Starting phenix.real_space_refine on Thu Sep 18 07:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3i_44141/09_2025/9b3i_44141.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3i_44141/09_2025/9b3i_44141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b3i_44141/09_2025/9b3i_44141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3i_44141/09_2025/9b3i_44141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3i_44141/09_2025/9b3i_44141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3i_44141/09_2025/9b3i_44141.map" } resolution = 2.88 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 163 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 42 5.16 5 C 9553 2.51 5 N 2447 2.21 5 O 2905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14951 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 944, 7531 Classifications: {'peptide': 944} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 917} Chain breaks: 2 Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1384 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "E" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2325 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain: "F" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2339 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.39, per 1000 atoms: 0.23 Number of scatterers: 14951 At special positions: 0 Unit cell: (115.866, 157.194, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 1 11.99 O 2905 8.00 N 2447 7.00 C 9553 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: 1.32 Conformation dependent library (CDL) restraints added in 655.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 9 sheets defined 71.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.546A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.848A pdb=" N THR A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 104 through 123 removed outlier: 4.079A pdb=" N VAL A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.667A pdb=" N THR A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 167 through 182 removed outlier: 3.509A pdb=" N ALA A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 removed outlier: 4.392A pdb=" N SER A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.898A pdb=" N PHE A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.720A pdb=" N PHE A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.558A pdb=" N PHE A 269 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 295 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 301 through 321 removed outlier: 4.672A pdb=" N GLU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.977A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 384 through 402 removed outlier: 3.651A pdb=" N LEU A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 4.669A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 452 through 470 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 522 through 542 removed outlier: 3.938A pdb=" N SER A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 544 No H-bonds generated for 'chain 'A' and resid 543 through 544' Processing helix chain 'A' and resid 545 through 546 No H-bonds generated for 'chain 'A' and resid 545 through 546' Processing helix chain 'A' and resid 547 through 561 Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.543A pdb=" N LEU A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 613 through 634 removed outlier: 3.559A pdb=" N TYR A 617 " --> pdb=" O ASN A 613 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 640 through 657 removed outlier: 4.527A pdb=" N LYS A 657 " --> pdb=" O PHE A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.877A pdb=" N ASN A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 727 through 732 Processing helix chain 'A' and resid 733 through 745 removed outlier: 4.340A pdb=" N LEU A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 752 through 767 removed outlier: 3.708A pdb=" N ALA A 759 " --> pdb=" O ARG A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 787 removed outlier: 3.527A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 805 through 817 removed outlier: 4.501A pdb=" N ARG A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 840 Processing helix chain 'A' and resid 841 through 847 Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 878 through 894 removed outlier: 3.557A pdb=" N LYS A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 941 removed outlier: 3.594A pdb=" N TYR A 939 " --> pdb=" O LYS A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 980 removed outlier: 3.664A pdb=" N ARG A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 991 Processing helix chain 'A' and resid 992 through 1004 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 27 through 39 removed outlier: 3.514A pdb=" N GLY B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 removed outlier: 3.903A pdb=" N VAL B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'C' and resid 40 through 52 Processing helix chain 'C' and resid 58 through 87 Processing helix chain 'C' and resid 93 through 105 removed outlier: 4.073A pdb=" N ILE C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 removed outlier: 3.717A pdb=" N HIS C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 35 Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 96 through 102 removed outlier: 3.776A pdb=" N TYR D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 removed outlier: 3.625A pdb=" N VAL D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.924A pdb=" N LYS D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 89 through 140 removed outlier: 3.707A pdb=" N LYS E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 146 through 161 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.563A pdb=" N LEU E 166 " --> pdb=" O THR E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.893A pdb=" N THR E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 203' Processing helix chain 'E' and resid 204 through 212 removed outlier: 3.600A pdb=" N GLU E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 4.073A pdb=" N ASP E 263 " --> pdb=" O TYR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 327 through 351 removed outlier: 4.392A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 362 Processing helix chain 'F' and resid 82 through 88 Processing helix chain 'F' and resid 89 through 140 Proline residue: F 130 - end of helix Processing helix chain 'F' and resid 146 through 159 Processing helix chain 'F' and resid 162 through 166 Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 187 through 195 Processing helix chain 'F' and resid 196 through 201 removed outlier: 4.096A pdb=" N ASP F 201 " --> pdb=" O PRO F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 212 removed outlier: 3.899A pdb=" N VAL F 210 " --> pdb=" O ARG F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 322 through 352 removed outlier: 3.920A pdb=" N GLU F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 330 " --> pdb=" O GLN F 326 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 338 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA2, first strand: chain 'A' and resid 852 through 854 removed outlier: 3.548A pdb=" N ARG A 873 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.815A pdb=" N ARG B 43 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 56 removed outlier: 3.648A pdb=" N GLY D 59 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE D 13 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP D 66 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU D 15 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR D 68 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU D 17 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA D 88 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS D 122 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 90 " --> pdb=" O CYS D 122 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN D 124 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE D 92 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 147 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 214 through 222 removed outlier: 6.039A pdb=" N ARG E 234 " --> pdb=" O GLN E 215 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE E 217 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU E 232 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU E 219 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS E 230 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TYR E 221 " --> pdb=" O GLY E 228 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY E 228 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE E 253 " --> pdb=" O HIS E 268 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS E 268 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 285 through 293 removed outlier: 3.620A pdb=" N THR E 307 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU E 288 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 216 through 221 removed outlier: 4.339A pdb=" N ASP F 216 " --> pdb=" O ARG F 234 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA F 249 " --> pdb=" O GLY F 271 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLY F 271 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR F 251 " --> pdb=" O ALA F 269 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA F 269 " --> pdb=" O THR F 251 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE F 253 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 285 through 294 936 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.83 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: 3674 1.33 - 1.45: 2774 1.45 - 1.57: 8702 1.57 - 1.69: 5 1.69 - 1.81: 64 Bond restraints: 15219 Sorted by residual: bond pdb=" N VAL A 848 " pdb=" CA VAL A 848 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.37e+00 bond pdb=" N VAL A 849 " pdb=" CA VAL A 849 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.92e+00 bond pdb=" N PHE A 514 " pdb=" CA PHE A 514 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.59e+00 bond pdb=" N VAL B 50 " pdb=" CA VAL B 50 " ideal model delta sigma weight residual 1.463 1.493 -0.030 1.14e-02 7.69e+03 6.87e+00 bond pdb=" N TYR D 148 " pdb=" CA TYR D 148 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.56e+00 ... (remaining 15214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 20154 2.27 - 4.54: 372 4.54 - 6.81: 58 6.81 - 9.08: 13 9.08 - 11.35: 3 Bond angle restraints: 20600 Sorted by residual: angle pdb=" C LEU F 160 " pdb=" CA LEU F 160 " pdb=" CB LEU F 160 " ideal model delta sigma weight residual 116.54 111.95 4.59 1.15e+00 7.56e-01 1.59e+01 angle pdb=" N VAL A 849 " pdb=" CA VAL A 849 " pdb=" C VAL A 849 " ideal model delta sigma weight residual 112.17 108.43 3.74 9.50e-01 1.11e+00 1.55e+01 angle pdb=" C TYR A 68 " pdb=" N TRP A 69 " pdb=" CA TRP A 69 " ideal model delta sigma weight residual 122.79 115.78 7.01 1.78e+00 3.16e-01 1.55e+01 angle pdb=" PB GTP D 202 " pdb=" O3B GTP D 202 " pdb=" PG GTP D 202 " ideal model delta sigma weight residual 120.50 131.85 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CA ASN A 850 " pdb=" C ASN A 850 " pdb=" O ASN A 850 " ideal model delta sigma weight residual 122.27 117.96 4.31 1.16e+00 7.43e-01 1.38e+01 ... (remaining 20595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.90: 9083 31.90 - 63.81: 166 63.81 - 95.71: 26 95.71 - 127.61: 1 127.61 - 159.52: 3 Dihedral angle restraints: 9279 sinusoidal: 3805 harmonic: 5474 Sorted by residual: dihedral pdb=" O5' GTP D 202 " pdb=" O3A GTP D 202 " pdb=" PA GTP D 202 " pdb=" PB GTP D 202 " ideal model delta sinusoidal sigma weight residual 274.12 114.61 159.52 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C8 GTP D 202 " pdb=" C1' GTP D 202 " pdb=" N9 GTP D 202 " pdb=" O4' GTP D 202 " ideal model delta sinusoidal sigma weight residual 104.59 -50.75 155.34 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O3B GTP D 202 " pdb=" O3A GTP D 202 " pdb=" PB GTP D 202 " pdb=" PA GTP D 202 " ideal model delta sinusoidal sigma weight residual 291.08 162.43 128.65 1 2.00e+01 2.50e-03 3.90e+01 ... (remaining 9276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1822 0.052 - 0.104: 447 0.104 - 0.155: 75 0.155 - 0.207: 18 0.207 - 0.259: 5 Chirality restraints: 2367 Sorted by residual: chirality pdb=" CB ILE C 57 " pdb=" CA ILE C 57 " pdb=" CG1 ILE C 57 " pdb=" CG2 ILE C 57 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE C 92 " pdb=" CA ILE C 92 " pdb=" CG1 ILE C 92 " pdb=" CG2 ILE C 92 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU A 833 " pdb=" CB LEU A 833 " pdb=" CD1 LEU A 833 " pdb=" CD2 LEU A 833 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2364 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 132 " 0.036 2.00e-02 2.50e+03 4.09e-02 4.18e+01 pdb=" CG TRP F 132 " -0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP F 132 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP F 132 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 132 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 132 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 132 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 132 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 132 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP F 132 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 189 " -0.020 2.00e-02 2.50e+03 1.80e-02 8.11e+00 pdb=" CG TRP E 189 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP E 189 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP E 189 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 189 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 189 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 189 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 189 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 189 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 189 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 813 " 0.021 2.00e-02 2.50e+03 1.62e-02 6.56e+00 pdb=" CG TRP A 813 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 813 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 813 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 813 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 813 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 813 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 813 " 0.006 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 39 2.40 - 3.02: 9470 3.02 - 3.65: 23480 3.65 - 4.27: 34895 4.27 - 4.90: 57212 Nonbonded interactions: 125096 Sorted by model distance: nonbonded pdb="MG MG D 201 " pdb=" O1G GTP D 202 " model vdw 1.769 2.170 nonbonded pdb="MG MG D 201 " pdb=" O3A GTP D 202 " model vdw 1.993 2.170 nonbonded pdb=" O SER A 78 " pdb=" OG1 THR A 79 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR F 252 " pdb=" OD1 ASP F 341 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN E 282 " pdb=" OG1 THR E 284 " model vdw 2.204 3.040 ... (remaining 125091 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 'E' selection = (chain 'F' and resid 83 through 365) } 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: 12.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.650 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 : 0.006 0.063 15219 Z= 0.259 Angle : 0.781 11.348 20600 Z= 0.430 Chirality : 0.048 0.259 2367 Planarity : 0.005 0.063 2640 Dihedral : 13.825 159.516 5711 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.30 % Allowed : 0.42 % Favored : 99.28 % 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 aren not related in a simple way. whole: 0.61 (0.19), residues: 1838 helix: 0.58 (0.15), residues: 1147 sheet: 1.36 (0.42), residues: 132 loop : 0.08 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 135 TYR 0.028 0.002 TYR A 511 PHE 0.030 0.003 PHE A 249 TRP 0.109 0.005 TRP F 132 HIS 0.010 0.001 HIS B 83 Details of bonding type rmsd covalent geometry : bond 0.00562 (15219) covalent geometry : angle 0.78065 (20600) hydrogen bonds : bond 0.16783 ( 936) hydrogen bonds : angle 6.49905 ( 2751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASN cc_start: 0.7819 (m110) cc_final: 0.6859 (m-40) REVERT: B 72 ARG cc_start: 0.8545 (mtm180) cc_final: 0.8252 (mtm180) REVERT: C 62 MET cc_start: 0.8485 (mpp) cc_final: 0.8222 (mpp) REVERT: E 95 LYS cc_start: 0.9098 (pttp) cc_final: 0.8746 (pptt) REVERT: E 96 LEU cc_start: 0.9433 (tp) cc_final: 0.9014 (tm) REVERT: E 107 PHE cc_start: 0.8665 (m-10) cc_final: 0.8313 (m-80) REVERT: E 316 PHE cc_start: 0.7289 (m-80) cc_final: 0.7058 (m-80) REVERT: E 333 ASP cc_start: 0.8665 (t70) cc_final: 0.8349 (p0) REVERT: F 107 PHE cc_start: 0.8546 (m-80) cc_final: 0.8249 (m-80) REVERT: F 123 LYS cc_start: 0.8836 (tttt) cc_final: 0.8613 (tppt) REVERT: F 315 PHE cc_start: 0.7327 (t80) cc_final: 0.7008 (t80) outliers start: 5 outliers final: 1 residues processed: 209 average time/residue: 0.6577 time to fit residues: 150.4019 Evaluate side-chains 150 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 50.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN A 967 GLN B 69 ASN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.159251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110205 restraints weight = 42843.744| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.68 r_work: 0.3244 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15219 Z= 0.179 Angle : 0.721 17.400 20600 Z= 0.365 Chirality : 0.044 0.246 2367 Planarity : 0.005 0.040 2640 Dihedral : 8.290 151.644 1993 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.72 % Allowed : 7.11 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1838 helix: 1.01 (0.14), residues: 1164 sheet: 0.95 (0.42), residues: 140 loop : 0.03 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 135 TYR 0.027 0.002 TYR E 221 PHE 0.030 0.002 PHE A 887 TRP 0.039 0.002 TRP E 189 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00393 (15219) covalent geometry : angle 0.72131 (20600) hydrogen bonds : bond 0.05293 ( 936) hydrogen bonds : angle 5.24037 ( 2751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.7679 (tmm160) cc_final: 0.7399 (tmm160) REVERT: A 648 GLU cc_start: 0.8290 (tt0) cc_final: 0.7925 (tp30) REVERT: A 755 ARG cc_start: 0.8624 (mpp-170) cc_final: 0.8356 (mtt90) REVERT: A 810 MET cc_start: 0.8966 (mmm) cc_final: 0.8376 (mpm) REVERT: A 813 TRP cc_start: 0.8968 (OUTLIER) cc_final: 0.8707 (p-90) REVERT: A 971 ARG cc_start: 0.9273 (ptt-90) cc_final: 0.9001 (ptt-90) REVERT: A 972 PHE cc_start: 0.9170 (t80) cc_final: 0.8890 (t80) REVERT: B 64 LEU cc_start: 0.9447 (mt) cc_final: 0.9108 (mt) REVERT: B 69 ASN cc_start: 0.8606 (m-40) cc_final: 0.8403 (m-40) REVERT: C 83 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8344 (mt) REVERT: D 177 GLU cc_start: 0.8387 (tp30) cc_final: 0.8178 (tp30) REVERT: E 189 TRP cc_start: 0.8039 (m-10) cc_final: 0.7686 (m-10) REVERT: E 316 PHE cc_start: 0.8934 (m-80) cc_final: 0.8554 (m-80) REVERT: E 333 ASP cc_start: 0.9133 (t70) cc_final: 0.8749 (p0) REVERT: F 107 PHE cc_start: 0.9350 (m-80) cc_final: 0.8865 (m-80) REVERT: F 123 LYS cc_start: 0.9049 (tttt) cc_final: 0.8774 (tppt) REVERT: F 132 TRP cc_start: 0.8429 (m100) cc_final: 0.8199 (m100) REVERT: F 312 PHE cc_start: 0.9249 (t80) cc_final: 0.8932 (t80) REVERT: F 315 PHE cc_start: 0.9053 (t80) cc_final: 0.8441 (t80) REVERT: F 332 GLU cc_start: 0.9130 (tt0) cc_final: 0.8898 (pp20) REVERT: F 346 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8817 (mp0) outliers start: 12 outliers final: 1 residues processed: 164 average time/residue: 0.6232 time to fit residues: 112.7787 Evaluate side-chains 150 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain C residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 138 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 143 optimal weight: 30.0000 chunk 110 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 786 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 = 0.4515 r_free = 0.4515 target = 0.161686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112945 restraints weight = 43308.787| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.71 r_work: 0.3227 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15219 Z= 0.171 Angle : 0.699 18.117 20600 Z= 0.345 Chirality : 0.043 0.293 2367 Planarity : 0.004 0.047 2640 Dihedral : 8.072 157.251 1991 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.25 % Allowed : 9.02 % Favored : 89.73 % 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 aren not related in a simple way. whole: 1.12 (0.19), residues: 1838 helix: 1.17 (0.15), residues: 1170 sheet: 0.87 (0.43), residues: 146 loop : -0.08 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 135 TYR 0.016 0.002 TYR A 697 PHE 0.044 0.002 PHE A 887 TRP 0.032 0.002 TRP E 189 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00390 (15219) covalent geometry : angle 0.69942 (20600) hydrogen bonds : bond 0.04758 ( 936) hydrogen bonds : angle 5.05216 ( 2751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8499 (t0) cc_final: 0.8237 (t0) REVERT: A 266 ARG cc_start: 0.7707 (tmm160) cc_final: 0.7425 (tmm160) REVERT: A 648 GLU cc_start: 0.8233 (tt0) cc_final: 0.7908 (tp30) REVERT: A 693 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8244 (tm-30) REVERT: A 732 MET cc_start: 0.8994 (ptp) cc_final: 0.8639 (mpp) REVERT: A 755 ARG cc_start: 0.8711 (mpp-170) cc_final: 0.8472 (mtt90) REVERT: A 757 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 810 MET cc_start: 0.9043 (mmm) cc_final: 0.8605 (mmm) REVERT: A 813 TRP cc_start: 0.8927 (OUTLIER) cc_final: 0.8625 (p-90) REVERT: A 870 MET cc_start: 0.7945 (ppp) cc_final: 0.7503 (tmm) REVERT: A 971 ARG cc_start: 0.9322 (ptt-90) cc_final: 0.9086 (ptt90) REVERT: A 972 PHE cc_start: 0.9099 (t80) cc_final: 0.8889 (t80) REVERT: B 69 ASN cc_start: 0.8640 (m-40) cc_final: 0.8331 (m-40) REVERT: B 72 ARG cc_start: 0.9135 (mtm180) cc_final: 0.8875 (mtm180) REVERT: C 62 MET cc_start: 0.9035 (mpp) cc_final: 0.8552 (mpp) REVERT: C 63 SER cc_start: 0.9155 (t) cc_final: 0.8939 (p) REVERT: C 83 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8369 (mt) REVERT: C 115 SER cc_start: 0.8422 (t) cc_final: 0.7894 (p) REVERT: E 316 PHE cc_start: 0.8947 (m-80) cc_final: 0.8530 (m-80) REVERT: E 333 ASP cc_start: 0.9156 (t70) cc_final: 0.8750 (p0) REVERT: F 107 PHE cc_start: 0.9333 (m-80) cc_final: 0.8815 (m-80) REVERT: F 123 LYS cc_start: 0.9020 (tttt) cc_final: 0.8789 (tppt) REVERT: F 129 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8111 (mmtp) REVERT: F 132 TRP cc_start: 0.8437 (m100) cc_final: 0.8190 (m100) REVERT: F 243 PHE cc_start: 0.6875 (p90) cc_final: 0.6669 (p90) REVERT: F 312 PHE cc_start: 0.9250 (t80) cc_final: 0.8911 (t80) REVERT: F 315 PHE cc_start: 0.9013 (t80) cc_final: 0.8416 (t80) REVERT: F 332 GLU cc_start: 0.9135 (tt0) cc_final: 0.8920 (pp20) REVERT: F 346 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8813 (mp0) REVERT: F 351 LYS cc_start: 0.8807 (mttt) cc_final: 0.8554 (mtmt) outliers start: 21 outliers final: 6 residues processed: 177 average time/residue: 0.5634 time to fit residues: 110.9919 Evaluate side-chains 164 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain F residue 94 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 150 optimal weight: 0.0020 chunk 170 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 172 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN E 103 GLN F 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.157694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108984 restraints weight = 42809.392| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.50 r_work: 0.3259 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15219 Z= 0.146 Angle : 0.675 18.267 20600 Z= 0.329 Chirality : 0.042 0.281 2367 Planarity : 0.004 0.045 2640 Dihedral : 7.977 157.290 1991 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.85 % Allowed : 10.22 % Favored : 87.93 % 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 aren not related in a simple way. whole: 1.27 (0.19), residues: 1838 helix: 1.32 (0.15), residues: 1165 sheet: 0.84 (0.43), residues: 146 loop : -0.06 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.034 0.002 TYR A 697 PHE 0.054 0.002 PHE A 887 TRP 0.038 0.002 TRP E 189 HIS 0.003 0.000 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00323 (15219) covalent geometry : angle 0.67455 (20600) hydrogen bonds : bond 0.04411 ( 936) hydrogen bonds : angle 4.92182 ( 2751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8435 (t0) cc_final: 0.8199 (t0) REVERT: A 266 ARG cc_start: 0.7657 (tmm160) cc_final: 0.7301 (tmm160) REVERT: A 648 GLU cc_start: 0.8209 (tt0) cc_final: 0.7894 (tp30) REVERT: A 693 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 755 ARG cc_start: 0.8738 (mpp-170) cc_final: 0.8533 (mtt90) REVERT: A 757 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7870 (mp) REVERT: A 810 MET cc_start: 0.9065 (mmm) cc_final: 0.8643 (mmm) REVERT: A 813 TRP cc_start: 0.8904 (OUTLIER) cc_final: 0.8628 (p-90) REVERT: B 69 ASN cc_start: 0.8648 (m-40) cc_final: 0.8342 (m110) REVERT: B 74 ASN cc_start: 0.7980 (m110) cc_final: 0.7411 (p0) REVERT: C 43 TYR cc_start: 0.8728 (m-10) cc_final: 0.8501 (m-10) REVERT: C 63 SER cc_start: 0.9200 (t) cc_final: 0.8981 (p) REVERT: C 83 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8409 (mt) REVERT: C 115 SER cc_start: 0.8337 (t) cc_final: 0.7786 (p) REVERT: D 18 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8642 (m) REVERT: E 316 PHE cc_start: 0.8781 (m-80) cc_final: 0.8483 (m-10) REVERT: E 333 ASP cc_start: 0.9124 (t70) cc_final: 0.8714 (p0) REVERT: F 107 PHE cc_start: 0.9327 (m-80) cc_final: 0.8822 (m-80) REVERT: F 108 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.9358 (mp0) REVERT: F 123 LYS cc_start: 0.8994 (tttt) cc_final: 0.8747 (tppt) REVERT: F 129 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8199 (mmtt) REVERT: F 133 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7661 (pt0) REVERT: F 233 PHE cc_start: 0.9072 (m-80) cc_final: 0.8758 (t80) REVERT: F 282 ASN cc_start: 0.8373 (m-40) cc_final: 0.8031 (m-40) REVERT: F 312 PHE cc_start: 0.9235 (t80) cc_final: 0.8827 (t80) REVERT: F 315 PHE cc_start: 0.8835 (t80) cc_final: 0.8624 (t80) REVERT: F 346 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8695 (mp0) outliers start: 31 outliers final: 11 residues processed: 177 average time/residue: 0.5746 time to fit residues: 112.7173 Evaluate side-chains 172 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 89 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 0.0000 chunk 114 optimal weight: 2.9990 chunk 168 optimal weight: 40.0000 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.160894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112282 restraints weight = 43153.225| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.65 r_work: 0.3231 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15219 Z= 0.168 Angle : 0.682 17.775 20600 Z= 0.335 Chirality : 0.043 0.272 2367 Planarity : 0.004 0.048 2640 Dihedral : 7.958 160.086 1991 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.85 % Allowed : 11.83 % Favored : 86.32 % 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 aren not related in a simple way. whole: 1.27 (0.19), residues: 1838 helix: 1.33 (0.15), residues: 1166 sheet: 0.80 (0.44), residues: 146 loop : -0.09 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 135 TYR 0.023 0.001 TYR A 697 PHE 0.029 0.002 PHE E 118 TRP 0.042 0.002 TRP E 189 HIS 0.004 0.001 HIS B 83 Details of bonding type rmsd covalent geometry : bond 0.00384 (15219) covalent geometry : angle 0.68175 (20600) hydrogen bonds : bond 0.04403 ( 936) hydrogen bonds : angle 4.93782 ( 2751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8465 (t0) cc_final: 0.8238 (t0) REVERT: A 173 MET cc_start: 0.8881 (mmm) cc_final: 0.8631 (mmm) REVERT: A 266 ARG cc_start: 0.7703 (tmm160) cc_final: 0.7349 (tmm160) REVERT: A 648 GLU cc_start: 0.8215 (tt0) cc_final: 0.7881 (tp30) REVERT: A 693 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 713 ASP cc_start: 0.7929 (m-30) cc_final: 0.7299 (m-30) REVERT: A 728 ASP cc_start: 0.8836 (p0) cc_final: 0.8050 (m-30) REVERT: A 732 MET cc_start: 0.8908 (ptp) cc_final: 0.8567 (mpp) REVERT: A 755 ARG cc_start: 0.8766 (mpp-170) cc_final: 0.8555 (mtt90) REVERT: A 757 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 810 MET cc_start: 0.9083 (mmm) cc_final: 0.8657 (mmm) REVERT: A 813 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.8639 (p-90) REVERT: A 825 ARG cc_start: 0.8831 (mtt90) cc_final: 0.8218 (mtt180) REVERT: A 833 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8685 (pp) REVERT: A 887 PHE cc_start: 0.8832 (m-80) cc_final: 0.8623 (m-80) REVERT: A 971 ARG cc_start: 0.9404 (ptt180) cc_final: 0.9183 (ptt90) REVERT: B 69 ASN cc_start: 0.8684 (m-40) cc_final: 0.8412 (m-40) REVERT: B 93 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: C 63 SER cc_start: 0.9203 (t) cc_final: 0.8958 (p) REVERT: C 83 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 115 SER cc_start: 0.8295 (t) cc_final: 0.7732 (p) REVERT: D 18 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8673 (m) REVERT: E 316 PHE cc_start: 0.8791 (m-80) cc_final: 0.8495 (m-10) REVERT: E 333 ASP cc_start: 0.9131 (t70) cc_final: 0.8717 (p0) REVERT: F 106 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9457 (mm) REVERT: F 107 PHE cc_start: 0.9332 (m-80) cc_final: 0.8824 (m-80) REVERT: F 108 GLU cc_start: 0.9623 (OUTLIER) cc_final: 0.9367 (mp0) REVERT: F 123 LYS cc_start: 0.9002 (tttt) cc_final: 0.8740 (tppt) REVERT: F 129 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8246 (mmtt) REVERT: F 133 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7628 (pt0) REVERT: F 146 LYS cc_start: 0.8267 (tptt) cc_final: 0.8052 (tptt) REVERT: F 282 ASN cc_start: 0.8402 (m-40) cc_final: 0.8020 (m-40) REVERT: F 312 PHE cc_start: 0.9268 (t80) cc_final: 0.8868 (t80) REVERT: F 315 PHE cc_start: 0.8982 (t80) cc_final: 0.8614 (t80) REVERT: F 346 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8688 (mp0) outliers start: 31 outliers final: 11 residues processed: 181 average time/residue: 0.5746 time to fit residues: 115.6939 Evaluate side-chains 171 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 5 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 30 optimal weight: 0.0870 chunk 134 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** 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 = 0.4527 r_free = 0.4527 target = 0.164509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115655 restraints weight = 42477.509| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.73 r_work: 0.3296 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15219 Z= 0.130 Angle : 0.664 18.117 20600 Z= 0.322 Chirality : 0.041 0.278 2367 Planarity : 0.004 0.056 2640 Dihedral : 7.840 158.572 1991 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.79 % Allowed : 12.60 % Favored : 85.60 % 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 aren not related in a simple way. whole: 1.33 (0.20), residues: 1838 helix: 1.41 (0.15), residues: 1166 sheet: 0.74 (0.43), residues: 148 loop : -0.13 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 135 TYR 0.027 0.001 TYR A 697 PHE 0.040 0.002 PHE E 113 TRP 0.013 0.001 TRP A 813 HIS 0.004 0.000 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00287 (15219) covalent geometry : angle 0.66434 (20600) hydrogen bonds : bond 0.04063 ( 936) hydrogen bonds : angle 4.85029 ( 2751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.7641 (tmm160) cc_final: 0.7282 (tmm160) REVERT: A 648 GLU cc_start: 0.8188 (tt0) cc_final: 0.7890 (tp30) REVERT: A 693 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 713 ASP cc_start: 0.7903 (m-30) cc_final: 0.7289 (m-30) REVERT: A 728 ASP cc_start: 0.8827 (p0) cc_final: 0.8249 (m-30) REVERT: A 755 ARG cc_start: 0.8769 (mpp-170) cc_final: 0.8502 (mtt90) REVERT: A 757 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7916 (mp) REVERT: A 810 MET cc_start: 0.9076 (mmm) cc_final: 0.8752 (mmm) REVERT: A 813 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.8649 (p-90) REVERT: A 825 ARG cc_start: 0.8807 (mtt90) cc_final: 0.8214 (mmm160) REVERT: A 833 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 887 PHE cc_start: 0.8792 (m-80) cc_final: 0.8549 (m-80) REVERT: A 971 ARG cc_start: 0.9396 (ptt180) cc_final: 0.9146 (ptt90) REVERT: B 35 LEU cc_start: 0.9629 (mt) cc_final: 0.9095 (pp) REVERT: B 69 ASN cc_start: 0.8638 (m-40) cc_final: 0.7938 (m110) REVERT: B 72 ARG cc_start: 0.9134 (mtm180) cc_final: 0.8794 (mtm180) REVERT: B 74 ASN cc_start: 0.7911 (m110) cc_final: 0.7429 (p0) REVERT: B 93 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: C 43 TYR cc_start: 0.8687 (m-10) cc_final: 0.8486 (m-10) REVERT: C 63 SER cc_start: 0.9151 (t) cc_final: 0.8930 (p) REVERT: C 83 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 115 SER cc_start: 0.8140 (t) cc_final: 0.7612 (p) REVERT: D 18 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8678 (m) REVERT: E 316 PHE cc_start: 0.8662 (m-80) cc_final: 0.8443 (m-10) REVERT: E 333 ASP cc_start: 0.9056 (t70) cc_final: 0.8621 (p0) REVERT: F 106 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9419 (mm) REVERT: F 107 PHE cc_start: 0.9326 (m-80) cc_final: 0.8814 (m-80) REVERT: F 108 GLU cc_start: 0.9618 (OUTLIER) cc_final: 0.9365 (mp0) REVERT: F 123 LYS cc_start: 0.8956 (tttt) cc_final: 0.8679 (tppt) REVERT: F 129 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8112 (mmtp) REVERT: F 133 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7598 (pt0) REVERT: F 146 LYS cc_start: 0.8138 (tptt) cc_final: 0.7882 (tptt) REVERT: F 233 PHE cc_start: 0.9058 (m-80) cc_final: 0.8856 (t80) REVERT: F 312 PHE cc_start: 0.9221 (t80) cc_final: 0.8758 (t80) REVERT: F 315 PHE cc_start: 0.8967 (t80) cc_final: 0.8546 (t80) REVERT: F 332 GLU cc_start: 0.9106 (tt0) cc_final: 0.8883 (pp20) outliers start: 30 outliers final: 11 residues processed: 184 average time/residue: 0.5428 time to fit residues: 111.5557 Evaluate side-chains 172 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 1 optimal weight: 0.9980 chunk 143 optimal weight: 40.0000 chunk 60 optimal weight: 0.0970 chunk 160 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** 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 = 0.4518 r_free = 0.4518 target = 0.161875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113263 restraints weight = 42557.996| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.67 r_work: 0.3261 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15219 Z= 0.144 Angle : 0.683 18.313 20600 Z= 0.331 Chirality : 0.042 0.249 2367 Planarity : 0.004 0.082 2640 Dihedral : 7.831 159.870 1991 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.21 % Allowed : 12.84 % Favored : 84.95 % 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 aren not related in a simple way. whole: 1.35 (0.19), residues: 1838 helix: 1.42 (0.15), residues: 1166 sheet: 0.84 (0.42), residues: 144 loop : -0.12 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 996 TYR 0.035 0.001 TYR A 697 PHE 0.030 0.002 PHE F 113 TRP 0.011 0.001 TRP A 813 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00326 (15219) covalent geometry : angle 0.68305 (20600) hydrogen bonds : bond 0.04054 ( 936) hydrogen bonds : angle 4.84154 ( 2751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.7686 (tmm160) cc_final: 0.7319 (tmm160) REVERT: A 648 GLU cc_start: 0.8186 (tt0) cc_final: 0.7857 (tp30) REVERT: A 693 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 713 ASP cc_start: 0.7848 (m-30) cc_final: 0.7250 (m-30) REVERT: A 728 ASP cc_start: 0.8872 (p0) cc_final: 0.8119 (m-30) REVERT: A 732 MET cc_start: 0.8882 (ptp) cc_final: 0.8644 (mpp) REVERT: A 755 ARG cc_start: 0.8781 (mpp-170) cc_final: 0.8520 (mtt90) REVERT: A 757 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 810 MET cc_start: 0.9208 (mmm) cc_final: 0.8764 (mpm) REVERT: A 813 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.8559 (p-90) REVERT: A 825 ARG cc_start: 0.8812 (mtt90) cc_final: 0.8190 (mtt180) REVERT: A 833 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8667 (pp) REVERT: A 971 ARG cc_start: 0.9407 (ptt180) cc_final: 0.9148 (ptt90) REVERT: B 69 ASN cc_start: 0.8670 (m-40) cc_final: 0.8075 (m110) REVERT: B 72 ARG cc_start: 0.9186 (mtm180) cc_final: 0.8856 (mtm180) REVERT: B 74 ASN cc_start: 0.7923 (m110) cc_final: 0.7352 (p0) REVERT: B 93 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: C 63 SER cc_start: 0.9181 (t) cc_final: 0.8961 (p) REVERT: C 83 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8412 (mt) REVERT: C 92 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7517 (tp) REVERT: C 115 SER cc_start: 0.8132 (t) cc_final: 0.7580 (p) REVERT: D 18 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8702 (m) REVERT: E 100 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9091 (mmmt) REVERT: E 316 PHE cc_start: 0.8779 (m-80) cc_final: 0.8531 (m-10) REVERT: E 333 ASP cc_start: 0.9126 (t70) cc_final: 0.8709 (p0) REVERT: F 106 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9449 (mm) REVERT: F 107 PHE cc_start: 0.9349 (m-80) cc_final: 0.8869 (m-80) REVERT: F 108 GLU cc_start: 0.9616 (OUTLIER) cc_final: 0.9358 (mp0) REVERT: F 123 LYS cc_start: 0.8953 (tttt) cc_final: 0.8665 (tppt) REVERT: F 129 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8142 (mmtp) REVERT: F 133 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7604 (pt0) REVERT: F 146 LYS cc_start: 0.8224 (tptt) cc_final: 0.7973 (tptt) REVERT: F 312 PHE cc_start: 0.9285 (t80) cc_final: 0.8819 (t80) REVERT: F 315 PHE cc_start: 0.9077 (t80) cc_final: 0.8647 (t80) REVERT: F 332 GLU cc_start: 0.9116 (tt0) cc_final: 0.8904 (pp20) REVERT: F 346 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8618 (mp0) outliers start: 37 outliers final: 17 residues processed: 182 average time/residue: 0.5559 time to fit residues: 113.3376 Evaluate side-chains 177 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 21 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.161411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112687 restraints weight = 42905.963| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.69 r_work: 0.3242 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15219 Z= 0.162 Angle : 0.710 18.154 20600 Z= 0.342 Chirality : 0.043 0.240 2367 Planarity : 0.004 0.072 2640 Dihedral : 7.851 162.614 1991 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.85 % Allowed : 13.80 % 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 aren not related in a simple way. whole: 1.31 (0.20), residues: 1838 helix: 1.40 (0.15), residues: 1168 sheet: 0.78 (0.42), residues: 144 loop : -0.18 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 996 TYR 0.029 0.001 TYR B 58 PHE 0.058 0.002 PHE A 887 TRP 0.014 0.001 TRP F 132 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00375 (15219) covalent geometry : angle 0.70961 (20600) hydrogen bonds : bond 0.04130 ( 936) hydrogen bonds : angle 4.88936 ( 2751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.7692 (tmm160) cc_final: 0.7325 (tmm160) REVERT: A 648 GLU cc_start: 0.8222 (tt0) cc_final: 0.7896 (tp30) REVERT: A 693 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 712 MET cc_start: 0.8195 (pmm) cc_final: 0.7946 (pmm) REVERT: A 713 ASP cc_start: 0.7814 (m-30) cc_final: 0.7160 (m-30) REVERT: A 728 ASP cc_start: 0.8853 (p0) cc_final: 0.8114 (m-30) REVERT: A 755 ARG cc_start: 0.8810 (mpp-170) cc_final: 0.8563 (mmt90) REVERT: A 757 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 772 THR cc_start: 0.7882 (m) cc_final: 0.7596 (p) REVERT: A 810 MET cc_start: 0.9179 (mmm) cc_final: 0.8779 (mmm) REVERT: A 813 TRP cc_start: 0.8901 (OUTLIER) cc_final: 0.8592 (p-90) REVERT: A 825 ARG cc_start: 0.8826 (mtt90) cc_final: 0.8203 (mtt180) REVERT: A 833 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 971 ARG cc_start: 0.9399 (ptt180) cc_final: 0.9133 (ptt90) REVERT: B 35 LEU cc_start: 0.9590 (mt) cc_final: 0.9013 (pp) REVERT: B 69 ASN cc_start: 0.8697 (m-40) cc_final: 0.8432 (m-40) REVERT: C 63 SER cc_start: 0.9151 (t) cc_final: 0.8943 (p) REVERT: C 83 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8438 (mt) REVERT: C 92 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7689 (tp) REVERT: C 115 SER cc_start: 0.8144 (t) cc_final: 0.7580 (p) REVERT: D 18 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8697 (m) REVERT: E 100 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9081 (mmmt) REVERT: E 117 MET cc_start: 0.7529 (ptt) cc_final: 0.6275 (mmp) REVERT: E 124 PHE cc_start: 0.8644 (m-10) cc_final: 0.8310 (m-10) REVERT: E 316 PHE cc_start: 0.8771 (m-80) cc_final: 0.8526 (m-10) REVERT: E 333 ASP cc_start: 0.9131 (t70) cc_final: 0.8722 (p0) REVERT: F 107 PHE cc_start: 0.9354 (m-80) cc_final: 0.8897 (m-80) REVERT: F 108 GLU cc_start: 0.9619 (OUTLIER) cc_final: 0.9391 (mp0) REVERT: F 113 PHE cc_start: 0.9391 (t80) cc_final: 0.8988 (m-80) REVERT: F 117 MET cc_start: 0.4866 (mtt) cc_final: 0.4414 (ptp) REVERT: F 123 LYS cc_start: 0.8942 (tttt) cc_final: 0.8646 (tppt) REVERT: F 129 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8151 (mmtp) REVERT: F 133 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7628 (pt0) REVERT: F 146 LYS cc_start: 0.8208 (tptt) cc_final: 0.7946 (tptt) REVERT: F 233 PHE cc_start: 0.9212 (m-80) cc_final: 0.8936 (t80) REVERT: F 282 ASN cc_start: 0.8488 (m-40) cc_final: 0.8077 (m-40) REVERT: F 312 PHE cc_start: 0.9272 (t80) cc_final: 0.8813 (t80) REVERT: F 315 PHE cc_start: 0.9078 (t80) cc_final: 0.8669 (t80) REVERT: F 332 GLU cc_start: 0.9121 (tt0) cc_final: 0.8898 (pp20) outliers start: 31 outliers final: 19 residues processed: 172 average time/residue: 0.5717 time to fit residues: 109.6855 Evaluate side-chains 173 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 65 optimal weight: 0.0370 chunk 103 optimal weight: 0.6980 chunk 135 optimal weight: 30.0000 chunk 146 optimal weight: 0.0570 chunk 149 optimal weight: 40.0000 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 599 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** 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 = 0.4530 r_free = 0.4530 target = 0.163445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115269 restraints weight = 42839.689| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.67 r_work: 0.3288 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15219 Z= 0.128 Angle : 0.741 18.322 20600 Z= 0.350 Chirality : 0.042 0.259 2367 Planarity : 0.004 0.075 2640 Dihedral : 7.762 159.790 1991 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.61 % Allowed : 14.28 % Favored : 84.11 % 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 aren not related in a simple way. whole: 1.34 (0.20), residues: 1838 helix: 1.46 (0.15), residues: 1166 sheet: 0.69 (0.42), residues: 146 loop : -0.23 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 996 TYR 0.022 0.001 TYR B 58 PHE 0.055 0.002 PHE E 360 TRP 0.021 0.001 TRP F 132 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00280 (15219) covalent geometry : angle 0.74054 (20600) hydrogen bonds : bond 0.03888 ( 936) hydrogen bonds : angle 4.85941 ( 2751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.7610 (tmm160) cc_final: 0.7221 (tmm160) REVERT: A 648 GLU cc_start: 0.8168 (tt0) cc_final: 0.7845 (tp30) REVERT: A 693 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 713 ASP cc_start: 0.7741 (m-30) cc_final: 0.7161 (m-30) REVERT: A 728 ASP cc_start: 0.8879 (p0) cc_final: 0.8430 (m-30) REVERT: A 755 ARG cc_start: 0.8771 (mpp-170) cc_final: 0.8518 (mmt90) REVERT: A 757 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 813 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.7509 (t-100) REVERT: A 825 ARG cc_start: 0.8781 (mtt90) cc_final: 0.8169 (mtt180) REVERT: A 833 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8632 (pp) REVERT: B 69 ASN cc_start: 0.8695 (m-40) cc_final: 0.7948 (m-40) REVERT: B 72 ARG cc_start: 0.9055 (mtm180) cc_final: 0.8735 (mtm180) REVERT: C 63 SER cc_start: 0.9135 (t) cc_final: 0.8931 (p) REVERT: C 83 LEU cc_start: 0.8828 (tp) cc_final: 0.8459 (mt) REVERT: C 92 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7500 (tp) REVERT: C 115 SER cc_start: 0.8056 (t) cc_final: 0.7487 (p) REVERT: D 18 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8725 (m) REVERT: E 100 LYS cc_start: 0.9296 (mmmt) cc_final: 0.9048 (mmmt) REVERT: E 124 PHE cc_start: 0.8661 (m-10) cc_final: 0.8319 (m-10) REVERT: E 316 PHE cc_start: 0.8733 (m-80) cc_final: 0.8508 (m-10) REVERT: E 333 ASP cc_start: 0.9112 (t70) cc_final: 0.8675 (p0) REVERT: F 107 PHE cc_start: 0.9336 (m-80) cc_final: 0.8877 (m-80) REVERT: F 108 GLU cc_start: 0.9618 (OUTLIER) cc_final: 0.9400 (mp0) REVERT: F 113 PHE cc_start: 0.9404 (t80) cc_final: 0.9018 (m-80) REVERT: F 117 MET cc_start: 0.4879 (mtt) cc_final: 0.4437 (ptp) REVERT: F 123 LYS cc_start: 0.8916 (tttt) cc_final: 0.8624 (tppt) REVERT: F 129 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8129 (mmtp) REVERT: F 133 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7603 (pt0) REVERT: F 146 LYS cc_start: 0.8148 (tptt) cc_final: 0.7854 (tptt) REVERT: F 233 PHE cc_start: 0.9219 (m-80) cc_final: 0.8963 (t80) REVERT: F 282 ASN cc_start: 0.8489 (m-40) cc_final: 0.8061 (m-40) REVERT: F 312 PHE cc_start: 0.9277 (t80) cc_final: 0.8825 (t80) REVERT: F 315 PHE cc_start: 0.9073 (t80) cc_final: 0.8666 (t80) outliers start: 27 outliers final: 15 residues processed: 175 average time/residue: 0.5683 time to fit residues: 110.8729 Evaluate side-chains 170 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 154 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 149 optimal weight: 30.0000 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** 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 = 0.4520 r_free = 0.4520 target = 0.161738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.112854 restraints weight = 42586.344| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.64 r_work: 0.3241 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15219 Z= 0.153 Angle : 0.767 17.890 20600 Z= 0.364 Chirality : 0.043 0.267 2367 Planarity : 0.004 0.081 2640 Dihedral : 7.800 161.840 1991 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.43 % Allowed : 14.87 % Favored : 83.69 % 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 aren not related in a simple way. whole: 1.28 (0.20), residues: 1838 helix: 1.39 (0.15), residues: 1170 sheet: 0.65 (0.42), residues: 146 loop : -0.20 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 843 TYR 0.021 0.001 TYR B 58 PHE 0.052 0.002 PHE E 360 TRP 0.029 0.001 TRP F 132 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00354 (15219) covalent geometry : angle 0.76720 (20600) hydrogen bonds : bond 0.04021 ( 936) hydrogen bonds : angle 4.90983 ( 2751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.7710 (tmm160) cc_final: 0.7330 (tmm160) REVERT: A 280 MET cc_start: 0.9186 (mtm) cc_final: 0.8898 (mtm) REVERT: A 648 GLU cc_start: 0.8221 (tt0) cc_final: 0.7880 (tp30) REVERT: A 693 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 712 MET cc_start: 0.8157 (pmm) cc_final: 0.7881 (pmm) REVERT: A 713 ASP cc_start: 0.7675 (m-30) cc_final: 0.7017 (m-30) REVERT: A 728 ASP cc_start: 0.9016 (p0) cc_final: 0.8551 (m-30) REVERT: A 755 ARG cc_start: 0.8766 (mpp-170) cc_final: 0.8517 (mmt90) REVERT: A 757 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 813 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.7521 (t-100) REVERT: A 825 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8189 (mtt180) REVERT: A 833 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8647 (pp) REVERT: A 843 ARG cc_start: 0.9363 (mmp80) cc_final: 0.8527 (ppt170) REVERT: B 69 ASN cc_start: 0.8810 (m-40) cc_final: 0.8535 (m-40) REVERT: C 83 LEU cc_start: 0.8821 (tp) cc_final: 0.8435 (mt) REVERT: C 92 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7557 (tp) REVERT: C 115 SER cc_start: 0.8078 (t) cc_final: 0.7490 (p) REVERT: D 18 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8710 (m) REVERT: E 100 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9088 (mmmt) REVERT: E 124 PHE cc_start: 0.8726 (m-10) cc_final: 0.8382 (m-10) REVERT: E 316 PHE cc_start: 0.8910 (m-80) cc_final: 0.8651 (m-10) REVERT: E 333 ASP cc_start: 0.9147 (t70) cc_final: 0.8724 (p0) REVERT: F 107 PHE cc_start: 0.9361 (m-80) cc_final: 0.8903 (m-80) REVERT: F 108 GLU cc_start: 0.9646 (OUTLIER) cc_final: 0.9443 (mp0) REVERT: F 113 PHE cc_start: 0.9438 (t80) cc_final: 0.9043 (m-80) REVERT: F 117 MET cc_start: 0.4997 (mtt) cc_final: 0.4544 (ptp) REVERT: F 123 LYS cc_start: 0.8917 (tttt) cc_final: 0.8617 (tppt) REVERT: F 129 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8220 (mmtp) REVERT: F 133 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7655 (pt0) REVERT: F 146 LYS cc_start: 0.8204 (tptt) cc_final: 0.7921 (tptt) REVERT: F 233 PHE cc_start: 0.9343 (m-80) cc_final: 0.9085 (t80) REVERT: F 282 ASN cc_start: 0.8637 (m-40) cc_final: 0.8233 (m-40) REVERT: F 312 PHE cc_start: 0.9358 (t80) cc_final: 0.8926 (t80) REVERT: F 315 PHE cc_start: 0.9210 (t80) cc_final: 0.8784 (t80) REVERT: F 332 GLU cc_start: 0.9119 (tt0) cc_final: 0.8865 (pp20) outliers start: 24 outliers final: 14 residues processed: 165 average time/residue: 0.5766 time to fit residues: 105.6949 Evaluate side-chains 171 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 119 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 176 optimal weight: 0.0970 chunk 7 optimal weight: 0.4980 chunk 150 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.168936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.119183 restraints weight = 41449.196| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.47 r_work: 0.3196 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15219 Z= 0.144 Angle : 0.770 17.758 20600 Z= 0.367 Chirality : 0.043 0.286 2367 Planarity : 0.005 0.079 2640 Dihedral : 7.794 162.026 1991 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.43 % Allowed : 14.99 % Favored : 83.57 % 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 aren not related in a simple way. whole: 1.26 (0.20), residues: 1838 helix: 1.40 (0.15), residues: 1169 sheet: 0.61 (0.43), residues: 136 loop : -0.22 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 843 TYR 0.021 0.001 TYR B 58 PHE 0.054 0.002 PHE E 360 TRP 0.034 0.002 TRP F 132 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00329 (15219) covalent geometry : angle 0.76989 (20600) hydrogen bonds : bond 0.04025 ( 936) hydrogen bonds : angle 4.93272 ( 2751) =============================================================================== Job complete usr+sys time: 6771.27 seconds wall clock time: 116 minutes 5.12 seconds (6965.12 seconds total)