Starting phenix.real_space_refine on Fri Jul 3 22:17:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpp_37722/07_2026/8wpp_37722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpp_37722/07_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_37722/07_2026/8wpp_37722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpp_37722/07_2026/8wpp_37722.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpp_37722/07_2026/8wpp_37722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpp_37722/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.41, per 1000 atoms: 0.20 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: 1.17 Conformation dependent library (CDL) restraints added in 746.2 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: 2.20 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: 5.04 Time building geometry restraints manager: 1.54 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=" N3 DT I 22 " pdb=" C4 DT I 22 " pdb=" O4 DT I 22 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+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: 1.810 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.990 Find NCS groups from input model: 0.100 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- 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 : 0.868 14.597 23670 Z= 0.524 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 0.86848 / 0.52 (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 : 0.605 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: 0.1114 time to fit residues: 47.8530 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 : 0.652 ------------------------------------------------------------------------------- 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 = 0.213976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.171402 restraints weight = 18577.068| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.64 r_work: 0.3466 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17297 Z= 0.255 Angle : 0.659 7.052 23670 Z= 0.364 Chirality : 0.047 0.264 2686 Planarity : 0.005 0.068 2755 Dihedral : 18.018 159.805 2854 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.91 % Allowed : 7.82 % Favored : 91.26 % 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: -1.00 (0.18), residues: 1895 helix: -0.07 (0.17), residues: 832 sheet: -1.05 (0.26), residues: 333 loop : -0.97 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 135 TYR 0.030 0.002 TYR A 668 PHE 0.032 0.002 PHE A 791 TRP 0.014 0.002 TRP A 8 HIS 0.009 0.002 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.26 (17297) covalent geometry : angle 0.65895 / 0.36 (23670) hydrogen bonds : bond 0.04615 / 3.07 ( 889) hydrogen bonds : angle 5.52921 / 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 : 0.399 Fit side-chains REVERT: A 211 GLN cc_start: 0.6874 (pm20) cc_final: 0.6543 (tp40) REVERT: A 268 ASP cc_start: 0.8397 (m-30) cc_final: 0.7583 (m-30) REVERT: A 519 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7469 (mtt90) REVERT: B 67 LYS cc_start: 0.7377 (mttt) cc_final: 0.7091 (ttmt) REVERT: C 58 ARG cc_start: 0.7721 (mpt-90) cc_final: 0.7233 (mmt180) REVERT: D 182 MET cc_start: 0.4096 (mmp) cc_final: 0.3300 (ptm) outliers start: 16 outliers final: 11 residues processed: 228 average time/residue: 0.1128 time to fit residues: 39.4899 Evaluate side-chains 198 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.7980 chunk 178 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 426 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.214182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172190 restraints weight = 18600.742| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.61 r_work: 0.3472 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17297 Z= 0.176 Angle : 0.579 8.871 23670 Z= 0.317 Chirality : 0.044 0.296 2686 Planarity : 0.004 0.049 2755 Dihedral : 17.982 161.829 2851 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.20 % Allowed : 9.71 % Favored : 89.09 % 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: -0.65 (0.18), residues: 1895 helix: 0.40 (0.17), residues: 832 sheet: -1.21 (0.27), residues: 325 loop : -0.86 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 39 TYR 0.021 0.002 TYR A 668 PHE 0.023 0.002 PHE A 534 TRP 0.010 0.001 TRP A 8 HIS 0.005 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (17297) covalent geometry : angle 0.57863 / 0.32 (23670) hydrogen bonds : bond 0.04242 / 2.82 ( 889) hydrogen bonds : angle 5.15375 / 3.52 ( 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: 21 poor density : 207 time to evaluate : 0.581 Fit side-chains REVERT: A 181 ASN cc_start: 0.7893 (m-40) cc_final: 0.7678 (m110) REVERT: A 211 GLN cc_start: 0.7030 (pm20) cc_final: 0.6719 (tp40) REVERT: A 357 MET cc_start: 0.8082 (mmp) cc_final: 0.7782 (mmp) REVERT: A 580 GLU cc_start: 0.8281 (tt0) cc_final: 0.8048 (tt0) REVERT: A 602 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6898 (pt0) REVERT: A 724 MET cc_start: 0.7945 (tmm) cc_final: 0.7619 (tmm) REVERT: B 67 LYS cc_start: 0.7382 (mttt) cc_final: 0.7169 (ttmt) REVERT: B 127 LEU cc_start: 0.7963 (mt) cc_final: 0.7661 (mt) REVERT: B 208 GLN cc_start: 0.6329 (mp10) cc_final: 0.6018 (mp10) REVERT: B 218 MET cc_start: 0.7232 (mtp) cc_final: 0.6967 (mtt) REVERT: B 351 GLN cc_start: 0.8082 (tt0) cc_final: 0.7835 (tt0) REVERT: B 365 GLU cc_start: 0.7961 (tp30) cc_final: 0.7688 (tm-30) REVERT: C 58 ARG cc_start: 0.7617 (mpt-90) cc_final: 0.7171 (mmt180) REVERT: C 114 ASP cc_start: 0.8059 (t70) cc_final: 0.7830 (t0) REVERT: D 182 MET cc_start: 0.4268 (mmp) cc_final: 0.3532 (ptm) outliers start: 21 outliers final: 12 residues processed: 219 average time/residue: 0.1178 time to fit residues: 39.8507 Evaluate side-chains 201 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER 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 451 ILE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 864 VAL 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 130 THR 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: 0.8980 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.212842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.169840 restraints weight = 18632.701| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.70 r_work: 0.3423 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17297 Z= 0.182 Angle : 0.563 9.476 23670 Z= 0.308 Chirality : 0.043 0.304 2686 Planarity : 0.004 0.047 2755 Dihedral : 18.002 161.942 2851 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.48 % Allowed : 10.97 % Favored : 87.55 % 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: 0.66 (0.17), residues: 829 sheet: -1.25 (0.27), residues: 323 loop : -0.80 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 39 TYR 0.038 0.002 TYR A 668 PHE 0.017 0.002 PHE A 791 TRP 0.010 0.001 TRP B 136 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (17297) covalent geometry : angle 0.56253 / 0.31 (23670) hydrogen bonds : bond 0.03954 / 2.64 ( 889) hydrogen bonds : angle 4.94893 / 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 226 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.626 Fit side-chains REVERT: A 211 GLN cc_start: 0.7184 (pm20) cc_final: 0.6846 (tp40) REVERT: A 345 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8306 (ptpt) REVERT: A 546 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 724 MET cc_start: 0.7932 (tmm) cc_final: 0.7651 (tmm) REVERT: A 889 LEU cc_start: 0.7903 (tp) cc_final: 0.7686 (tp) REVERT: B -10 MET cc_start: 0.5764 (ptm) cc_final: 0.5540 (ptm) REVERT: B 67 LYS cc_start: 0.7278 (mttt) cc_final: 0.7037 (ttmt) REVERT: B 127 LEU cc_start: 0.7936 (mt) cc_final: 0.7629 (mt) REVERT: B 351 GLN cc_start: 0.8068 (tt0) cc_final: 0.7740 (tt0) REVERT: C 58 ARG cc_start: 0.7590 (mpt-90) cc_final: 0.7168 (mmt180) REVERT: C 114 ASP cc_start: 0.8000 (t70) cc_final: 0.7784 (t0) REVERT: D 182 MET cc_start: 0.4403 (mmp) cc_final: 0.3625 (ptm) outliers start: 26 outliers final: 15 residues processed: 216 average time/residue: 0.1172 time to fit residues: 39.3802 Evaluate side-chains 200 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 28 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 168 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 chunk 19 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.214159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.172278 restraints weight = 18546.374| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.67 r_work: 0.3448 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17297 Z= 0.138 Angle : 0.543 10.109 23670 Z= 0.296 Chirality : 0.042 0.303 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.947 162.010 2851 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.54 % Allowed : 12.51 % Favored : 85.95 % 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: -0.27 (0.19), residues: 1895 helix: 0.83 (0.17), residues: 831 sheet: -1.33 (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 0.023 0.001 TYR A 668 PHE 0.014 0.001 PHE A 838 TRP 0.009 0.001 TRP B 136 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (17297) covalent geometry : angle 0.54324 / 0.30 (23670) hydrogen bonds : bond 0.03696 / 2.46 ( 889) hydrogen bonds : angle 4.81858 / 3.30 ( 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 215 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.469 Fit side-chains REVERT: A 130 GLN cc_start: 0.7733 (pm20) cc_final: 0.7527 (pt0) REVERT: A 346 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8663 (tp) REVERT: A 546 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 724 MET cc_start: 0.7889 (tmm) cc_final: 0.7620 (tmm) REVERT: A 996 MET cc_start: 0.7105 (mmm) cc_final: 0.6707 (mmt) REVERT: B -10 MET cc_start: 0.5609 (ptm) cc_final: 0.5396 (ptm) REVERT: B 67 LYS cc_start: 0.7208 (mttt) cc_final: 0.6978 (ttmt) REVERT: B 127 LEU cc_start: 0.7922 (mt) cc_final: 0.7632 (mt) REVERT: B 218 MET cc_start: 0.7348 (mtp) cc_final: 0.7083 (mtt) REVERT: C 40 ASP cc_start: 0.6858 (m-30) cc_final: 0.6657 (m-30) REVERT: C 58 ARG cc_start: 0.7569 (mpt-90) cc_final: 0.7179 (mmt180) REVERT: D 182 MET cc_start: 0.4349 (mmp) cc_final: 0.3624 (ptm) outliers start: 27 outliers final: 16 residues processed: 206 average time/residue: 0.1074 time to fit residues: 34.5096 Evaluate side-chains 197 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 413 ILE Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 166 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 0.0770 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.213149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171965 restraints weight = 18421.170| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.62 r_work: 0.3411 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17297 Z= 0.155 Angle : 0.539 9.775 23670 Z= 0.294 Chirality : 0.043 0.306 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.949 161.971 2851 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.23 % Allowed : 12.11 % Favored : 85.67 % 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 (0.19), residues: 1895 helix: 0.89 (0.17), residues: 837 sheet: -1.33 (0.27), residues: 321 loop : -0.64 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 39 TYR 0.022 0.001 TYR A 668 PHE 0.024 0.001 PHE A 930 TRP 0.011 0.001 TRP B 136 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (17297) covalent geometry : angle 0.53880 / 0.29 (23670) hydrogen bonds : bond 0.03686 / 2.46 ( 889) hydrogen bonds : angle 4.75758 / 3.27 ( 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: 39 poor density : 196 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8364 (ptpt) REVERT: A 346 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 546 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8374 (mt) REVERT: A 724 MET cc_start: 0.8051 (tmm) cc_final: 0.7794 (tmm) REVERT: A 996 MET cc_start: 0.7064 (mmm) cc_final: 0.6749 (mmt) REVERT: B 67 LYS cc_start: 0.7231 (mttt) cc_final: 0.6992 (ttmt) REVERT: B 76 TYR cc_start: 0.4749 (m-80) cc_final: 0.4457 (m-80) REVERT: B 127 LEU cc_start: 0.7829 (mt) cc_final: 0.7521 (mt) REVERT: B 218 MET cc_start: 0.7321 (mtp) cc_final: 0.7091 (mtt) REVERT: B 351 GLN cc_start: 0.8297 (tt0) cc_final: 0.7975 (tt0) REVERT: B 424 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7271 (mp) REVERT: C 58 ARG cc_start: 0.7569 (mpt-90) cc_final: 0.7186 (mmt180) REVERT: C 114 ASP cc_start: 0.8059 (t70) cc_final: 0.7856 (t0) REVERT: D 182 MET cc_start: 0.4264 (mmp) cc_final: 0.3555 (ptm) outliers start: 39 outliers final: 21 residues processed: 226 average time/residue: 0.1257 time to fit residues: 44.6023 Evaluate side-chains 212 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET 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 346 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 188 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 151 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.213610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170286 restraints weight = 18348.036| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.55 r_work: 0.3445 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17297 Z= 0.144 Angle : 0.542 9.883 23670 Z= 0.295 Chirality : 0.042 0.305 2686 Planarity : 0.004 0.042 2755 Dihedral : 17.923 162.218 2851 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.00 % Allowed : 12.45 % Favored : 85.55 % 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: -0.14 (0.19), residues: 1895 helix: 0.92 (0.17), residues: 839 sheet: -1.29 (0.27), residues: 321 loop : -0.56 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 39 TYR 0.039 0.001 TYR A 668 PHE 0.022 0.001 PHE A 930 TRP 0.010 0.001 TRP B 136 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17297) covalent geometry : angle 0.54192 / 0.29 (23670) hydrogen bonds : bond 0.03609 / 2.41 ( 889) hydrogen bonds : angle 4.69575 / 3.22 ( 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 220 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8272 (m-30) cc_final: 0.7740 (m-30) REVERT: A 346 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8669 (tp) REVERT: A 546 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 996 MET cc_start: 0.7060 (mmm) cc_final: 0.6751 (mmt) REVERT: B 127 LEU cc_start: 0.7811 (mt) cc_final: 0.7561 (mp) REVERT: B 218 MET cc_start: 0.7383 (mtp) cc_final: 0.7122 (mtt) REVERT: B 424 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7262 (mp) REVERT: C 58 ARG cc_start: 0.7430 (mpt-90) cc_final: 0.7071 (mmt180) REVERT: D 182 MET cc_start: 0.4299 (mmp) cc_final: 0.3572 (ptm) outliers start: 35 outliers final: 22 residues processed: 209 average time/residue: 0.1251 time to fit residues: 40.7859 Evaluate side-chains 202 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 346 LEU 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 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 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: 0.7980 chunk 180 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 67 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.211358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.168297 restraints weight = 18576.992| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.76 r_work: 0.3385 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17297 Z= 0.185 Angle : 0.570 10.098 23670 Z= 0.308 Chirality : 0.043 0.308 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.975 162.715 2851 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.00 % Allowed : 12.96 % Favored : 85.04 % 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: -0.19 (0.19), residues: 1895 helix: 0.90 (0.17), residues: 839 sheet: -1.31 (0.27), residues: 328 loop : -0.61 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 146 TYR 0.042 0.002 TYR A 668 PHE 0.023 0.002 PHE A 838 TRP 0.011 0.001 TRP B 136 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (17297) covalent geometry : angle 0.56973 / 0.31 (23670) hydrogen bonds : bond 0.03792 / 2.53 ( 889) hydrogen bonds : angle 4.71998 / 3.25 ( 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 226 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7838 (m-40) cc_final: 0.7573 (m-40) REVERT: A 268 ASP cc_start: 0.8323 (m-30) cc_final: 0.7863 (m-30) REVERT: A 345 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8366 (ptpt) REVERT: A 546 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 580 GLU cc_start: 0.8285 (tt0) cc_final: 0.8010 (tt0) REVERT: A 744 ARG cc_start: 0.7367 (tpp-160) cc_final: 0.6765 (ttp-170) REVERT: A 842 MET cc_start: 0.7150 (ttm) cc_final: 0.6933 (ttm) REVERT: A 996 MET cc_start: 0.7009 (mmm) cc_final: 0.6772 (mmt) REVERT: B 127 LEU cc_start: 0.7841 (mt) cc_final: 0.7586 (mp) REVERT: B 218 MET cc_start: 0.7596 (mtp) cc_final: 0.7353 (mtt) REVERT: B 351 GLN cc_start: 0.8297 (tt0) cc_final: 0.7969 (tt0) REVERT: B 424 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7296 (mp) REVERT: C 41 GLU cc_start: 0.6930 (tp30) cc_final: 0.6672 (pm20) REVERT: C 58 ARG cc_start: 0.7623 (mpt-90) cc_final: 0.7259 (mmt180) REVERT: D 182 MET cc_start: 0.4371 (mmp) cc_final: 0.3639 (ptm) outliers start: 35 outliers final: 24 residues processed: 216 average time/residue: 0.1305 time to fit residues: 43.6994 Evaluate side-chains 208 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 455 MET 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: 0.7980 chunk 148 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 186 optimal weight: 50.0000 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** 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 = 0.4367 r_free = 0.4367 target = 0.213159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169665 restraints weight = 18425.385| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.67 r_work: 0.3434 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17297 Z= 0.139 Angle : 0.548 10.335 23670 Z= 0.298 Chirality : 0.042 0.303 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.917 162.706 2851 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.48 % Allowed : 13.99 % Favored : 84.52 % 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: -0.07 (0.19), residues: 1895 helix: 0.98 (0.17), residues: 837 sheet: -1.38 (0.27), residues: 329 loop : -0.46 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 286 TYR 0.027 0.001 TYR A 668 PHE 0.022 0.001 PHE A 838 TRP 0.008 0.001 TRP B 136 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17297) covalent geometry : angle 0.54804 / 0.30 (23670) hydrogen bonds : bond 0.03568 / 2.38 ( 889) hydrogen bonds : angle 4.65840 / 3.20 ( 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 212 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7700 (m-40) cc_final: 0.7423 (m-40) REVERT: A 268 ASP cc_start: 0.8308 (m-30) cc_final: 0.7721 (m-30) REVERT: A 345 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8303 (ptpt) REVERT: A 546 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 580 GLU cc_start: 0.8234 (tt0) cc_final: 0.7626 (tt0) REVERT: A 744 ARG cc_start: 0.7401 (tpp-160) cc_final: 0.6824 (ttp-170) REVERT: A 842 MET cc_start: 0.7228 (ttm) cc_final: 0.7020 (ttm) REVERT: A 996 MET cc_start: 0.6988 (mmm) cc_final: 0.6746 (mmt) REVERT: B 67 LYS cc_start: 0.7338 (ttmt) cc_final: 0.6986 (ttmt) REVERT: B 127 LEU cc_start: 0.7809 (mt) cc_final: 0.7550 (mp) REVERT: B 218 MET cc_start: 0.7509 (mtp) cc_final: 0.7280 (mtt) REVERT: B 424 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7298 (mp) REVERT: C 58 ARG cc_start: 0.7514 (mpt-90) cc_final: 0.7161 (mmt180) REVERT: D 182 MET cc_start: 0.4394 (mmp) cc_final: 0.3687 (ptm) outliers start: 26 outliers final: 21 residues processed: 205 average time/residue: 0.1241 time to fit residues: 40.1549 Evaluate side-chains 203 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 227 LEU 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 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 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 424 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 143 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: 8.9990 chunk 135 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.212621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173332 restraints weight = 18412.024| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.55 r_work: 0.3403 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2911 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= 0.153 Angle : 0.558 10.559 23670 Z= 0.302 Chirality : 0.042 0.305 2686 Planarity : 0.004 0.045 2755 Dihedral : 17.916 162.173 2851 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.60 % Allowed : 14.16 % 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: -0.06 (0.19), residues: 1895 helix: 0.98 (0.17), residues: 844 sheet: -1.37 (0.27), residues: 329 loop : -0.44 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 286 TYR 0.029 0.001 TYR A 668 PHE 0.019 0.001 PHE A 930 TRP 0.008 0.001 TRP B 136 HIS 0.004 0.001 HIS B -9 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (17297) covalent geometry : angle 0.55776 / 0.30 (23670) hydrogen bonds : bond 0.03606 / 2.40 ( 889) hydrogen bonds : angle 4.63938 / 3.19 ( 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 207 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7760 (m-40) cc_final: 0.7493 (m-40) REVERT: A 268 ASP cc_start: 0.8319 (m-30) cc_final: 0.7753 (m-30) REVERT: A 345 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8371 (ptpt) REVERT: A 546 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8340 (mt) REVERT: A 580 GLU cc_start: 0.8270 (tt0) cc_final: 0.7664 (tt0) REVERT: A 744 ARG cc_start: 0.7376 (tpp-160) cc_final: 0.6737 (ttp-170) REVERT: A 842 MET cc_start: 0.7176 (ttm) cc_final: 0.6952 (ttm) REVERT: A 996 MET cc_start: 0.6933 (mmm) cc_final: 0.6696 (mmt) REVERT: B 127 LEU cc_start: 0.7731 (mt) cc_final: 0.7461 (mp) REVERT: B 218 MET cc_start: 0.7510 (mtp) cc_final: 0.7255 (mtt) REVERT: B 424 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7324 (mp) REVERT: C 58 ARG cc_start: 0.7546 (mpt-90) cc_final: 0.7189 (mmt180) REVERT: D 182 MET cc_start: 0.4389 (mmp) cc_final: 0.3670 (ptm) outliers start: 28 outliers final: 20 residues processed: 198 average time/residue: 0.1252 time to fit residues: 38.9766 Evaluate side-chains 198 residues out of total 1753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 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 226 ASP Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.212897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172725 restraints weight = 18298.310| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.34 r_work: 0.3433 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17297 Z= 0.150 Angle : 0.561 10.427 23670 Z= 0.303 Chirality : 0.042 0.302 2686 Planarity : 0.004 0.043 2755 Dihedral : 17.914 162.470 2851 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.43 % Allowed : 14.62 % Favored : 83.95 % 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 (0.19), residues: 1895 helix: 1.00 (0.17), residues: 844 sheet: -1.38 (0.27), residues: 331 loop : -0.39 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 286 TYR 0.028 0.001 TYR A 668 PHE 0.019 0.001 PHE A 930 TRP 0.013 0.001 TRP B 136 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17297) covalent geometry : angle 0.56055 / 0.30 (23670) hydrogen bonds : bond 0.03572 / 2.38 ( 889) hydrogen bonds : angle 4.62066 / 3.18 ( 2547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.60 seconds wall clock time: 64 minutes 5.28 seconds (3845.28 seconds total)