Starting phenix.real_space_refine on Thu Aug 6 17:56:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpp_37722/08_2026/8wpp_37722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpp_37722/08_2026/8wpp_37722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpp_37722/08_2026/8wpp_37722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpp_37722/08_2026/8wpp_37722.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpp_37722/08_2026/8wpp_37722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpp_37722/08_2026/8wpp_37722.cif" } resolution = 3.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 77 5.16 5 C 10515 2.51 5 N 2830 2.21 5 O 3335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16826 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8223 Classifications: {'peptide': 1006} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 968} Chain: "B" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3557 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 426} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1773 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 525 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "F" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 481 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 778 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Time building chain proxies: 2.60, per 1000 atoms: 0.15 Number of scatterers: 16826 At special positions: 0 Unit cell: (108.73, 136.12, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 69 15.00 O 3335 8.00 N 2830 7.00 C 10515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 446.5 milliseconds 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 19 sheets defined 46.4% alpha, 18.9% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.505A pdb=" N SER A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.665A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.802A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.856A pdb=" N GLY A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 621 through 643 Processing helix chain 'A' and resid 646 through 673 removed outlier: 4.314A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 836 through 857 removed outlier: 3.501A pdb=" N GLY A 857 " --> pdb=" O MET A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 883 removed outlier: 3.727A pdb=" N VAL A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.658A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 983 removed outlier: 4.337A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 removed outlier: 4.092A pdb=" N CYS A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 19 Processing helix chain 'B' and resid 24 through 43 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 147 through 158 removed outlier: 4.294A pdb=" N ILE B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.579A pdb=" N SER B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 298 Processing helix chain 'B' and resid 315 through 323 removed outlier: 4.296A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 removed outlier: 3.677A pdb=" N LEU B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.657A pdb=" N LEU B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.919A pdb=" N CYS B 394 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 406 through 426 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.509A pdb=" N GLU C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 22 through 38 removed outlier: 3.797A pdb=" N GLU C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.698A pdb=" N PHE C 49 " --> pdb=" O PRO C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 133 through 152 removed outlier: 5.439A pdb=" N LYS C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 211 through 214 Processing helix chain 'D' and resid 142 through 174 removed outlier: 3.583A pdb=" N ASP D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 174 " --> pdb=" O VAL D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 198 Processing helix chain 'E' and resid 141 through 164 Processing helix chain 'E' and resid 168 through 196 Processing helix chain 'F' and resid 142 through 173 removed outlier: 4.025A pdb=" N LEU F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 200 Processing helix chain 'G' and resid 141 through 164 Processing helix chain 'G' and resid 168 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 136 removed outlier: 7.081A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.161A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 58 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 56 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.317A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.581A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 3.677A pdb=" N LEU A 361 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 372 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 420 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 405 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.916A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 822 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.775A pdb=" N PHE B 69 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 167 removed outlier: 3.924A pdb=" N LEU B 166 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 208 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 103 through 104 removed outlier: 4.275A pdb=" N MET B 95 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG B 128 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 132 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 220 through 227 Processing sheet with id=AB6, first strand: chain 'B' and resid 220 through 227 removed outlier: 3.528A pdb=" N VAL B 237 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 273 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 264 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 218 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 379 Processing sheet with id=AB8, first strand: chain 'C' and resid 2 through 5 removed outlier: 3.518A pdb=" N ILE C 13 " --> pdb=" O VAL C 4 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 116 through 120 Processing sheet with id=AC1, first strand: chain 'C' and resid 107 through 108 821 hydrogen bonds defined for protein. 2391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4079 1.33 - 1.46: 3945 1.46 - 1.58: 9016 1.58 - 1.70: 137 1.70 - 1.82: 120 Bond restraints: 17297 Sorted by residual: bond pdb=" CG PRO A 821 " pdb=" CD PRO A 821 " ideal model delta sigma weight residual 1.503 1.258 0.245 3.40e-02 8.65e+02 5.21e+01 bond pdb=" C3' DA H 27 " pdb=" O3' DA H 27 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" N PRO A 821 " pdb=" CD PRO A 821 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" C3' DT H 32 " pdb=" C2' DT H 32 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" CB PRO A 821 " pdb=" CG PRO A 821 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 ... (remaining 17292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 23357 2.92 - 5.84: 259 5.84 - 8.76: 42 8.76 - 11.68: 7 11.68 - 14.60: 5 Bond angle restraints: 23670 Sorted by residual: angle pdb=" CA PRO A 821 " pdb=" N PRO A 821 " pdb=" CD PRO A 821 " ideal model delta sigma weight residual 112.00 97.90 14.10 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N PRO A 821 " pdb=" CD PRO A 821 " pdb=" CG PRO A 821 " ideal model delta sigma weight residual 103.20 88.60 14.60 1.50e+00 4.44e-01 9.47e+01 angle pdb=" CA PRO A 821 " pdb=" CB PRO A 821 " pdb=" CG PRO A 821 " ideal model delta sigma weight residual 104.50 94.33 10.17 1.90e+00 2.77e-01 2.86e+01 angle pdb=" O4' DC I 37 " pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 108.00 111.33 -3.33 7.00e-01 2.04e+00 2.26e+01 angle pdb=" C3' DA H 27 " pdb=" O3' DA H 27 " pdb=" P DC H 28 " ideal model delta sigma weight residual 119.70 125.18 -5.48 1.20e+00 6.94e-01 2.09e+01 ... (remaining 23665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 9725 30.52 - 61.04: 564 61.04 - 91.56: 21 91.56 - 122.08: 0 122.08 - 152.60: 1 Dihedral angle restraints: 10311 sinusoidal: 4660 harmonic: 5651 Sorted by residual: dihedral pdb=" CA GLU G 168 " pdb=" C GLU G 168 " pdb=" N ASP G 169 " pdb=" CA ASP G 169 " ideal model delta harmonic sigma weight residual -180.00 -146.00 -34.00 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA ARG A 497 " pdb=" C ARG A 497 " pdb=" N ALA A 498 " pdb=" CA ALA A 498 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA HIS B -9 " pdb=" C HIS B -9 " pdb=" N HIS B -8 " pdb=" CA HIS B -8 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 10308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2315 0.074 - 0.148: 332 0.148 - 0.222: 33 0.222 - 0.297: 2 0.297 - 0.371: 4 Chirality restraints: 2686 Sorted by residual: chirality pdb=" CB ILE C 117 " pdb=" CA ILE C 117 " pdb=" CG1 ILE C 117 " pdb=" CG2 ILE C 117 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL E 166 " pdb=" CA VAL E 166 " pdb=" CG1 VAL E 166 " pdb=" CG2 VAL E 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB ILE B 45 " pdb=" CA ILE B 45 " pdb=" CG1 ILE B 45 " pdb=" CG2 ILE B 45 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 2683 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 820 " 0.107 5.00e-02 4.00e+02 1.48e-01 3.52e+01 pdb=" N PRO A 821 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 930 " 0.017 2.00e-02 2.50e+03 2.42e-02 1.02e+01 pdb=" CG PHE A 930 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 930 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 930 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 930 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 930 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 930 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 668 " -0.023 2.00e-02 2.50e+03 1.78e-02 6.35e+00 pdb=" CG TYR A 668 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 668 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 668 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 668 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 668 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 668 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 668 " -0.001 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3082 2.78 - 3.31: 15354 3.31 - 3.84: 30760 3.84 - 4.37: 35467 4.37 - 4.90: 58403 Nonbonded interactions: 143066 Sorted by model distance: nonbonded pdb=" OH TYR A 162 " pdb=" OE1 GLU A 476 " model vdw 2.245 3.040 nonbonded pdb=" O SER F 161 " pdb=" OG1 THR F 165 " model vdw 2.305 3.040 nonbonded pdb=" OG SER C 153 " pdb=" OD2 ASP C 205 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 89 " pdb=" OD1 ASN B 115 " model vdw 2.313 3.040 nonbonded pdb=" O PHE F 179 " pdb=" OG1 THR F 183 " model vdw 2.315 3.040 ... (remaining 143061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 139 through 201 or (resid 202 through 203 and (name N or n \ ame CA or name C or name O or name CB )))) selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 1.670 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.005 0.245 17297 Z= 0.302 Angle : 0.870 14.597 23670 Z= 0.526 Chirality : 0.053 0.371 2686 Planarity : 0.007 0.148 2755 Dihedral : 16.997 152.597 6655 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.85 (0.17), residues: 1895 helix: -1.24 (0.15), residues: 833 sheet: -0.76 (0.28), residues: 322 loop : -1.20 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 234 TYR 0.043 0.002 TYR A 668 PHE 0.055 0.002 PHE A 930 TRP 0.041 0.002 TRP C 19 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.30 (17297) covalent geometry : angle 0.87012 / 0.53 (23670) hydrogen bonds : bond 0.16308 / 11.00 ( 889) hydrogen bonds : angle 7.46542 / 5.11 ( 2547) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.526 Fit side-chains REVERT: A 519 ARG cc_start: 0.7309 (mtt-85) cc_final: 0.7080 (mtt90) REVERT: B 263 PHE cc_start: 0.7240 (m-80) cc_final: 0.7008 (m-80) REVERT: C 55 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.6724 (mm110) REVERT: C 58 ARG cc_start: 0.6720 (mpt-90) cc_final: 0.6304 (mmt180) REVERT: D 182 MET cc_start: 0.4629 (mmp) cc_final: 0.3948 (ptm) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.1123 time to fit residues: 48.2195 Evaluate side-chains 206 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 HIS A 147 ASN A 336 GLN A 426 ASN A 543 ASN A 785 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.214006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.170720 restraints weight = 18572.025| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.62 r_work: 0.3476 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17297 Z= 0.254 Angle : 0.660 6.981 23670 Z= 0.364 Chirality : 0.047 0.292 2686 Planarity : 0.005 0.066 2755 Dihedral : 17.977 158.382 2854 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.91 % Allowed : 7.77 % Favored : 91.32 % 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: -0.99 (0.18), residues: 1895 helix: -0.06 (0.17), residues: 833 sheet: -1.05 (0.26), residues: 333 loop : -0.97 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 135 TYR 0.027 0.002 TYR A 668 PHE 0.034 0.002 PHE A 791 TRP 0.014 0.002 TRP A 8 HIS 0.008 0.002 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (17297) covalent geometry : angle 0.65953 / 0.36 (23670) hydrogen bonds : bond 0.04605 / 3.06 ( 889) hydrogen bonds : angle 5.52574 / 3.77 ( 2547) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.583 Fit side-chains REVERT: A 211 GLN cc_start: 0.6850 (pm20) cc_final: 0.6541 (tp40) REVERT: A 268 ASP cc_start: 0.8364 (m-30) cc_final: 0.7559 (m-30) REVERT: A 519 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.7471 (mtt90) REVERT: B 67 LYS cc_start: 0.7392 (mttt) cc_final: 0.7107 (ttmt) REVERT: B 218 MET cc_start: 0.7306 (mtp) cc_final: 0.6955 (mtt) REVERT: C 58 ARG cc_start: 0.7623 (mpt-90) cc_final: 0.7134 (mmt180) REVERT: D 182 MET cc_start: 0.4199 (mmp) cc_final: 0.3399 (ptm) outliers start: 16 outliers final: 11 residues processed: 228 average time/residue: 0.1209 time to fit residues: 42.0085 Evaluate side-chains 201 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 161 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 351 GLN B 374 ASN B 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.215554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.172983 restraints weight = 18590.103| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.59 r_work: 0.3508 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17297 Z= 0.151 Angle : 0.566 8.814 23670 Z= 0.310 Chirality : 0.043 0.317 2686 Planarity : 0.004 0.047 2755 Dihedral : 17.909 160.270 2851 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.03 % Allowed : 9.94 % Favored : 89.03 % 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: -0.60 (0.18), residues: 1895 helix: 0.45 (0.17), residues: 831 sheet: -1.14 (0.27), residues: 322 loop : -0.87 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 39 TYR 0.018 0.001 TYR A 668 PHE 0.018 0.001 PHE A 9 TRP 0.009 0.001 TRP B 136 HIS 0.005 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (17297) covalent geometry : angle 0.56608 / 0.31 (23670) hydrogen bonds : bond 0.04107 / 2.74 ( 889) hydrogen bonds : angle 5.12236 / 3.50 ( 2547) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.399 Fit side-chains REVERT: A 181 ASN cc_start: 0.7806 (m-40) cc_final: 0.7552 (m-40) REVERT: A 211 GLN cc_start: 0.6929 (pm20) cc_final: 0.6654 (tp40) REVERT: A 357 MET cc_start: 0.8071 (mmp) cc_final: 0.7795 (mmp) REVERT: A 519 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7515 (mtt90) REVERT: A 602 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6856 (pt0) REVERT: A 724 MET cc_start: 0.7828 (tmm) cc_final: 0.7502 (tmm) REVERT: B 67 LYS cc_start: 0.7399 (mttt) cc_final: 0.7187 (ttmt) REVERT: B 127 LEU cc_start: 0.7943 (mt) cc_final: 0.7680 (mt) REVERT: B 208 GLN cc_start: 0.6352 (mp10) cc_final: 0.6045 (mp10) REVERT: B 218 MET cc_start: 0.7196 (mtp) cc_final: 0.6929 (mtt) REVERT: B 351 GLN cc_start: 0.8072 (tt0) cc_final: 0.7819 (tt0) REVERT: B 365 GLU cc_start: 0.7846 (tp30) cc_final: 0.7600 (tm-30) REVERT: C 58 ARG cc_start: 0.7494 (mpt-90) cc_final: 0.7063 (mmt180) REVERT: D 182 MET cc_start: 0.4272 (mmp) cc_final: 0.3525 (ptm) outliers start: 18 outliers final: 8 residues processed: 219 average time/residue: 0.1085 time to fit residues: 37.0733 Evaluate side-chains 193 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN A 426 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.212663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169587 restraints weight = 18622.165| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.84 r_work: 0.3413 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17297 Z= 0.191 Angle : 0.574 9.664 23670 Z= 0.313 Chirality : 0.043 0.325 2686 Planarity : 0.004 0.047 2755 Dihedral : 17.975 160.581 2851 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.43 % Allowed : 11.19 % Favored : 87.38 % 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: -0.45 (0.18), residues: 1895 helix: 0.64 (0.17), residues: 829 sheet: -1.25 (0.27), residues: 323 loop : -0.79 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 39 TYR 0.028 0.002 TYR A 668 PHE 0.018 0.002 PHE A 791 TRP 0.011 0.001 TRP B 136 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (17297) covalent geometry : angle 0.57369 / 0.31 (23670) hydrogen bonds : bond 0.03975 / 2.64 ( 889) hydrogen bonds : angle 4.94520 / 3.39 ( 2547) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.626 Fit side-chains REVERT: A 211 GLN cc_start: 0.7170 (pm20) cc_final: 0.6838 (tp40) REVERT: A 345 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8322 (ptpt) REVERT: A 357 MET cc_start: 0.8222 (mmp) cc_final: 0.7917 (mmp) REVERT: A 519 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7487 (mtt90) REVERT: A 546 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8393 (mt) REVERT: A 724 MET cc_start: 0.8026 (tmm) cc_final: 0.7740 (tmm) REVERT: B -10 MET cc_start: 0.5809 (ptm) cc_final: 0.5592 (ptm) REVERT: B 67 LYS cc_start: 0.7263 (mttt) cc_final: 0.7021 (ttmt) REVERT: B 127 LEU cc_start: 0.7952 (mt) cc_final: 0.7636 (mt) REVERT: B 351 GLN cc_start: 0.8102 (tt0) cc_final: 0.7765 (tt0) REVERT: C 58 ARG cc_start: 0.7682 (mpt-90) cc_final: 0.7247 (mmt180) REVERT: D 182 MET cc_start: 0.4435 (mmp) cc_final: 0.3647 (ptm) outliers start: 25 outliers final: 15 residues processed: 215 average time/residue: 0.1177 time to fit residues: 38.9534 Evaluate side-chains 197 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 0.0000 chunk 28 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.214169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171613 restraints weight = 18517.689| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.73 r_work: 0.3454 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17297 Z= 0.139 Angle : 0.542 10.054 23670 Z= 0.295 Chirality : 0.042 0.324 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.916 161.106 2851 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.54 % Allowed : 11.94 % Favored : 86.52 % 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: -0.28 (0.19), residues: 1895 helix: 0.82 (0.17), residues: 831 sheet: -1.34 (0.27), residues: 332 loop : -0.64 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 39 TYR 0.017 0.001 TYR A 190 PHE 0.013 0.001 PHE A 9 TRP 0.008 0.001 TRP B 136 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (17297) covalent geometry : angle 0.54226 / 0.30 (23670) hydrogen bonds : bond 0.03685 / 2.46 ( 889) hydrogen bonds : angle 4.82051 / 3.31 ( 2547) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.582 Fit side-chains REVERT: A 130 GLN cc_start: 0.7739 (pm20) cc_final: 0.7536 (pt0) REVERT: A 346 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 357 MET cc_start: 0.8205 (mmp) cc_final: 0.7897 (mmp) REVERT: A 519 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7554 (mtt-85) REVERT: A 546 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8392 (mt) REVERT: A 724 MET cc_start: 0.7935 (tmm) cc_final: 0.7673 (tmm) REVERT: B 67 LYS cc_start: 0.7198 (mttt) cc_final: 0.6970 (ttmt) REVERT: B 127 LEU cc_start: 0.7908 (mt) cc_final: 0.7622 (mt) REVERT: B 218 MET cc_start: 0.7321 (mtp) cc_final: 0.7067 (mtt) REVERT: C 58 ARG cc_start: 0.7554 (mpt-90) cc_final: 0.7171 (mmt180) REVERT: D 182 MET cc_start: 0.4359 (mmp) cc_final: 0.3621 (ptm) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 0.1310 time to fit residues: 42.7213 Evaluate side-chains 202 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 166 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 122 ASN ** B 374 ASN ** 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 = 0.4353 r_free = 0.4353 target = 0.211731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.168682 restraints weight = 18382.904| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.69 r_work: 0.3404 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17297 Z= 0.184 Angle : 0.567 9.609 23670 Z= 0.307 Chirality : 0.044 0.330 2686 Planarity : 0.004 0.044 2755 Dihedral : 17.959 161.149 2851 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.17 % Allowed : 11.82 % Favored : 86.01 % 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 (0.19), residues: 1895 helix: 0.85 (0.17), residues: 835 sheet: -1.22 (0.28), residues: 320 loop : -0.71 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 39 TYR 0.042 0.002 TYR A 668 PHE 0.024 0.002 PHE A 930 TRP 0.009 0.001 TRP A 8 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (17297) covalent geometry : angle 0.56724 / 0.31 (23670) hydrogen bonds : bond 0.03840 / 2.57 ( 889) hydrogen bonds : angle 4.78521 / 3.29 ( 2547) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7794 (pm20) cc_final: 0.7589 (pt0) REVERT: A 211 GLN cc_start: 0.7336 (pm20) cc_final: 0.7111 (tp40) REVERT: A 345 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8395 (ptpt) REVERT: A 357 MET cc_start: 0.8261 (mmp) cc_final: 0.7972 (mmp) REVERT: A 519 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7598 (mtt-85) REVERT: A 546 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 724 MET cc_start: 0.7961 (tmm) cc_final: 0.7716 (tmm) REVERT: B 67 LYS cc_start: 0.7235 (mttt) cc_final: 0.7012 (ttmt) REVERT: B 127 LEU cc_start: 0.7863 (mt) cc_final: 0.7594 (mp) REVERT: B 218 MET cc_start: 0.7406 (mtp) cc_final: 0.7199 (mtt) REVERT: B 351 GLN cc_start: 0.8246 (tt0) cc_final: 0.7982 (tt0) REVERT: B 424 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7308 (mp) REVERT: C 58 ARG cc_start: 0.7491 (mpt-90) cc_final: 0.7144 (mmt180) REVERT: D 182 MET cc_start: 0.4376 (mmp) cc_final: 0.3607 (ptm) outliers start: 38 outliers final: 21 residues processed: 226 average time/residue: 0.1197 time to fit residues: 42.3957 Evaluate side-chains 209 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 188 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.212600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.169168 restraints weight = 18250.183| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.64 r_work: 0.3418 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17297 Z= 0.157 Angle : 0.558 10.686 23670 Z= 0.301 Chirality : 0.043 0.327 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.922 161.807 2851 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.83 % Allowed : 12.91 % Favored : 85.27 % 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: -0.20 (0.19), residues: 1895 helix: 0.87 (0.17), residues: 837 sheet: -1.21 (0.27), residues: 322 loop : -0.66 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 39 TYR 0.030 0.001 TYR A 668 PHE 0.025 0.001 PHE A 838 TRP 0.010 0.001 TRP B 136 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (17297) covalent geometry : angle 0.55780 / 0.30 (23670) hydrogen bonds : bond 0.03664 / 2.45 ( 889) hydrogen bonds : angle 4.71509 / 3.24 ( 2547) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7803 (pm20) cc_final: 0.7596 (pt0) REVERT: A 181 ASN cc_start: 0.7725 (m-40) cc_final: 0.7424 (m-40) REVERT: A 268 ASP cc_start: 0.8355 (m-30) cc_final: 0.7753 (m-30) REVERT: A 357 MET cc_start: 0.8214 (mmp) cc_final: 0.7925 (mmp) REVERT: A 519 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7619 (mtt-85) REVERT: A 546 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8361 (mt) REVERT: B 127 LEU cc_start: 0.7790 (mt) cc_final: 0.7538 (mp) REVERT: B 218 MET cc_start: 0.7432 (mtp) cc_final: 0.7169 (mtt) REVERT: B 351 GLN cc_start: 0.8280 (tt0) cc_final: 0.7897 (tt0) REVERT: B 424 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7275 (mp) REVERT: C 58 ARG cc_start: 0.7498 (mpt-90) cc_final: 0.7124 (mmt180) REVERT: D 182 MET cc_start: 0.4308 (mmp) cc_final: 0.3572 (ptm) outliers start: 32 outliers final: 22 residues processed: 222 average time/residue: 0.1134 time to fit residues: 39.3695 Evaluate side-chains 211 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 42 optimal weight: 0.0020 chunk 121 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 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 = 0.4345 r_free = 0.4345 target = 0.210933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167557 restraints weight = 18584.823| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.78 r_work: 0.3388 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17297 Z= 0.192 Angle : 0.578 10.381 23670 Z= 0.312 Chirality : 0.043 0.331 2686 Planarity : 0.004 0.044 2755 Dihedral : 17.957 161.789 2851 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.77 % Allowed : 13.59 % Favored : 84.64 % 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: -0.23 (0.19), residues: 1895 helix: 0.88 (0.17), residues: 837 sheet: -1.32 (0.27), residues: 328 loop : -0.66 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 39 TYR 0.031 0.002 TYR A 668 PHE 0.027 0.002 PHE A 838 TRP 0.010 0.001 TRP A 8 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (17297) covalent geometry : angle 0.57762 / 0.31 (23670) hydrogen bonds : bond 0.03813 / 2.54 ( 889) hydrogen bonds : angle 4.71679 / 3.24 ( 2547) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7851 (pm20) cc_final: 0.7623 (pt0) REVERT: A 181 ASN cc_start: 0.7824 (m-40) cc_final: 0.7596 (m-40) REVERT: A 268 ASP cc_start: 0.8403 (m-30) cc_final: 0.7886 (m-30) REVERT: A 345 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8413 (ptpt) REVERT: A 357 MET cc_start: 0.8288 (mmp) cc_final: 0.7996 (mmp) REVERT: A 519 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7616 (mtt-85) REVERT: A 546 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 127 LEU cc_start: 0.7843 (mt) cc_final: 0.7578 (mp) REVERT: B 218 MET cc_start: 0.7604 (mtp) cc_final: 0.7360 (mtt) REVERT: B 351 GLN cc_start: 0.8236 (tt0) cc_final: 0.7882 (tt0) REVERT: B 424 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7322 (mp) REVERT: C 58 ARG cc_start: 0.7549 (mpt-90) cc_final: 0.7170 (mmt180) REVERT: D 182 MET cc_start: 0.4407 (mmp) cc_final: 0.3664 (ptm) outliers start: 31 outliers final: 23 residues processed: 210 average time/residue: 0.1257 time to fit residues: 41.4180 Evaluate side-chains 214 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 4 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 186 optimal weight: 50.0000 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS A 426 ASN ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** 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 = 0.4361 r_free = 0.4361 target = 0.212652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170607 restraints weight = 18393.740| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.52 r_work: 0.3412 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17297 Z= 0.146 Angle : 0.559 10.651 23670 Z= 0.302 Chirality : 0.043 0.327 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.912 161.853 2851 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.48 % Allowed : 14.16 % Favored : 84.35 % 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 (0.19), residues: 1895 helix: 0.93 (0.17), residues: 844 sheet: -1.39 (0.27), residues: 329 loop : -0.55 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 39 TYR 0.024 0.001 TYR A 668 PHE 0.020 0.001 PHE A 930 TRP 0.009 0.001 TRP B 136 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (17297) covalent geometry : angle 0.55856 / 0.30 (23670) hydrogen bonds : bond 0.03591 / 2.40 ( 889) hydrogen bonds : angle 4.66996 / 3.21 ( 2547) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7822 (pm20) cc_final: 0.7590 (pt0) REVERT: A 181 ASN cc_start: 0.7750 (m-40) cc_final: 0.7507 (m-40) REVERT: A 268 ASP cc_start: 0.8374 (m-30) cc_final: 0.7912 (m-30) REVERT: A 357 MET cc_start: 0.8227 (mmp) cc_final: 0.7907 (mmp) REVERT: A 519 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7536 (mtt-85) REVERT: A 546 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 744 ARG cc_start: 0.7381 (tpp-160) cc_final: 0.6782 (ttp-170) REVERT: A 842 MET cc_start: 0.7196 (ttm) cc_final: 0.6868 (ttm) REVERT: B 67 LYS cc_start: 0.7348 (ttmt) cc_final: 0.6996 (ttmt) REVERT: B 127 LEU cc_start: 0.7789 (mt) cc_final: 0.7506 (mp) REVERT: B 218 MET cc_start: 0.7522 (mtp) cc_final: 0.7286 (mtt) REVERT: B 424 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7317 (mp) REVERT: C 58 ARG cc_start: 0.7498 (mpt-90) cc_final: 0.7164 (mmt180) REVERT: D 182 MET cc_start: 0.4355 (mmp) cc_final: 0.3608 (ptm) outliers start: 26 outliers final: 19 residues processed: 221 average time/residue: 0.1032 time to fit residues: 35.8384 Evaluate side-chains 209 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 184 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** 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 = 0.4360 r_free = 0.4360 target = 0.212432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170870 restraints weight = 18380.166| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.55 r_work: 0.3417 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17297 Z= 0.151 Angle : 0.566 10.654 23670 Z= 0.305 Chirality : 0.043 0.327 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.907 161.321 2851 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.31 % Allowed : 14.45 % Favored : 84.24 % 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 (0.19), residues: 1895 helix: 0.97 (0.17), residues: 837 sheet: -1.37 (0.27), residues: 329 loop : -0.50 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 286 TYR 0.025 0.001 TYR A 668 PHE 0.019 0.001 PHE A 930 TRP 0.010 0.001 TRP B 136 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (17297) covalent geometry : angle 0.56600 / 0.31 (23670) hydrogen bonds : bond 0.03650 / 2.43 ( 889) hydrogen bonds : angle 4.65070 / 3.20 ( 2547) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7851 (pm20) cc_final: 0.7617 (pt0) REVERT: A 181 ASN cc_start: 0.7711 (m-40) cc_final: 0.7486 (m-40) REVERT: A 357 MET cc_start: 0.8254 (mmp) cc_final: 0.7948 (mmp) REVERT: A 519 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7533 (mtt-85) REVERT: A 546 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8347 (mt) REVERT: A 566 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: A 744 ARG cc_start: 0.7391 (tpp-160) cc_final: 0.6827 (ttp-170) REVERT: A 842 MET cc_start: 0.7193 (ttm) cc_final: 0.6927 (ttm) REVERT: B 127 LEU cc_start: 0.7860 (mt) cc_final: 0.7599 (mp) REVERT: B 218 MET cc_start: 0.7573 (mtp) cc_final: 0.7356 (mtt) REVERT: B 424 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7273 (mp) REVERT: C 58 ARG cc_start: 0.7608 (mpt-90) cc_final: 0.7292 (mmt180) REVERT: D 182 MET cc_start: 0.4491 (mmp) cc_final: 0.3737 (ptm) outliers start: 23 outliers final: 20 residues processed: 207 average time/residue: 0.1010 time to fit residues: 33.1413 Evaluate side-chains 211 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 176 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.212639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.171522 restraints weight = 18290.272| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.62 r_work: 0.3414 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17297 Z= 0.147 Angle : 0.563 10.557 23670 Z= 0.304 Chirality : 0.043 0.326 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.900 161.386 2851 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.54 % Allowed : 14.45 % Favored : 84.01 % 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: -0.04 (0.19), residues: 1895 helix: 1.01 (0.17), residues: 837 sheet: -1.34 (0.27), residues: 329 loop : -0.46 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 286 TYR 0.024 0.001 TYR A 668 PHE 0.019 0.001 PHE A 930 TRP 0.010 0.001 TRP B 136 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (17297) covalent geometry : angle 0.56265 / 0.30 (23670) hydrogen bonds : bond 0.03607 / 2.40 ( 889) hydrogen bonds : angle 4.63492 / 3.19 ( 2547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.71 seconds wall clock time: 61 minutes 12.85 seconds (3672.85 seconds total)