (mm) cc_final: 0.6905 (tt) REVERT: C 979 GLU cc_start: 0.7232 (tt0) cc_final: 0.7015 (tt0) REVERT: C 1017 ASP cc_start: 0.7493 (t70) cc_final: 0.7199 (t0) REVERT: C 1022 MET cc_start: 0.8659 (mmt) cc_final: 0.8446 (tpp) REVERT: C 1084 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7279 (tttt) REVERT: C 1091 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6580 (mt-10) REVERT: D 37 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8078 (ttp80) REVERT: D 158 LEU cc_start: 0.2628 (OUTLIER) cc_final: 0.1349 (pp) REVERT: D 170 ASP cc_start: 0.7985 (m-30) cc_final: 0.7405 (p0) REVERT: D 191 ASP cc_start: 0.8310 (m-30) cc_final: 0.7989 (m-30) REVERT: D 194 GLU cc_start: 0.6891 (pt0) cc_final: 0.6227 (tp30) REVERT: D 220 GLU cc_start: 0.6169 (mt-10) cc_final: 0.5714 (mp0) REVERT: D 378 ARG cc_start: 0.7266 (mtp85) cc_final: 0.6786 (mtt-85) REVERT: D 388 ILE cc_start: 0.9107 (mt) cc_final: 0.8746 (tt) REVERT: D 506 THR cc_start: 0.6192 (OUTLIER) cc_final: 0.5963 (p) outliers start: 42 outliers final: 28 residues processed: 239 average time/residue: 0.1173 time to fit residues: 41.9625 Evaluate side-chains 208 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 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 506 THR 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 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 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 Chi-restraints excluded: chain D residue 536 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 155 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 B 339 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 HIS B 380 HIS B 509 GLN C 860 ASN C 867 ASN C1014 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS D 379 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106829 restraints weight = 22476.235| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.28 r_work: 0.3092 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15592 Z= 0.199 Angle : 0.606 8.044 21050 Z= 0.312 Chirality : 0.043 0.166 2286 Planarity : 0.004 0.045 2688 Dihedral : 4.692 25.712 2036 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.47 % Allowed : 13.40 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1862 helix: 1.26 (0.18), residues: 870 sheet: -0.45 (0.42), residues: 166 loop : -2.60 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 387 TYR 0.015 0.002 TYR D 70 PHE 0.030 0.002 PHE B 550 TRP 0.010 0.002 TRP A 692 HIS 0.007 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00477 (15582) covalent geometry : angle 0.60422 (21040) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.79370 ( 4) hydrogen bonds : bond 0.04018 ( 659) hydrogen bonds : angle 3.77577 ( 1899) metal coordination : bond 0.00797 ( 8) metal coordination : angle 2.42245 ( 6) *********************** 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 245 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.587 Fit side-chains REVERT: A 675 GLU cc_start: 0.7267 (mp0) cc_final: 0.6896 (mp0) REVERT: A 736 MET cc_start: 0.8640 (mmm) cc_final: 0.8251 (mmm) REVERT: A 881 PRO cc_start: 0.8343 (Cg_endo) cc_final: 0.8081 (Cg_exo) REVERT: A 893 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 925 ASN cc_start: 0.6918 (m-40) cc_final: 0.6699 (t0) REVERT: A 930 ILE cc_start: 0.7721 (mm) cc_final: 0.7382 (tt) REVERT: A 1084 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7733 (tttt) REVERT: A 1091 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6669 (mt-10) REVERT: B 37 ARG cc_start: 0.8670 (ttm170) cc_final: 0.8327 (ttp80) REVERT: B 144 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8519 (tt0) REVERT: B 158 LEU cc_start: 0.3421 (OUTLIER) cc_final: 0.2380 (pt) REVERT: B 194 GLU cc_start: 0.7165 (pt0) cc_final: 0.6241 (tp30) REVERT: B 219 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7434 (tptp) REVERT: B 221 ILE cc_start: 0.7900 (tt) cc_final: 0.7645 (tt) REVERT: B 270 LYS cc_start: 0.7864 (mtpp) cc_final: 0.7638 (mtmm) REVERT: B 299 CYS cc_start: 0.7573 (m) cc_final: 0.7191 (m) REVERT: B 379 HIS cc_start: 0.7560 (t70) cc_final: 0.6853 (t-90) REVERT: B 483 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8588 (mtpp) REVERT: C 893 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7106 (mm-30) REVERT: C 930 ILE cc_start: 0.7628 (mm) cc_final: 0.7336 (tt) REVERT: C 1084 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7572 (tttt) REVERT: C 1091 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6464 (mt-10) REVERT: C 1093 GLU cc_start: 0.8159 (tp30) cc_final: 0.7953 (tp30) REVERT: D 37 ARG cc_start: 0.8395 (ttm170) cc_final: 0.8186 (ttp80) REVERT: D 158 LEU cc_start: 0.3411 (OUTLIER) cc_final: 0.1963 (pt) REVERT: D 194 GLU cc_start: 0.7186 (pt0) cc_final: 0.6210 (tp30) REVERT: D 299 CYS cc_start: 0.7557 (m) cc_final: 0.7004 (m) REVERT: D 378 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7296 (mtt-85) REVERT: D 388 ILE cc_start: 0.9255 (mt) cc_final: 0.8818 (tt) REVERT: D 506 THR cc_start: 0.6494 (OUTLIER) cc_final: 0.6191 (p) REVERT: D 526 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7109 (mtm180) REVERT: D 536 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8543 (mttp) outliers start: 58 outliers final: 35 residues processed: 237 average time/residue: 0.1251 time to fit residues: 43.5528 Evaluate side-chains 212 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 764 VAL 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 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 324 VAL Chi-restraints excluded: chain B residue 329 VAL 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 B residue 506 THR 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 282 LYS 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 506 THR Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 536 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 462 GLN ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** 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 = 0.3622 r_free = 0.3622 target = 0.135762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109793 restraints weight = 22299.897| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.29 r_work: 0.3135 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15592 Z= 0.123 Angle : 0.534 9.009 21050 Z= 0.273 Chirality : 0.040 0.155 2286 Planarity : 0.004 0.046 2688 Dihedral : 4.349 23.943 2036 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.09 % Allowed : 14.83 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1862 helix: 1.54 (0.18), residues: 872 sheet: -0.08 (0.43), residues: 164 loop : -2.46 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 880 TYR 0.011 0.001 TYR D 301 PHE 0.031 0.001 PHE B 550 TRP 0.008 0.001 TRP A1086 HIS 0.008 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00290 (15582) covalent geometry : angle 0.53241 (21040) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.65523 ( 4) hydrogen bonds : bond 0.03160 ( 659) hydrogen bonds : angle 3.53323 ( 1899) metal coordination : bond 0.00693 ( 8) metal coordination : angle 2.23490 ( 6) *********************** 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 217 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.518 Fit side-chains REVERT: A 675 GLU cc_start: 0.7242 (mp0) cc_final: 0.6962 (mp0) REVERT: A 736 MET cc_start: 0.8557 (mmm) cc_final: 0.8217 (mmm) REVERT: A 893 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 925 ASN cc_start: 0.6800 (m-40) cc_final: 0.6569 (t0) REVERT: A 930 ILE cc_start: 0.7684 (mm) cc_final: 0.7425 (tt) REVERT: A 1084 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7661 (tttt) REVERT: A 1091 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6772 (mt-10) REVERT: B 37 ARG cc_start: 0.8516 (ttm170) cc_final: 0.8313 (ttp80) REVERT: B 144 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8470 (tt0) REVERT: B 158 LEU cc_start: 0.3570 (OUTLIER) cc_final: 0.2357 (pt) REVERT: B 194 GLU cc_start: 0.7163 (pt0) cc_final: 0.6220 (tp30) REVERT: B 221 ILE cc_start: 0.7810 (tt) cc_final: 0.7561 (tt) REVERT: B 299 CYS cc_start: 0.7515 (m) cc_final: 0.7171 (m) REVERT: B 483 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8531 (mtpp) REVERT: B 526 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7039 (mtt180) REVERT: B 561 ASP cc_start: 0.6492 (p0) cc_final: 0.5792 (t0) REVERT: C 893 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7036 (mm-30) REVERT: C 930 ILE cc_start: 0.7609 (mm) cc_final: 0.7355 (tt) REVERT: C 984 LEU cc_start: 0.8626 (mt) cc_final: 0.8416 (mp) REVERT: C 1084 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7581 (tttt) REVERT: C 1091 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6548 (mt-10) REVERT: D 158 LEU cc_start: 0.3289 (OUTLIER) cc_final: 0.1928 (pt) REVERT: D 194 GLU cc_start: 0.7222 (pt0) cc_final: 0.6163 (tp30) REVERT: D 299 CYS cc_start: 0.7485 (m) cc_final: 0.7015 (m) REVERT: D 378 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7089 (mtt-85) REVERT: D 413 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6557 (mm-30) outliers start: 35 outliers final: 28 residues processed: 209 average time/residue: 0.1111 time to fit residues: 35.2948 Evaluate side-chains 195 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 984 LEU 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 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 500 LEU 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 214 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 302 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 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 457 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 147 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 56 optimal weight: 0.0020 chunk 173 optimal weight: 5.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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** ** B 380 HIS ** 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** D 509 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110109 restraints weight = 22304.330| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.29 r_work: 0.3144 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 15592 Z= 0.121 Angle : 0.528 9.471 21050 Z= 0.269 Chirality : 0.040 0.152 2286 Planarity : 0.004 0.045 2688 Dihedral : 4.259 23.393 2036 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.81 % Allowed : 15.01 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1862 helix: 1.68 (0.18), residues: 872 sheet: -0.16 (0.43), residues: 168 loop : -2.36 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 37 TYR 0.021 0.001 TYR D 301 PHE 0.029 0.001 PHE D 550 TRP 0.007 0.001 TRP A1086 HIS 0.006 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00288 (15582) covalent geometry : angle 0.52688 (21040) SS BOND : bond 0.00082 ( 2) SS BOND : angle 0.74024 ( 4) hydrogen bonds : bond 0.03108 ( 659) hydrogen bonds : angle 3.47079 ( 1899) metal coordination : bond 0.00527 ( 8) metal coordination : angle 1.98458 ( 6) *********************** 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 224 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.565 Fit side-chains REVERT: A 736 MET cc_start: 0.8543 (mmm) cc_final: 0.8214 (mmm) REVERT: A 893 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 925 ASN cc_start: 0.6792 (m-40) cc_final: 0.6558 (t0) REVERT: A 930 ILE cc_start: 0.7686 (mm) cc_final: 0.7453 (tt) REVERT: A 1084 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7638 (tttt) REVERT: A 1091 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6761 (mt-10) REVERT: B 144 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 158 LEU cc_start: 0.3671 (OUTLIER) cc_final: 0.2542 (pt) REVERT: B 194 GLU cc_start: 0.7178 (pt0) cc_final: 0.6194 (tp30) REVERT: B 196 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7839 (mt) REVERT: B 221 ILE cc_start: 0.7881 (tt) cc_final: 0.7607 (tt) REVERT: B 299 CYS cc_start: 0.7519 (m) cc_final: 0.7229 (m) REVERT: B 483 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8522 (mtpp) REVERT: B 506 THR cc_start: 0.6130 (OUTLIER) cc_final: 0.5813 (p) REVERT: B 526 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7312 (mtt180) REVERT: B 561 ASP cc_start: 0.6534 (p0) cc_final: 0.5823 (t0) REVERT: C 887 ILE cc_start: 0.8588 (tp) cc_final: 0.8359 (tt) REVERT: C 930 ILE cc_start: 0.7633 (mm) cc_final: 0.7375 (tt) REVERT: C 984 LEU cc_start: 0.8496 (mt) cc_final: 0.8264 (mp) REVERT: C 1084 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7558 (tttt) REVERT: C 1091 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6576 (mt-10) REVERT: D 158 LEU cc_start: 0.3311 (OUTLIER) cc_final: 0.1950 (pt) REVERT: D 194 GLU cc_start: 0.7113 (pt0) cc_final: 0.6167 (tp30) REVERT: D 299 CYS cc_start: 0.7527 (m) cc_final: 0.7172 (m) REVERT: D 378 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7087 (mtt-85) REVERT: D 506 THR cc_start: 0.5970 (OUTLIER) cc_final: 0.5744 (p) REVERT: D 526 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7080 (mtt180) outliers start: 47 outliers final: 34 residues processed: 216 average time/residue: 0.1088 time to fit residues: 35.7653 Evaluate side-chains 205 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 924 VAL 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 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 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 282 LYS 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 411 CYS 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 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 65 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 37 optimal weight: 0.0050 chunk 175 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 130 optimal weight: 0.0470 overall best weight: 1.4096 ------------------------------------------------------------------------------- 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** ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1014 ASN D 339 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.135320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109269 restraints weight = 22245.695| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.29 r_work: 0.3133 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15592 Z= 0.135 Angle : 0.534 9.790 21050 Z= 0.274 Chirality : 0.041 0.152 2286 Planarity : 0.004 0.046 2688 Dihedral : 4.261 23.660 2036 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.93 % Allowed : 15.31 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1862 helix: 1.68 (0.18), residues: 872 sheet: -0.12 (0.43), residues: 168 loop : -2.32 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 397 TYR 0.016 0.001 TYR D 301 PHE 0.029 0.001 PHE D 550 TRP 0.006 0.001 TRP C1086 HIS 0.006 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00325 (15582) covalent geometry : angle 0.53283 (21040) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.69169 ( 4) hydrogen bonds : bond 0.03227 ( 659) hydrogen bonds : angle 3.50110 ( 1899) metal coordination : bond 0.00527 ( 8) metal coordination : angle 1.99726 ( 6) *********************** 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 223 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.458 Fit side-chains REVERT: A 736 MET cc_start: 0.8550 (mmm) cc_final: 0.8200 (mmm) REVERT: A 893 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7464 (mt-10) REVERT: A 925 ASN cc_start: 0.6750 (m-40) cc_final: 0.6523 (t0) REVERT: A 930 ILE cc_start: 0.7743 (mm) cc_final: 0.7490 (tt) REVERT: A 1084 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7651 (tttt) REVERT: A 1091 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6788 (mt-10) REVERT: B 144 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 194 GLU cc_start: 0.7236 (pt0) cc_final: 0.6191 (tp30) REVERT: B 196 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7934 (mt) REVERT: B 221 ILE cc_start: 0.7888 (tt) cc_final: 0.7605 (tt) REVERT: B 299 CYS cc_start: 0.7608 (m) cc_final: 0.7349 (m) REVERT: B 378 ARG cc_start: 0.7602 (mtp85) cc_final: 0.7180 (mtt-85) REVERT: B 483 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8508 (mtpp) REVERT: B 506 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5893 (p) REVERT: B 526 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7072 (mtt180) REVERT: C 887 ILE cc_start: 0.8602 (tp) cc_final: 0.8384 (tt) REVERT: C 930 ILE cc_start: 0.7626 (mm) cc_final: 0.7371 (tt) REVERT: C 984 LEU cc_start: 0.8478 (mt) cc_final: 0.8234 (mp) REVERT: C 1084 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7586 (tttt) REVERT: C 1091 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6455 (mt-10) REVERT: D 158 LEU cc_start: 0.3550 (OUTLIER) cc_final: 0.2201 (pt) REVERT: D 194 GLU cc_start: 0.7162 (pt0) cc_final: 0.6127 (tp30) REVERT: D 196 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7801 (mt) REVERT: D 299 CYS cc_start: 0.7644 (m) cc_final: 0.7120 (m) REVERT: D 378 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7147 (mtt-85) REVERT: D 506 THR cc_start: 0.6065 (OUTLIER) cc_final: 0.5828 (p) REVERT: D 526 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7113 (mtt180) outliers start: 49 outliers final: 34 residues processed: 213 average time/residue: 0.1133 time to fit residues: 36.3747 Evaluate side-chains 210 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 984 LEU 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 371 LEU 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 215 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 282 LYS 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 411 CYS 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 500 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS ** 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 = 0.3618 r_free = 0.3618 target = 0.135574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109514 restraints weight = 22509.444| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.29 r_work: 0.3134 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 15592 Z= 0.130 Angle : 0.543 12.106 21050 Z= 0.274 Chirality : 0.041 0.157 2286 Planarity : 0.004 0.046 2688 Dihedral : 4.253 23.591 2036 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.75 % Allowed : 16.21 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1862 helix: 1.75 (0.18), residues: 872 sheet: -0.05 (0.44), residues: 168 loop : -2.31 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 397 TYR 0.015 0.001 TYR D 301 PHE 0.029 0.001 PHE D 550 TRP 0.006 0.001 TRP C1086 HIS 0.005 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00310 (15582) covalent geometry : angle 0.54156 (21040) SS BOND : bond 0.00054 ( 2) SS BOND : angle 0.90206 ( 4) hydrogen bonds : bond 0.03133 ( 659) hydrogen bonds : angle 3.47346 ( 1899) metal coordination : bond 0.00491 ( 8) metal coordination : angle 1.93820 ( 6) *********************** 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 221 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.561 Fit side-chains REVERT: A 736 MET cc_start: 0.8541 (mmm) cc_final: 0.8187 (mmm) REVERT: A 893 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 925 ASN cc_start: 0.6695 (m-40) cc_final: 0.6489 (t0) REVERT: A 930 ILE cc_start: 0.7747 (mm) cc_final: 0.7484 (tt) REVERT: A 1084 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7660 (tttt) REVERT: A 1091 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6801 (mt-10) REVERT: B 144 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 194 GLU cc_start: 0.7180 (pt0) cc_final: 0.6298 (tp30) REVERT: B 196 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7855 (mt) REVERT: B 221 ILE cc_start: 0.7962 (tt) cc_final: 0.7686 (tt) REVERT: B 276 PHE cc_start: 0.8195 (m-80) cc_final: 0.7750 (m-80) REVERT: B 299 CYS cc_start: 0.7616 (m) cc_final: 0.7305 (m) REVERT: B 378 ARG cc_start: 0.7593 (mtp85) cc_final: 0.7159 (mtt-85) REVERT: B 380 HIS cc_start: 0.6542 (m-70) cc_final: 0.5844 (m-70) REVERT: B 483 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8472 (mtpp) REVERT: B 506 THR cc_start: 0.5762 (OUTLIER) cc_final: 0.5509 (p) REVERT: B 526 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7078 (mtt180) REVERT: C 887 ILE cc_start: 0.8619 (tp) cc_final: 0.8408 (tt) REVERT: C 930 ILE cc_start: 0.7635 (mm) cc_final: 0.7389 (tt) REVERT: C 984 LEU cc_start: 0.8437 (mt) cc_final: 0.8187 (mp) REVERT: C 1084 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7580 (tttt) REVERT: C 1091 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6450 (mt-10) REVERT: D 158 LEU cc_start: 0.3599 (OUTLIER) cc_final: 0.2237 (pt) REVERT: D 194 GLU cc_start: 0.7192 (pt0) cc_final: 0.6137 (tp30) REVERT: D 196 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7822 (mt) REVERT: D 299 CYS cc_start: 0.7609 (m) cc_final: 0.7145 (m) REVERT: D 378 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7150 (mtt-85) REVERT: D 526 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7056 (mtt180) outliers start: 46 outliers final: 32 residues processed: 210 average time/residue: 0.1085 time to fit residues: 34.7524 Evaluate side-chains 205 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 984 LEU 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 371 LEU 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 215 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 282 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 69 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 147 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 40 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN B 360 ASN D 360 ASN D 479 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112315 restraints weight = 22091.873| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.30 r_work: 0.3172 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 15592 Z= 0.103 Angle : 0.527 10.059 21050 Z= 0.264 Chirality : 0.039 0.167 2286 Planarity : 0.003 0.046 2688 Dihedral : 4.085 21.724 2036 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.97 % Allowed : 17.05 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1862 helix: 1.91 (0.18), residues: 872 sheet: 0.03 (0.44), residues: 168 loop : -2.24 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 397 TYR 0.013 0.001 TYR D 301 PHE 0.028 0.001 PHE D 550 TRP 0.008 0.001 TRP A 932 HIS 0.005 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00237 (15582) covalent geometry : angle 0.52620 (21040) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.49417 ( 4) hydrogen bonds : bond 0.02769 ( 659) hydrogen bonds : angle 3.36016 ( 1899) metal coordination : bond 0.00515 ( 8) metal coordination : angle 2.02722 ( 6) *********************** 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 214 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.575 Fit side-chains REVERT: A 736 MET cc_start: 0.8502 (mmm) cc_final: 0.8160 (mmm) REVERT: A 893 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 925 ASN cc_start: 0.6559 (m-40) cc_final: 0.6313 (t0) REVERT: A 1084 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7654 (tttt) REVERT: A 1091 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6807 (mt-10) REVERT: B 144 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 194 GLU cc_start: 0.7260 (pt0) cc_final: 0.6309 (tp30) REVERT: B 221 ILE cc_start: 0.7885 (tt) cc_final: 0.7589 (tt) REVERT: B 257 LEU cc_start: 0.7465 (mt) cc_final: 0.7174 (mp) REVERT: B 276 PHE cc_start: 0.8105 (m-80) cc_final: 0.7724 (m-80) REVERT: B 299 CYS cc_start: 0.7704 (m) cc_final: 0.7441 (m) REVERT: B 353 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 378 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7353 (mtt-85) REVERT: B 483 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8319 (mtpp) REVERT: C 887 ILE cc_start: 0.8574 (tp) cc_final: 0.8354 (tt) REVERT: C 930 ILE cc_start: 0.7606 (mm) cc_final: 0.7341 (tt) REVERT: C 1084 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7558 (tttt) REVERT: C 1091 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6572 (mt-10) REVERT: D 158 LEU cc_start: 0.3474 (OUTLIER) cc_final: 0.2170 (pt) REVERT: D 194 GLU cc_start: 0.7109 (pt0) cc_final: 0.6127 (tp30) REVERT: D 196 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7876 (mt) REVERT: D 254 MET cc_start: 0.6828 (tpt) cc_final: 0.6135 (tpt) REVERT: D 299 CYS cc_start: 0.7695 (m) cc_final: 0.7200 (m) REVERT: D 378 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7264 (mtt-85) REVERT: D 526 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7064 (mtt180) outliers start: 33 outliers final: 25 residues processed: 208 average time/residue: 0.1087 time to fit residues: 34.7620 Evaluate side-chains 195 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 301 TYR 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 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET 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 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 282 LYS 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 526 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111436 restraints weight = 22357.933| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.33 r_work: 0.3159 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15592 Z= 0.110 Angle : 0.534 10.088 21050 Z= 0.271 Chirality : 0.040 0.149 2286 Planarity : 0.004 0.045 2688 Dihedral : 4.053 21.647 2036 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 2.09 % Allowed : 16.75 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1862 helix: 1.97 (0.18), residues: 872 sheet: 0.10 (0.44), residues: 168 loop : -2.20 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 397 TYR 0.013 0.001 TYR D 301 PHE 0.027 0.001 PHE B 550 TRP 0.010 0.001 TRP A 932 HIS 0.005 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00257 (15582) covalent geometry : angle 0.53336 (21040) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.63066 ( 4) hydrogen bonds : bond 0.02821 ( 659) hydrogen bonds : angle 3.37835 ( 1899) metal coordination : bond 0.00442 ( 8) metal coordination : angle 1.78509 ( 6) ********************** 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 205 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.609 Fit side-chains REVERT: A 736 MET cc_start: 0.8400 (mmm) cc_final: 0.8041 (mmm) REVERT: A 893 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7219 (mt-10) REVERT: A 1084 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7603 (tttt) REVERT: A 1091 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6736 (mt-10) REVERT: B 144 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 194 GLU cc_start: 0.7121 (pt0) cc_final: 0.6272 (tp30) REVERT: B 196 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 221 ILE cc_start: 0.7852 (tt) cc_final: 0.7590 (tt) REVERT: B 257 LEU cc_start: 0.7434 (mt) cc_final: 0.7202 (mp) REVERT: B 276 PHE cc_start: 0.8044 (m-80) cc_final: 0.7776 (m-80) REVERT: B 299 CYS cc_start: 0.7721 (m) cc_final: 0.7516 (m) REVERT: B 353 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 378 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7178 (mtt-85) REVERT: C 887 ILE cc_start: 0.8534 (tp) cc_final: 0.8319 (tt) REVERT: C 930 ILE cc_start: 0.7574 (mm) cc_final: 0.7323 (tt) REVERT: C 1084 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7516 (tttt) REVERT: C 1091 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6552 (mt-10) REVERT: D 158 LEU cc_start: 0.3405 (OUTLIER) cc_final: 0.2195 (pt) REVERT: D 194 GLU cc_start: 0.6964 (pt0) cc_final: 0.6107 (tp30) REVERT: D 196 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7841 (mt) REVERT: D 254 MET cc_start: 0.6769 (tpt) cc_final: 0.6056 (tpt) REVERT: D 299 CYS cc_start: 0.7673 (m) cc_final: 0.7183 (m) REVERT: D 378 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7177 (mtt-85) REVERT: D 526 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6958 (mtt180) outliers start: 35 outliers final: 27 residues processed: 199 average time/residue: 0.1121 time to fit residues: 34.4669 Evaluate side-chains 201 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 984 LEU 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 301 TYR 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 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET 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 264 ILE Chi-restraints excluded: chain D residue 282 LYS 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 526 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 0.0170 chunk 69 optimal weight: 0.0370 chunk 83 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.140509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114510 restraints weight = 22117.680| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.31 r_work: 0.3204 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 15592 Z= 0.100 Angle : 0.531 11.634 21050 Z= 0.265 Chirality : 0.039 0.173 2286 Planarity : 0.003 0.043 2688 Dihedral : 3.955 20.342 2036 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 1.97 % Allowed : 17.05 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1862 helix: 2.08 (0.18), residues: 872 sheet: 0.17 (0.44), residues: 168 loop : -2.16 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 397 TYR 0.015 0.001 TYR A 716 PHE 0.026 0.001 PHE D 550 TRP 0.012 0.001 TRP A 932 HIS 0.005 0.000 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00228 (15582) covalent geometry : angle 0.52985 (21040) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.37696 ( 4) hydrogen bonds : bond 0.02600 ( 659) hydrogen bonds : angle 3.30812 ( 1899) metal coordination : bond 0.00517 ( 8) metal coordination : angle 1.95907 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.81 seconds wall clock time: 56 minutes 59.49 seconds (3419.49 seconds total)